Protein Prospector Revision History
prospector.ucsf.edu runs the basic version of Protein Prospector
prospector2.ucsf.edu runs the full version of Protein Prospector
For Protein Prospector quantitation one computer in the cluster must be running Windows

V 5.12.0 04/07/2014 (2000/XP/XPx64/LINUX)
  • There is a new feature in Batch-Tag/Search Compare and MS-Tag to search for cross-linked peptides.
  • Added a ETD high resolution iinstrument to Batch-Tag, MS-Tag and MS-Product.
  • MS-Viewer now has a "Tab Delimited Text with URL option". This column contains a URL link to the MS-Product spectrum.
  • MS-Viewer Tab Delimited text output options now create a link to the output. This is to enable the output to be saved to a file without displaying the report.
  • MS-Viewer now displays 100 raw by default.
  • MS-Tag now has the option to filter peak lists.
  • Crosslinking usermods now in params/usermod_xlink.txt.
  • Glycopeptide usermods now in params/usermod_glyco.txt.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/msbridge.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
  • Changed param file:
    • params/disc_score.txt - added ESI-ETD-high-res
    • params/disc_score2.txt - added ESI-ETD-high-res
    • params/fragmentation.txt - added ESI-ETD-high-res
    • params/instrument.txt - added ESI-ETD-high-res
    • params/links.txt
    • params/msbridge/default.xml
    • params/mstag/default.xml
    • params/msviewer/default.xml
    • params/quan.txt - added Xlink:DSS1:2H(4) (K) and Xlink:DSS1:2H(12) (K)
    • params/searchCompare/default.xml
    • params/usermod.txt
  • New param file:
    • params/usermod_glyco.txt
    • params/usermod_xlink.txt

V 5.10.19 03/19/2014 (2000/XP/XPx64/LINUX)
  • Support added for NIST msp files added to MS-Viewer.
  • Fixed the following bugs:
    • Search-Compare and MS-Display can crash if attempting to access raw data with an associated mgf file created by msconvert.
    • MS-Viewer can't display spectra from peptides with an M+H less than 600 Da.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
  • Changed param file:
    • params/mgf.xml - added msconvert option.
    • params/usermod_msproduct.txt

V 5.10.18 03/05/2014 (2000/XP/XPx64/LINUX)
  • There is now an additional modifications file for MS-Product. This is mainly to add modifications for use by MS-Viewer which aren't available on the menus in Batch-Tag, MS-Tag, etc.
  • Multiple items may now be specified as MS-Viewer filters. Eg you could specify multiple accession numbers as a filter and include them all in the report.
  • Prefix and Suffix added as MS-Viewer filter options.
  • Fixed the following bugs:
    • If blib output was created by Search Compare from the command line and the output file was already present then the created blib database was invalid.
    • In a Search Compare Time report if multiple hits were reported for a given spectrum they all had the same accession number.
    • blib generation in Search Compare did not function properly in Multi Sample mode. If Multi Sample mode is chosen a blib library is now created for each fraction. The number for the fraction is appended to the library file name.
    • The modifications in the modifications column in MS-Viewer can now have space characters after the semi colon. This was done to make it compatible with Protein Pilot output.
    • If the page number in an MS-Viewer report is greater than the number of pages in the report then the page number is reset to the last page in the report. This can happen for, for example, if you set a filter without changing the page number.
    • Java applet now has a trusted certificate.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/java/SpectrumGraph.jar
    • html/misc/revhist.htm
  • Changed param file:
    • params/mgf.xml - added Protein Pilot option.
    • params/usermod.txt - changed instructions at top of file.
  • New param file:
    • params/usermod_msproduct.txt

V 5.10.17 02/07/2014 (2000/XP/XPx64/LINUX)
  • BiblioSpec output in Search Compare now generated much faster.
  • The MS-Viewer Constant Mods option is now better explained.
  • The MS-Viewer Results File Format item now has PRIDE XML, pepXML, BiblioSpec and Thermo MSF as specific options.
  • Once a data set has been uploaded MS-Viewer items containing column numbers are limited to the number of columns in the report.
  • MS-Viewer now has a Remove Column option which can be used to hide columns and thus restrict the width of a report.
  • MS-Viewer now has a Filtering option which can be used to only display rows with specific information in them.
  • The MS-Viewer sort options are now only available once a data set has been uploaded.
  • MS-Viewer now has more options for displaying a report once the data set has been saved.
  • In Search Compare coverage maps are now not displayed for single protein peptide reports if the Coverage checkbox is deselected.
  • Fixed the following bugs:
    • Some MS-Viewer uploads didn't work if the uploaded file was placed in some archived formats. An example was a blib file in a zip archive.
    • MS-Viewer reports generated from pepXML files had incorrect modification masses.
    • The bug fix addressed in release 5.10.15 didn't work if the sequence database was indexed by FA-Index on Windows.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/viewerman.htm
    • html/misc/revhist.htm
  • Changed param file:
    • params/link_aa.txt - added C->K,Protein N-term

V 5.10.16 01/14/2014 (2000/XP/XPx64/LINUX)
  • Search Compare now has a normalized RT option for BiblioSpec output.
  • The Search Compare Discr Score Graph option is now turned off during BiblioSpec output.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm

V 5.10.15 12/17/2013 (2000/XP/XPx64/LINUX)
  • Fixed the following bugs:
    • Search Compare can fail when reporting on a search against the UniProt random database on a Windows 32-bit operating system. To fix this bug the code has been rewritten to use a lot less memory. This should result in quantitation reports being generated faster and more reliably.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
V 5.10.14 12/2/2013 (2000/XP/XPx64/LINUX)
  • Added support for BiblioSpec in MS-Viewer and Search Compare.
  • Thermo MSF files now supported by MS-Viewer.
  • MS-Viewer can now have Scan Number as a spectrum identifier.
  • MS-Viewer can now be run from the command line. This is useful for processing very large files or multiple files.
  • MS-Viewer manual added.
  • Modified the Batch-Tag daemon init.d script so it is compatible with Red Hat, Debian and openSUSE LINUX.
  • Fixed the following bugs:
    • Fixed a bug with reading mgf peak lists from the Sciex 5600 data converter software.
    • autofaindex.pl didn't work on Red Hat LINUX.
    • Filtering Search Compare results by accession number sometimes didn't work if the preferred species option was used.
    • The reporting of search progress sometimes reported a negative percentage and time remaining.
    • There was a problem using Search Compare with the full UniProtKB and UniProtKB random database on Windows 32-bit XP.
  • Changed cgi-bin files:
    • autofaindex.pl
  • New cgi-bin file:
    • automsviewer.pl added
  • Changed HTML files:
    • mshome.htm
    • html/js/info.js
    • html/misc/revhist.htm
  • New HTML files:
    • html/images/mascot1.png
    • html/images/mascot2.png
    • html/images/tandem1.png
    • html/images/tandem2.png
    • html/instruct/viewerman.htm
  • Changed param files:
    • params/msviewer/default.xml

V 5.10.13 9/18/2013 (2000/XP/XPx64/LINUX)
  • There is now a possibility of setting a directive called max_jobs_per_user that limits the number of simultaneous jobs that can be run by a given user on a given server.
  • ms2 files now supported in MS-Tag, Batch-Tag, Search Compare and MS-Viewer.
  • MS-Viewer now supports ms2 and pepXML files.
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm

V 5.10.12 9/3/2013 (2000/XP/XPx64/LINUX)
  • MS-Viewer now supports pepXML and PrideXML files.
  • There is now a more compact way of representing modification site ambiguity.
  • Search Compare and MS-Digest can now report cosine similarity values between experimental raw data and theoretical isotope distributions.
  • A version is now available for reporting Chem Score in MS-Digest (available on request).
  • Maximum fragment ion in MS-Product increased from 20 to 30.
  • Fixed the following bugs:
    • If a species term appears multiple times in the taxonomy tree then the lowest rather than the highest occurrence was being used. Eg the term Drosophila occurs 3 times.
    • DB-Stat could crash if the pre-search gave zero entries.
    • Sometimes the names of searches were being scrambled when importing Batch-Tag projects using Results Management.
    • The average masses of modified amino acids in MS-Product and MS-Comp were using the monoisotopic values.
    • Raw data access to Thermo files didn't work for the last scan in a run.
    • The RT information is now only written to an mgf file if it is available.
    • In MS-Viewer a restricted number of lines is shown in the report when a data set is first uploaded.
    • MS-Viewer now has Tab delimited text and Viewer files output options for saved results.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/faman.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
  • Changed param file:
    • params/dbhosts.txt
    • params/mgf.xml - added PROSPECTOR_2
  • New param file (optional):
    • params/chem_score.txt

V 5.10.11 3/19/2013 (2000/XP/XPx64/LINUX)
  • All database search programs now have an N Term AA Limit option which limits searches to the amino acids at the protein N-Termini.
  • MS-Homology and MS-Pattern now have Start AA columns.
  • Thermo MSF viewer option added to MS-Viewer.
  • Fixed the following bugs:
    • Mass modifications didn't work in MS-Product if average masses were selected.
    • N15 quantitation didn't work if the heavy peptide contained any light nitrogen. For example Carbamidomethyl modified Cysteine.
    • DNA sequences don't work in MS-Digest. Bug introduced in v5.9.4
    • XML reports in MS-Pattern didn't have information on the hits.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/misc/revhist.htm
  • New cgi-bin file:
    • msfviewer_converter.pl added
  • Changed param file:
    • params/usermod.txt - added Label:15N(1)+Carbamidomethyl
    • params/viewer_conv.txt - added Thermo MSF Viewer

V 5.10.10 2/15/2013 (2000/XP/XPx64/LINUX)
  • A Perl script has been written to allow automatic download and indexing of sequence databases.
  • The login form now has an option for changing the password.
  • Search Compare now has an optional column for displaying the MSMS Information. This is generally contains the scan(s) used to create the MSMS spectrum.
  • MS-Display now reports the cosine similarity of the fit between the theoretical and experimental isotope distributions.
  • Fixed the following bugs:
    • There was sometimes a problem reporting the names of missing files on the Windows version.
    • If a User Protein was searched in conjunction with a random or reverse database then the randomized/reversed version of the user protein wasn't being created. This bug was introduced in version 5.10.7.
    • If MS-Digest considered multiple proteins in a joint report and the last protein had no modifications then the modifications column was missing.
    • MS-Viewer sometimes had missing rows at the top of a report.
    • The scan number was sometimes incorrectly extracted from mzML peak list files.
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm
  • New cgi-bin file:
    • autofaindex.pl added
  • New param file:
    • params/dbhosts.txt

V 5.10.9 1/2/2013 (2000/XP/XPx64/LINUX)
  • MS-Viewer now has a form for setting the parameters for the MS-Tag links.
  • There are now some examples of MS-Viewer data sets on the public server.
  • Search Compare now has an option for directly preparing files to upload to MS-Viewer.
  • In Search Compare accession number are now sorted so that O-Z are preferred to A-N. This is so more appropriate UniProtKB accession numbers are chosen.
  • Fixed the following bugs:
    • A problem was introduced in v5.10.8 if directories were moved on the same partition.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/msviewer/default.xml
    • params/usermod.txt - added PhosphoHexNAc mod

V 5.10.8 12/3/2012 (2000/XP/XPx64/LINUX)
  • Some changes made to make the code compile on Ubuntu LINUX.
  • Results Management now has a Check option for checking if all the necessary files for a Batch-Tag project are present. Files not present are reported.
  • Fixed the following bugs:
    • There was a problem with the LINUX version if uploaded files were moved between disk partitions.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm

V 5.10.7 11/14/2012 (2000/XP/XPx64/LINUX)
  • Fixed the following bugs:
    • If a Batch-Tag search was done the a temporary User Protein database was created for each process and each pass through the database. Now one is only created for each process.
    • In Search Compare the link which creates a single protein peptide report. This has been a bug since v5.10.2.
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm

V 5.10.6 11/7/2012 (2000/XP/XPx64/LINUX)
  • MS-Viewer now supports crosslinked peptides.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/links.txt - added DSS:2H(4) and DSS:2H(12)
    • params/usermod.txt - added DSS:2H(4) and DSS:2H(12) mods

V 5.10.5 10/31/2012 (2000/XP/XPx64/LINUX)
  • New program MS-Filter added. The program can filter MSMS peak lists to only retain spectra matching filter parameters. These currently include precursor M+H, precursor charge, the presence of a loss fragment from the precursor ion and the presence of an ion of a given m/z.
  • Fixed the following bugs:
    • zip archives created on a Mac are now supported.
    • Sometimes Batch-Tag errors aren't caught and a message saying that the search was aborted for an unknown reason is output.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • New HTML files:
    • html/images/msfilter.jpg
    • html/instruct/filterman.htm
  • Changed param files:
    • params/info.txt
  • New param files:
    • params/msfilter/default.xml

V 5.10.4 10/17/2012 (2000/XP/XPx64/LINUX)
  • Results Management now has a facility for compressing and uncompressing projects. Currently all project related files in the user repository are compressed if a project is compressed. Data in the centroid and raw data file repositories is not compressed.
  • Results Management now has a date filter. Note that the project accessed by filter will only work going forward. This is based on the last time the project was accessed by either Search Compare or Batch-Tag.
  • Messages from the 7za compression/uncompression program are now suppressed on the LINUX version.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • New HTML files:
    • html/images/compressed.jpg
  • Changed param files:
    • params/usermod.txt - added HexNAc (Y)

V 5.10.3 09/07/2012 (2000/XP/XPx64/LINUX)
  • Results Management now has a facility for import and export of Batch-Tag projects. The export option produces an archive file which can be imported either by another user or to a different server. There is a 2 GByte limit on the size of an archive file that can be imported. If the project is just being moved between users and the data is in a lab repository then the Data to Export option should be set to No Data. There is also an option for just exporting the peaklists and not the raw data. Projects containing searches from newer versions of Prospector cannot be imported. Also parameters used in the project (eg amino acid modifications) must match between the Prospector instances.
  • If a Batch-Tag search is split into more than one serial search then any pre-search is now only done once.
  • Fixed the following bugs:
    • MS-Tag and Batch-Tag searches now support a combination of a Met Loss and an N-terminal protein modification.
    • If residues a residue has two different modifications representing different quantification states then unmodified residues may also be present in a peptide.
    • The LINUX web version of FA-Index can abort when using one of the DNA to Protein, Random database, Reverse Database or Concat database options. This is caused by an Apache timeout. It has been solved by writing periodic messages to the browser.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/usermod.txt - added Incorrect Mono -1Da (Neutral loss), Incorrect Mono -2Da (Neutral loss), Incorrect Mono 1Da (Neutral loss), Incorrect Mono 2Da (Neutral loss)

V 5.10.2 07/03/2012 (2000/XP/XPx64/LINUX)
  • MS-Digest now has a tab delimited text output option.
  • Specified peaks in an MS-Bridge search can now have additional filters applied to them. See the MS-Bridge manual for details.
  • MS-Tag can now search peak lists with multiple spectra. This is for users who want to use options not available in Batch-Tag.
  • MS-Tag now has an expectation value column if appropriate.
  • MS-Product now has an mgf output option.
  • Mass modification searches in MS-Tag/Batch-Tag should be now somewhat faster. This will be most noticable for single spectrum searches.
  • In Search Compare the precursor error histogram no longer includes mass modified peptides.
  • MS-Viewer now has a paging option.
  • Search Compare now has filtered and unfiltered pepXML outputs. The unfiltered output has all the hits from the Batch-Tag program.
  • Fixed the following bugs:
    • Mass modification searches now have the correct precursor tolerance applied to non mass-modified peptides.
    • Batch-Tag hits from mass modification searches which contain both a mass modification and a methionine oxidation and/or a phosphorylation have incorrect scores.
    • If you specify something in Spot/Fraction on the Search Compare form with Multi Sample unchecked, a blank report is generated. Now it filters the results to just contain results from the specified fractions.
    • If you specify something in Spot/Fraction on the Search Compare form they have to be in alphabetic (rather than numeric) order for it to work correctly. Now both are acceptable.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/bridgeman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm

V 5.10.1 04/11/2012 (2000/XP/XPx64/LINUX)
  • The PepXML option in Search Compare can now be used by all users.
  • There is now an output_filename variable for Search Compare. This works for the Tab Delimited Text and pepXML output options. For Tab Delimited Text output it is the name of the output text file; if no name is specified the report is named report.txt. For pepXML output it is the name of the zip file (don't include the .zip suffix); if no name is specified the output file is named after the project.
  • Added support for Proteo Wizard mgf files..
  • Fixed the following bugs:
    • There was a problem with the FA-Index Database Summary Report.
    • There was a problem in Search Compare if searches with different constant modifications were compared.
    • MS-Product didn't work in the Windows basic version.
    • The allow_incorrect_charge flag in params/instrument.txt didn't work properly.
    • The number of Max Losses allowed on the MS-Product form has been increased to 10.
    • MS-Viewer didn't work correctly if some of the cells in a report at the end of a line were empty.
    • Some peptide hits were not included in PepXML reports.
    • Command line Batch-Tag didn't work if a project had more than one fraction.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/bridgeman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/mgf.xml added PROTEO_WIZARD
    • params/usermod.txt added Ethanolyl (C), HexNAcHexSAOx (ST), HexNACHExSAOxSAOx (ST), HexNACHexSASAOx (ST), HexNAcSAOx (ST)
  • New param files:
    • params/distribution.txt
    • params/link_aa.txt - added K,Protein N-term->Protein C-term

V 5.10.0 01/12/2012 (2000/XP/XPx64/LINUX)
  • Database search programs can now search multiple protein databases at the same time. One of these can be one or more user proteins. Note that searching multiple databases is equivalent to searching a single larger database.
  • If a .random or .reverse database is generated by FA-Index then a concat option always appears on the database menu. Thus .random.concat amd .reverse.concat databases are no longer necessary (they will still work however).
  • Read DB can now display the disk use of each user and the remaining disk space.
  • Accession numbers from random or reverse databases are now labelled as decoy in the results.
  • MS-Fit now has a Report Homologous Proteins option.
  • mgf format peak Lists from the Sciex 5600 data converter software are now supported.
  • The Accession Number Pre-Searches and Additional Accession Numbers options can be used with multiple databases. See manual for details.
  • Database option now removed from Search Compare. This should now be automatically assigned.
  • MS-Product can now set a maximum peptide length for reporting internal ions.
  • Fixed the following bugs:
    • If a Batch-Tag search is done with Expectation Calc Method set to None the peptides in the Search Compare peptide report should be sorted by disciminant score by default.
    • Batch-Tag searching with the mySQL database didn't work in non-MPI mode.
    • The HTML form generation program (msform.cgi) crashes if mySQL is supposed to be installed but isn't.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/faman.htm
    • html/instruct/fitman.htm
    • html/instruct/prodman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/acclinks.txt - reformatted text
    • params/mgf.xml added 5600_MS_DATA_CONVERTER and 5600_MZML_TO_MGF_MS_DATA_CONVERTER
    • params/usermod.txt added HexNAcHexSA2 (ST)

V 5.9.4 10/27/2011 (2000/XP/XPx64/LINUX)
  • All database search programs now have a user protein sequence option. The User Protein option needs to be selected from the database option to activate this. When using the user protein sequence option other pre-search options such as species and protein MW filters are disabled. It is possible to have multiple protein sequences if the FASTA format is used. See the manual for details.
  • MS-Tag now has a hidden form item for msms_min_precursor_mass which is set to 200 Da. This overrides the limit of 600 Da used in Batch-Tag.
  • Fixed the following bugs:
    • If Search Compare is used to compare multiple searches from different databases the databases aren't all set on the Search Compare form. This means that accession number links and protein species/name information isn't reported.
    • Search Compare crashes if using the run_msproduct option on a Time report with reporting of unmatched spectra.
    • There is now a mechanism for reporting an accession number without a link if there is no entry in the acclinks.txt parameter file.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/enzyme_comb.txt added Asp-N/Asp-C
    • params/usermod.txt added Carboxy (E)

V 5.9.3 10/06/2011 (2000/XP/XPx64/LINUX)
  • The graphs in the MS-Fit, MS-Bridge and MS-NonSpecific reports now have checkboxes for matched and unmatched peaks.
  • The categories for the MS-Product report are now passed to the Java applet rather than built into it.
  • FA-Index now uses somewhat less memory by using sort rather than stable_sort. Also the order of writing out the index files has changed. This can help with indexing random concat UniProt and NCBInr database on Windows.
  • Results file conversion scripts can now be added to a Prospector distribution without a new version being necessary.
  • Taxonomy files updated.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/instruct/servadmn.htm
    • html/java/SpectrumGraph.jar
    • html/misc/revhist.htm
  • Changed param files:
    • params/enzyme.txt added Lys-C-Pro
    • params/taxonomy/citations.dmp
    • params/taxonomy/delnodes.dmp
    • params/taxonomy/gc.prt
    • params/taxonomy/gencode.dmp
    • params/taxonomy/merged.dmp
    • params/taxonomy/names.dmp
    • params/taxonomy/nodes.dmp
    • params/taxonomy/speclist.dmp
    • params/taxonomy/taxonomy_cache.txt
    • params/viewer_conv.txt

V 5.9.2 09/26/2011 (2000/XP/XPx64/LINUX)
  • The FA-Index Database Summary Report now displays Uniprot ID, organism, gene name, existence and version columns for Uniprot databases with this information.
  • MS-Digest, MS-Bridge, MSNonSpecific and MS-Fit now display the Uniprot ID, organism, gene name, existence and version for Uniprot databases with this information.
  • The MS-Viewer form has been redesigned so that Protein Prospector, Mascot and XTandem hits can be uploaded without specifying the column numbers.
  • Fixed the following bugs:
    • The link to MS-Product from Search Compare didn't work in cases where one of the alternatives to a modification was no modification. This can occur for example with N15 labelling and deamidation where the mass shift is very small.
    • It is currently an error to try to build a concatenated Pdefault or Ddefault database. On detection of this problem the partially written database was not deleted.
    • The peptide sequences at the top of MS-Product can wrap if the sequence contains a '-' character. This was fixed by adding "white-space: nowrap" directives to pform.css and print.css.
    • The links to MS-Product from MS-Tag did not work if MS-Tag was invoked from MS-Viewer and the results were from either XTandem or Mascot.
  • New cgi-bin files:
    • mascot_converter.pl added
    • tandem_converter.pl added
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/instruct/faman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
    • html/pform.css
    • html/print.css
  • Changed param files:
    • params/genelinks.txt replaced with params/upidlinks.txt
    • params/usermod.txt - Label:15N(2)+Deamidated name changed to Label:15N(1)+Deamidated

V 5.9.1 08/29/2011 (2000/XP/XPx64/LINUX)
  • Fixed the following bugs:
    • N15 quantitation didn't work for peptides with modifications whose delta formula included nitrogen.
    • The link from Search Compare to MS-Product sometimes didn't work properly if a residue with a constant mod on it was overidden by a variable mod.
    • The mass window of data saved when doing N15 quantitation was too small in some cases.
    • The spectral viewer program failed to find spectra when the scan identifier was a retention time and the strings didn't match exactly. Eg. 39.0 and 39 were considered different strings.
    • The accession number links for SwissProt no longer worked.
    • The formula for the low mass Q ion at 84 Da was incorrect in imm.txt.
    • The link from Search Compare to MS-Display (for displaying raw data) no longer worked.
    • Some lines in the peak lists output by the Search Compare Filtered Peak Lists option were incorrectly terminated in some cases.
    • wiffread.htm contains incorrect reference to js/instrument.js which no longer exists.
  • Changed HTML files:
    • mshome.htm
    • html/wiffread.htm
    • html/instruct/batchtagman.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/acclinks.txt - changed accession number links for Swiss Prot
    • params/enzyme.txt - added Pro-N
    • params/imm.txt - corrected formula for low mass associated with Q at 84 Da
    • params/info.txt - added comment about single_server directive
    • params/quan.txt - Entry for N15 labelling changed
    • params/usermod.txt - added AMTzGalNAcGlcNAc (N), Formyl (ST)

V 5.9.0 07/13/2011 (2000/XP/XPx64/LINUX)
  • A spectral viewer program called MS-Viewer has been added to the package.
  • The Batch-Tag and Search Compare programs can now be run from the command line without a mySQL database.
  • Fixed the following bugs:
    • In Search Compare the N-term, C-term and Neutral loss elements of modified peptides are not reported in the HTML report if mods are reported in peptide.
    • The new features introduced to support SLIP scoring caused problems in Search Compare for searches (or spectra) for which expectation values have not been calculated.
    • There was a problem with the MS-Product links from Search Compare if the ambiguity in a peptide sequence involved a constant modification.
    • A few source code modules have been modified slightly to allow compilation on the CentOS LINUX platform.
    • The word composition was spelt "compositon" some program outputs.
    • When either saving the form settings on the Batch-Tag and Search Compare forms, using the Make/Import Project form or using the Create Calibrated Project form the log file was incorrectly terminated.
    • In Search Compare the search end time and search time are now only reported if they are non-zero.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/info.txt - added viewer_repository directive
    • params/usermod.txt - added Nitrosyl (C), Thiophospho (ST)

V 5.8.0 05/20/2011 (2000/XP/XPx64/LINUX)
  • A SLIP (site location in peptide) score has been introduced to associate a score with a modification location. The score corresponds to (-10log10 E1) - (-10log10 E2) where E1 is the expectation value of the peptide hit with the modification in its highest scoring position and E2 is the expectation value of the peptide hit with the modification in its second best scoring position. Each modification in a peptide will have an associated SLIP score if there is an alternative location for it in the peptide. Search Compare now has a SLIP score threshold. Any modifications with a SLIP score below the threshold are reported as ambiguous in which case all possible modification positions are reported. As a rough guide using a SLIP score threshold of 6 gives a 5% false localization rate. Note that to fully utilize SLIP scores existing searches need to be redone.
  • If a peptide in Search Compare is reported as ambiguous then all possible peptides are now passed to MS-Product. Note that as MS-Product can only display 6 simultaneous peptides then the user can choose up to 6 of the available peptides via checkboxes.
  • Batch-Tag now has options for Max MSMS peaks in a spectrum and the maximum number of peaks per 100 Da.
  • The columns for reporting peptides and modifications in Search Compare have changed. Modifications can now be reported either in the peptide as before or as separate constant and variable modification columns. The variable modification column will also report any ambiguity in the modification position dependent on the value of the SLIP score threshold option. It is also possible to report variable modification relative to their position in the protein.
  • Mass modification searches now apply a charge dependent precursor tolerance to ensure that mass modifications of any mass defect can be found. The tolerance is equivalent to +/- 0.5 Da for charge 1. Thus it is +/- 0.5 Da for charge 2, +/- 0.33 Da at charge 3, etc. This tolerance is only applied to hits with mass modifications, otherwise the tolerance on the form is used. If the precursor tolerance on the form is larger than this tolerence then the one on the form is used.
  • Search Compare now has an option to create filtered mgf peak lists form all the data displayed in a report.
  • Options have been added to delete the cookies used to store the user's default Batch-Tag and Search Compare parameters.
  • Fixed the following bugs:
    • Under certain rare circumstances it is possible to get very low expectation values. This has been seen to occur for data with large N-termini such as SY tags or 8-plex iTRAQ. In such cases the calculated disciminant score is infinite and Search Compare gives a memory allocation error if the discriminant score graph is displayed. If an expectation value of zero is encountered then the disciminant score calculation using expectation values is now replaced by the old one using score differences.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/expectation.xml
    • params/searchCompare/default.xml
    • params/usermod.txt - added Cation:Na (C-term), Cation:Na (DE), Delta:H(2)C(2) (N-term), Dioxidation (C)
  • New param files:
    • params/msviewer/default.xml

V 5.7.3 03/29/2011 (2000/XP/XPx64/LINUX)
  • MS-Isotope can now plot up to 6 different isotope distributions on the same plot. These can have different charges and relative intensities. The command line version of the program can deal with an unlimited number of distributions.
  • New ESI-Q-high-res instrument added which can assign fragment ions up to charge 4.
  • Search Compare tab delimited text reports are now written to a file which can be accessed via a link. They thus don't have to be written to the browser.
  • MS-Product will now label c1 ions.
  • The Protein Prospector publication list is now just maintained on the public web site.
  • Fixed the following bugs:
    • If there is a single server with a lot of processors servicing Batch-Tag Daemon requests then the searches take longer and longer to start. A single_server directive has been added to params/info.txt to deal with this situation. If this is set then there is no longer a wait dependent on the number of searches running before a new search is started.
    • MSMS peak list in mgf format cannot be read if there is a space at the start of a line containing the fragment ion data.
    • MS-Product crashed for ECD/ETD data if either the precursor charge was 1 or was unspecified.
    • mgf files where there were spaces on the lines before the fragment ion masses were problematic.
    • There was a problem making projects with raw data where some of the raw data files were present and some weren't.
    • Search Compare now only uses the code to generate the discriminant score graph when doing a HTML report.
    • In Search Compare the header for Next AA sometimes didn't line up with the column.
    • In Search Compare there is now a check for whether or not the discriminant score cache file is of zero length.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/instruct/isoman.htm
    • html/instruct/patternman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/disc_score.txt - added ESI-Q-high-res
    • params/disc_score2.txt - added ESI-Q-high-res
    • params/instrument.txt - added ESI-Q-high-res
    • params/link_aa.txt - added E,D,Protein C-term->K,Protein N-term
    • params/taxonomy.txt
    • params/usermod.txt - added APTA

V 5.7.2 01/20/2011 (2000/XP/XPx64/LINUX)
  • A test version of pepXML output for Search Compare has been added.
  • Search Compare can now report the search number if multiple searches are being compared.
  • MS-Homology now prints the number of peptide hits.
  • MS-Pattern max hits increased from 100000 to 1000000.
  • Added N15 quantitation option.
  • Fixed the following bugs:
    • Batch-Tag and MS-Tag now check for Proline for c and z type ions.
    • MS-Pattern hits were not allowed to overlap. This caused the number of hits reported by MS-Homology and MS-Pattern to be different.
    • FA-Index couldn't convert databases that were in Mac text format.
    • Numbers weren't allowed in the MS-Pattern regular expression box.
    • There was a problem with mgf files from dta files in that the TITLE line needed to have dta at the end for the software to correctly pick up the start and end scan.
    • Search Compare Time reports sometimes had the wrong accession number in the last line of the report.
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm
  • Additional HTML files:
    • html/pepxml_std.xsl
  • Changed param files:
    • params/enzyme.txt - added KR-N
    • params/enzyme_comb.txt - added Lys-C/Lys-N and Trypsin/KR-N
    • params/mspattern/default.xml - max_hits modified
    • params/quan.txt - added N15 option
    • params/taxonomy.txt - added ARABIDOPSIS, HORDEUM, ORYZA, SECALE, TRITICUM and ZEA
    • params/usermod.txt - added Acetyl:2H(3)+Methyl (K), Acetyl:2H(3)+Methyl (Uncleaved K), Acetohydrazide (C-term), Acetohydrazide (DE), Ammonia-loss (K), Ammonia-loss (R), GirardT (N), GlnGlnGlnThrGlyGly (Uncleaved K), GlnGluGlnThrGlyGly (Uncleaved K), HexNAc (Neutral loss), HexNAc (N), several N15 labels, NIPCAM (C), SerTyrLys(OAc) (N-term), SerTyrLys(OAcs) (N-term)

V 5.7.1 10/07/2010 (2000/XP/XPx64/LINUX)
  • Graph backgrounds are now white rather than grey.
  • Fixed the following bugs:
    • If a Search Compare Time report is used to report the merged search results of 2 different searches on the same project then any spectra with only hits from the second search will have an extra unmatched spectrum line added. This only happens if unmatched spectra are reported.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
  • R Scripts:
    • initGraph.R
  • Changed param files:
    • params/elements.txt - added silicon
    • params/enzyme_comb.txt - added Asp-C/Cys-N
    • params/pr_graph.par.txt
    • params/sp_graph.par.txt
    • params/usermod.txt - added Piperidine (K, N-term), Pyro-carbamidomethyl (N-term C), TMT (Y), TMT2plex (Y), TMT6plex (Y)

V 5.7.0 09/17/2010 (2000/XP/XPx64/LINUX)
  • Some changes have been made to the HTML to make it more XHTML compliant. This work is not finished yet.
  • The repository.xml file now has an option for having a single raw data directory and multiple associated centroid directories.
  • The repository.xml file can now be set up to save raw data links when creating a project without the raw data file being in place.
  • Some data flow diagrams have been added to the automation guidance document.
  • Some Prospector publications have been added.
  • Changed HTML files:
    • mshome.htm
    • html/peakSpotter.htm
    • html/pform.css
    • html/print.css
    • html/readDB.htm
    • html/wiffread.htm
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/bridgeman.htm
    • html/instruct/compman.htm
    • html/instruct/dbstatman.htm
    • html/instruct/digestman.htm
    • html/instruct/faman.htm
    • html/instruct/fitman.htm
    • html/instruct/homologyman.htm
    • html/instruct/isoman.htm
    • html/instruct/nonspecificman.htm
    • html/instruct/patternman.htm
    • html/instruct/prodman.htm
    • html/instruct/seqman.htm
    • html/instruct/servadmn.htm
    • html/instruct/tagman.htm
    • html/js/info.js
    • html/misc/bughist.htm
    • html/misc/dipep.htm
    • html/misc/faq.htm
    • html/misc/invar.htm
    • html/misc/links.htm
    • html/misc/mutation.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
    • html/misc/trypsin.htm
  • New HTML files:
    • html/images/btag-daemon.jpg
    • html/images/dbstat.jpg
    • html/images/faindex1.jpg
    • html/images/faindex2.jpg
    • html/images/faindex3.jpg
    • html/images/msbridge.jpg
    • html/images/mscomp.jpg
    • html/images/msdigest.jpg
    • html/images/msfit.jpg
    • html/images/mshomology.jpg
    • html/images/msisotope.jpg
    • html/images/msnonspecific.jpg
    • html/images/mspattern.jpg
    • html/images/msseq.jpg
    • html/images/mstag.jpg
    • html/misc/publications/1996_asms_1.jpg
    • html/misc/publications/1996_asms_2.jpg
    • html/misc/publications/1998_asms_1.txt
    • html/misc/publications/1998_asms_2.txt
    • html/misc/publications/2000_asms_1.pdf
    • html/misc/publications/2000_asms_2.pdf
    • html/misc/publications/2001_asms_1.pdf
    • html/misc/publications/2002_asms_1.pdf
    • html/misc/publications/2002_asms_2.pdf
    • html/misc/publications/2003_asms_1.pdf
    • html/misc/publications/2004_asms_1.pdf
    • html/misc/publications/2005_asms_1.pdf
    • html/misc/publications/2005_asms_2.pdf
    • html/misc/publications/2006_asms_1.pdf
    • html/misc/publications/2007_asms_2.pdf
    • html/misc/publications/2007_asms_3.pdf
    • html/misc/publications/2008_asms_2.pdf
    • html/misc/publications/2008_asms_4.pdf
    • html/misc/publications/2009_asms_1.pdf
    • html/misc/publications/2010_asms_2.pdf
    • html/misc/publications/2010_asms_3.pdf
    • html/misc/publications/2010_asms_4.pdf
    • html/misc/publications/2010_asms_5.pdf
  • Changed param files:
    • params/usermod.txt - added AMTzGalNAcGlcNAc

V 5.6.2 08/24/2010 (2000/XP/XPx64/LINUX)
  • The maximum length of the sequence field on the MS-Product form has been increased from 500 to 1000.
  • There is now a display graph option on MS-Isotope.
  • Fixed the following bugs:
    • Some accession numbers in protein sequence databases have several species associated with them. Use a preferred species on the Search Compare form sometimes caused the correct species but the wrong accession number to be reported.
    • The Search Compare Report Homologous Proteins (All/Interesting/None) option didn't work properly is the results contained peptides with different N-terminal/C-terminal or neutral loss versions of the same peptide.
    • Search Compare and MS-Display could crash if the scan number requested was greater than the number of scans in the file.
  • Changed HTML files:
    • mshome.htm
    • html/misc/invar.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/enzyme.txt - added Elastase
    • params/enzyme_comb.txt - added DE-N/Cys-N
    • params/taxonomy.txt - added NATRIALBA MAGADII
    • params/usermod.txt - added iTRAQ8Plex of Y
    • params/msisotope/default.xml

V 5.6.1 07/19/2010 (2000/XP/XPx64/LINUX)
  • A parameter score_histogram_only can now be set in the params/mstag/default.xml file which makes MS-Tag produce a histogram of scores rather than the standard report. This used to be done if the Maximum Reported Hits parameter was set to a value of 1000 or more.
  • MS-Isotope now has a tab delimited text option.
  • Search Compare now has gradient and offset options for reporting the gradient and offsets of the survival functions used to calculate expectation values.
  • The options on the MS-Bridge Link AAs menu are now contained in the file params/link_aa.txt.
  • MS-Bridge now supports crosslinks to the Protein C-terminus.
  • MS-Bridge now has 6 rather than 4 user-defined dead end link modifications.
  • Fixed the following bugs:
    • The MS-Isotope XML output now works correctly.
    • The save to file option now also works for tab delimited text output
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/msbridge/default.xml
  • New param files:
    • params/link_aa.txt

V 5.6.0 06/22/2010 (2000/XP/XPx64/LINUX)
  • Batch-Tag can now consider b and y ions of +3 charge for the ESI-ION-TRAP-low-res instrument.
  • A new set of precursor charge and sequence dependent scoring coefficients has been introduced for the ESI-ION-TRAP-low-res instrument.
  • MS-Product now has checkboxes for turning peptides on and off it multiple peptides are entered.
  • MS-Product now can now plot a given number of peaks per 100 Da interval.
  • The MS-Product multiple losses checkbox has been replaced by a max losses menu.
  • The MS-Product raw data checkbox has been replaced by a menu allowing the display of either centroid data, raw data or raw data combined with centroid data.
  • MS-Product can now show ions which discriminate between a different peptides.
  • MS-Product now reports theoretical peaks outside the measured mass range in italics.
  • When proteins are sorted in Search Compare then accession numbers which don't form part of the gene name are preferred over those that do.
  • A directive called keep_r_data_file in params/info.txt can now be used to retain the temporary data files used to R scripts when drawing graphs. These are normally deleted.
  • DNA databases with sequences in lower case letters are now supported.
  • Fixed the following bugs:
    • mgf files with title lines similar to "TITLE=A20100611-04.10000.10000.3.dta" cause a "Spectrum not found in datafile" error when peptide matches from the search results are viewed in Search Compare. The error only occurs if the file is uploaded using Windows but the search is done by a LINUX computer.
    • A message is now printed for each mgf file created for a set of dta files uploaded by Batch-Tag Web. There is a potential problem with Apache timeouts if this isn't done.
  • Changed HTML files:
    • mshome.htm
    • html/pform.css
    • html/print.css
    • html/instruct/batchtagman.htm
    • html/instruct/prodman.htm
    • html/instruct/servadmn.htm
    • html/java/SpectrumGraph.jar
    • html/misc/invar.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
    • html/misc/publications/2006_asms_2.pdf
    • html/misc/publications/2008_asms_1.pdf
    • html/misc/publications/2010_asms_1.pdf
  • Changed param files:
    • params/fragmentation.txt
    • params/info.txt
    • params/pr_graph.par.txt

V 5.5.1 05/31/2010 (2000/XP/XPx64/LINUX)
  • The Batch-Tag and Search-Compare form settings can now be saved.
  • MS-Bridge now reports the accession number rather than the protein number if multiple proteins are involved in the search.
  • Guest accounts now have more checks to stop them doing illegal actions such as deleting data or calibrating a project.
  • Fixed the following bugs:
    • The default number of missed cleavages for a Batch-Tag expectation value search was 3 (as set is params/expectation.xml). If an enzyme such as ChymotrypsinFWYMEDLN was chosen with missed cleavages set to a high number (say 8) then insufficient precursors were available to calculate expectation values from some high mass spectra. Thus the expectation value was reported as -1.0. Now a new expecation value search is done for each setting of the missed_cleavage above the value is params/expectation.xml.
    • An error message is output if a cookie length is too long. The limit is currently around 4096 characters.
    • Quantitation doesn't work if one of the peptides contains a B or a Z as an amino acid.
    • Peptides which are "illegal" from a quantitation point of view - such as peptides where only some of the amino acids have an isotopic label - stop the quantitation working.
    • In some cases the number of unmatched masses was printed to the right of rather than underneath the spectrum graph in an MS-Fit detailed report.
    • Some combinations of modifications in MS-Fit cause the program to run for a very long time. The happened when there were more than around 25 sites of modification in a peptide from an identified protein. The program now exits with an error code if this happens.
    • There were problems with some Batch-Tag Web uploaded archives such as .tar.gz archives.
    • Quantitation scatterplots weren't drawn if there was a # character in the project or results name.
    • The R scripts initArgs.R and initGraph.R have been modified so that installations are independent of the version of R installed. This was necessitated as in version 2.6.0 of R a new units argument was added to the bitmap and png functions.
    • Systems without a data repository (eg the public server) now don't offer a Make Project option when Batch-Tag is run.
    • There were problems reading the charge from an mgf file if it was a floating point number.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/compman.htm
    • html/instruct/fitman.htm
    • html/instruct/patternman.htm
    • html/instruct/prodman.htm
    • html/instruct/seqman.htm
    • html/instruct/tagman.htm
    • html/misc/faq.htm
    • html/misc/invar.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
  • R Scripts:
    • initArgs.R
    • initGraph.R
    • quan.R
  • Changed param files:
    • params/enzyme.txt
    • params/quan.txt
    • params/taxonomy_groups.txt
    • params/usermod.txt
    • params/taxonomy/citations.dmp
    • params/taxonomy/delnodes.dmp
    • params/taxonomy/gc.prt
    • params/taxonomy/gencode.dmp
    • params/taxonomy/merged.dmp
    • params/taxonomy/names.dmp
    • params/taxonomy/nodes.dmp
    • params/taxonomy/speclist.dmp
    • params/taxonomy/taxonomy_cache.txt

V 5.5.0 03/17/2010 (2000/XP/XPx64/LINUX)
  • More file types which are uploaded to Batch-Tag Web can now be recognized. The archive formats .rar, .7z and .cmn are now recognized. Also the code used to recognize dta, pkl, mzData and mzXML files has been improved. Some support for mzML and Mascot Search Results files has been added.
  • Improved error messages if a Batch-Tag Web upload fails.
  • Most Batch-Tag Web uploads are now deleted if the upload fails.
  • MS quantitation methods like SILAC can now have more than 2 quantitation states.
  • The public server can now have a guest user.
  • MS-Product now reports the yn ion if there is an N-terminus that is in the b1.txt parameter file.
  • Fixed the following bugs:
    • An error message is now printed if the name of an uploaded Batch-Tag Web file, and hence the project name, is too long. The current limit is 58 characters.
    • There was a problem deleting a tar upload with an unrecogized format if some of the files were read only.
    • The elemental formulae reported in MS-Display (with links to MS-Isotope) were 1 hydrogen too light.
    • There were problems using Batch-Tag Web with uploads that were just compressed files (.gz, .Z) as distinct from compressed archives.
    • There were problems using Batch-Tag Web with uploaded filenames that didn't have a filename extension (such as .mgf, .dta or .txt).
    • There was a problem with uncompressed 64-bit conversion for mzXML and mzData files.
    • MS-Isotope graph sometimes didn't have a properly labelled x-axis.
    • If the Batch-Tag Web error message was longer than 512 characters then the program gave reported an unknown error. Such errors are now truncated so they fit in the database aborted_jobs table.
    • If the accession number list from a Search Compare report is posted into Batch-Tag Web then rather than a list of accession numbers it is treated as a single accession number with spaces. This can lead to a very long error message causing the above bug. An error message is now generated if the accession number is longer than 100 characters to intercept this problem.
    • The multiple losses option in MS-Product didn't work properly for S(Phospho), T(Phospho), Y(Phospho) and M(Oxidation).
  • Changed cgi-bin files:
    • 7za.exe added
    • common.exe added. Note on LINUX the binary should be installed and called common.
    • tar.exe removed
    • unrar.exe added
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/faq.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/quan.txt
    • params/sp_graph.par.txt

V 5.4.2 02/01/2010 (2000/XP/XPx64/LINUX)
  • Search Compare can now report p-values and -10 log10 (P value).
  • If the merge option is used in Search Compare the results are now merged based on p-values rather the discriminant scores. The exception to this is if one or more of the searches being merged didn't have an expectation value search.
  • Searches done prior to v5.4.2 will have a new expectation value search if the user does another Batch-Tag search on them.
  • Sizes of taxonomy, constant modifications and variable modifications form options increased.
  • Protein index now included in the XML output for MS-Digest.
  • Fixed the following bugs:
    • Spectra in mgf files where multiple charge were specified were only searched for the first specified charge.
    • wiffTOXIC program now tries to catch COM errors from the Sciex library.
    • Spot/RT option in Search Compare now renamed Fraction/RT.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/js/info.js
    • html/misc/revhist.htm
  • Changed param files:
    • params/enzyme_comb.txt
V 5.4.0 12/02/2009 (2000/XP/XPx64/LINUX)
  • A new scoring mechanism has been introduced for ETD data which allows different scoring weights and ion types to be considered for different charge states. The mechanism now also considers doubly charged fragment ions where appropriate which were previously not scored.
  • In cases in Batch-Tag/MS-Tag where a precursor match has multiple possible matches corresponding to different modification positions only the best matching score is used in the expectation value calculations.
  • Batch-Tag and MS-Tag now have a Max Peptide Permutations option. Peptides which exceed the maximum number of permuations are skipped in the search. Using this can greatly speed up searches looking for things like phosphorylations. Note that the number of permutations is calculated separately for each given number of modifications. Thus if the match has 5 modifications and there are only 5 modifiable sites then that is only a single permuation. If the Max Peptide Permuations field is left blank then all permuations are considered.
  • The pre-search peak filtering for Batch-Tag and MS-Tag can now attempt to remove specified ETD/ECD neutral loss peaks if desired. These are specified via a directive in params/fragmentation.txt. Note that only the tolerance region around multiply charged peaks is removed but for singly charged peaks the whole region is removed up to the highest specified loss.
  • MS-Product can now label neutral loss peaks in ETD/ECD spectra. These are generally removed from processed peak lists but can be seen if the Unprocessed MSMS tick box is selected.
  • ETD/ECD reduced charge peaks are now calculated using the precursor charge.
  • A file params/repository.xml can now be used as an alternative to params/inst_dir.txt. This file allows multiple centroid files to be associated with a single raw data file via the use of different suffixes. This has mainly been introduced to allow ETD and CID peak lists to share the same raw data file in a repository. There can also be a parameters block in the file to allow different default parameters (such as mass tolerances) to be set up for different instruments.
  • Search Compare can now report quantitation results from MSMS reporter ions without the raw data being present. It uses the centroid file if the raw data file isn't present. Note that currently this only works with mgf files. As most uploaded files are converted to mgf files this is only a restriction if other file formats are used in a user repository. If you want to see the actual data in such cases you need to use the MS-Product link from the peptide sequence and the Unprocessed MSMS tick box.
  • Search Compare now outputs the search time for each reported search. This is just the end time minus the start time and could be affected by such things as other searches taking place on the computer.
  • Precursor charge ranges on the Batch-Tag form can now include dash separated ranges (such as 2-5). Thus if you for example you wanted to search charges 2-5 and 7 but not charge 6 the selection would be "2-5 7". Note that none of these have yet been included on the default form but could be included in the file params/batchtag/default.xml if required.
  • Code has been written to allow the selection and upload of an unrestricted number of files. Only one such upload item is currently allowed per form. This hasn't been implemented anywhere yet.
  • The peak intensity has now been added to the match element of the MS-Product XML output.
  • Uploaded files are now written to the temporary directory in 1 MByte chunks rather than all at once.
  • The cgi parameters from a multipart form can now be written to a log file by setting the max_upload_content_length parameter in params/info.txt to 1.
  • Fixed the following bugs:
    • If a raw data directory matching the centroid directory is not present in a user repository the Make Project operation fails. This only affects the LINUX version.
    • Centroid files in the user repository are not now converted to UNIX text files by MS-Batch on LINUX systems.
    • The last peptide in a Peptide Difference Time report was incorrectly displayed.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/servdmn.htm
    • html/misc/invar.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
  • New HTML files:
    • html/js/multifile.js
  • Changed param files:
    • params/fragmentation.txt - Extensive changes to ESI-ETD-low-res option
    • params/info.txt - Some comments changed
    • params/inst_dir.txt - Can be replaced by repository.xml
    • params/instrument.txt - New peak filtering instruction for ESI-ETD-low-res option
  • New param files:
    • params/repository.xml - optional replacement for inst_dir.txt
V 5.3.2 10/13/2009 (2000/XP/XPx64/LINUX)
  • If the MSMS precursor tolerance on the Batch-Tag form is greater than the value in the parameters section of the params/expectation.xml file (and is in the same units) then it overrides it. Thus each specific MSMS precursor tolerance which is greater than the value in the file will result in an expectation value search.
  • If there are multiple MS-Product matches to an ion from different ion types they are sorted into order of increasing absolute mass error. The matches are be labelled <match1>, <match2>, etc in the XML output. Also the XML output has been slightly modified to allow the match information to be input into a spreadsheet.
  • Search Compare now has an unmatched spectra option that is off by default. This is used by some sort options of the Time report to output rows for spectra that didn't match.
  • There is now an option available to a systems administrator to allow Search Compare to output an MS-Product XML report for every peptide reported in a Search Compare report.
  • In MS-Tag and Batch-Tag sequence ions which include all the amino acids in the peptide are no longer scored.
  • c+1, c+2, z+2 and z+3 ions added to MS-Tag instrument ion types form.
  • The name of the score coefficient in params/fragmentation.txt for c-1 ions has been changed from cm1_score to c_minus_1_score.
  • The name of the score coefficient in params/fragmentation.txt for z+1 ions has been changed from zp1_score to z_plus_1_score.
  • When MS-Product is accessed from Search Compare there is a hidden part of the form called ion types. This is now left open if the instrument specific defaults tick box is not ticked.
  • The wiffToXIC program can now output a "note" for each precursor/product transition when used with Sciex Analyst 1.5.
  • Fixed the following bugs:
    • The MS-Fit option to search for another component doesn't work properly as the taxonomy options aren't correctly passed.
    • If multiple user proteins are entered into MS-Digest or MS-NonSpecific and the separate proteins option is selected then the first protein sequence is output for all proteins.
    • The Hits to File option now works correctly if XML is selected. Also only the HTML file is written if HTML is selected.
    • The Search Compare mods options only reports the correct position for the first modification in the peptide.
    • The protein information is not correctly reported in the Search Compare Time report.
    • Occasionally MS-Tag/Batch-Tag didn't match a doubly charged ion due to the wrong tolerance being applied.
    • If MS-Tag has 2 or more subsequent hits from the same peptide (say different modification positions) and there are multiple comment lines then the second and subsequent hits don't report the accession number from the first comment line.
    • In MS-Tag if instrument specific defaults are disabled then immonium ions are counted as matches when the tick box isn't selected.
    • MS-Product sometimes displays matches incorrectly if the charge is specified in the peak list.
    • The list of databases to search sometimes included incompletely indexed ones.
    • FA-Index creates .mw and .pi files for dna databases if it is run with the faindex_parallel flag set in params/info.txt.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/instruct/faman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/enzyme.txt - Lys-N added
    • params/fragmentation.txt - Names of c-1 and z+1 score coefficients changed

V 5.3.1 7/27/2009 (2000/XP/XPx64/LINUX)
  • New parameter virtual_dir_proxy in info.txt used for setting up a system with a proxy server.
  • Fixed the following bugs:
    • Quantitation methods using MS data now just work out the quantitation ratio for a particular peptide once per LC fraction. The one used is the first one encountered independent of whether it is the light or heavy peptide.
    • Batch-Tag Daemon, MS-Batch, MS-Form and Job-Status now close the mySQL database connection at the end of the program.
    • mysql_library_init and mysql_libary_end functions now used.
    • Link to MS-Display from Search-Compare didn't work for O18 data.
    • Java applet, links to data files and links in the MS-Fit results now use relative rather than absolute paths.
    • The error message generated when a constant modification wasn't present in the parameter file referred to the defunct const_mod.txt file rather than usermod.txt.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/faq.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/info.txt

V 5.3.0 7/15/2009 (2000/XP/XPx64/LINUX)
  • Search Compare now has a Separated or Merged option when comparing searches. If the Merged option is chosen then the results are displayed in a single set of report columns. This can be useful for example when combining CID and ETD results from the same sample.
  • In Search Compare the Difference option has been replaced with Protein and Peptide Difference options. These now result in multiple columns which report what is unique to each search being compared. There are also now Protein and Peptide Intersection options.
  • There is now a directive in the info.txt called faindex_parallel. If this is set then FA-Index runs with 2 passes through the database. If not then it runs with 5 passes through the database. If it is set the program runs faster but uses more memory. It may be appropriate not to have this set is you have a computer with a small amount of memory and large databases.
  • The ions defined for the fragmentation types ESI-TRAP-CID-low-res, ESI-Q-CID and ESI-ETD-low-res have now been built into the source code. This allows new ion types to be added without potentially slowing Batch-Tag/MS-Tag down.
  • New ion types c+1, c+2, z+2 and z+3 have been introduced to Batch-Tag/MS-Tag and MS-Product. These are to deal with cases when centroiding algorithms don't detect the monoisotopic peak.
  • The form item for entering the database name on the FA-Index form had been increased from 25 to 50 characters.
  • The Search Compare discriminant score graph is now cached. Once it has been displayed once it is stored in a file. This greatly decreases the program's memory requirements.
  • The Search Compare discriminant score graph is now red.
  • The Search Compare S column is now labelled RT.
  • On the Search Compare form the Keep Replicate Peptides option has been replaced by a 3 item menu with the following items: Best Peptide Only, Best Per Charge and Keep Replicates.
  • The black banner gif now uses a relative rather than an absolute path.
  • The color for protein coverage maps and MS-Product ion hits is now explictly defined rather than defined via a style sheet. This means it is preseved when pasted into Word.
  • MS-Product when run from Search Compare now has a form for selecting individual ion types.
  • MS-Product can now accept up to 6 sequences.
  • A message is now printed out when the modifications are being initialized in an MS-Tag search.
  • There is now an option to redirect requests which require raw data to a different server.
  • The default Search Compare maximum peptide expectation value has been changed from 0.01 to 0.05.
  • Only the root Batch-Tag binary now keeps its mySQL database connection open for the duration of the search.
  • Some code changes to allow the code to be compiled on Visual C++ 2008.
  • Fixed the following bugs:
    • An error message is now reported if a Thermo RAW file is corrupt and the raw data can't be read from it.
    • In Search Compare the Report Homologous Proteins options now work when searches are being compared.
    • On LINUX cluster systems with the repository on a network drive it was possible that projects could get accidentally deleted if something went wrong with the automounter. The daemon now aborts if this situation is detected.
    • The expectation value file could get corrupted if 2 or more searches are running simultaneously on the same project. If this occurs then Search Compare could show less results than were actually obtained. The Batch-Tag daemon has been modified to prevent simultaneous searches on the same project (they are now queued). Also Search Compare can now detect if any results are missing and prints an error message. If you get such an error message it is best to delete the project and rerun all the searches.
    • Deleting a project from Results Management whilst a search was running on it could cause the daemon to crash. An error message is now printed if a user attempts to do this,
    • Accession numbers from the Swiss Prot database downloaded from the Swiss Prot site now have version numbers. These have now been removed so that accession number links now work. Also the name field contained more information than was necessary to present.
    • On LINUX systems if the daemon is started automatically when the system is booted the path to the mpich2 executable needs to be defined in the startup script. If this didn't happen then previously the system said that any subsequent Batch-Tag searches had finished unexpectedly. Now it prints out a more meaningful error message.
    • FA-Index could crash if a comment line is longer than 1000 characters.
    • The Search Compare form was being loaded by the accession numbers used in an accession number limited Batch-Tag search. This was inappropriate if multiple such searches were being compared.
    • Some instruments didn't have minimum precursor masses defined. This could cause Batch-Tag searches to crash with very large N-terminus modifications.
    • For Thermo data the last scan of an averaged range was calculated incorrectly if the start retention time was greater than zero.
    • The font family was not being properly passed to Java applets.
  • Changed HTML files:
    • mshome.htm
    • html/pform.css
    • html/print.css
    • html/instruct/batchtagman.htm
    • html/instruct/servadmn.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/aa.txt
    • params/dbstat_hist.par.txt
    • params/enzyme.txt - Asp-C added
    • params/enzyme_comb.txt - CNBr/Asp-C and Chymotrypsin/Arg-C added
    • params/error_hist.par.txt
    • params/fit_graph.par.txt
    • params/hist.par.txt
    • params/idxlinks.txt
    • params/info.txt - faindex_parallel and raw_data_forwarding directives added
    • params/inst_dir.txt
    • params/instrument.txt - msms_min_precursor_mass 600.0 added from some instruments
    • params/mmod_hist.par.txt
    • params/pr_graph.par.txt
    • params/sp_graph.par.txt
    • params/searchCompare/default.xml
  • Perl Scripts in cgi-bin:
    • Modified Perl script mssearchmpi.pl.
  • R Scripts:
    • initGraph.R - bitmap function needs an extra argument
  • Windows now needs mySQL version 5.0.77
  • LINUX now needs R version 2.7.1 or later

V 5.2.2 3/17/2009 (2000/XP/XPx64/LINUX)
  • Batch-Tag/MS-Tag mass modification searches now have a protein/peptide switch for N and C terminus modifications. Also there is an uncleaved option to restrict modifications to residues that haven't been cleaved by the digestion.
  • Search Compare now has separate expectation value thresholds for proteins and peptides.
  • Fixed the following bugs:
    • If FA-Index is used with an invalid database name then the database appears in the list afterwards even though an error message is generated.
    • Batch-Tag project and results names could be entered that had a greater length than could be stored in the database.
    • Batch-Tag sometimes reports that the search finished for an unknown reason if there are less spectra than processors.
    • In some cases the wrong database is set when performing a Batch-Tag From Accession Number in Search Compare if a database suffix is used.
    • If any of the entries in the taxonomy names option is a not a UniProt organism code and a Batch-Tag search goes through the database more than once (not including the expectation search) then the search will not complete.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/batchtagman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/b1.txt - TMT6plex added
    • params/searchCompare/default.xml

V 5.2.1 2/16/2009 (2000/XP/XPx64/LINUX)
  • MS-Isotope now has a maximum resolution of 10,000,000. This is reduced to 200,000 for Lorentzian distributions.
  • MS-Isotope now plots out the detailed distribution on the graph if a detailed report is specified.
  • MS-Isotope now only plots intensities that are greater than 0.01% for Gaussian and Lorentzian distribution or 0.001% for Stick distributions.
  • The taxonomy cache file is no longer updated by FA-Index. It is updated if necessary whilst doing a taxonomy pre-search.
  • Fixed the following bugs:
    • The DTT modification was incorrect for Ser and Thr.
    • The MS-Isotope graph doesn't draw peaks at the correct heights if the resolution is too high.
    • The FA-Index Database Summary Report didn't work (introduced in 5.2.0).
    • If FA-Index is run from the command line a species parameter is required (introduced in 5.2.0).
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/quan.txt - DTT modification replaced by DTT_C and DTT_ST
    • params/usermod.txt - DTT option corrected

V 5.2.0 2/5/2009 (2000/XP/XPx64/LINUX)
  • FA-Index must be run on all databases before using the database search programs.
  • The species pre-search has now been replaced with a taxomomy pre-search. If a higher level taxonomy is chosen such as GREEN PLANTS then all database entries below it in the taxonomy are automatically searched without the server administrator having to worry about the relevant species names. Also if a species is chosen then the relevant sub-species are also included in the search. Any name in the NCBI taxonomy browser can now be added to the Taxonomy menu. Also names can be grouped together to produce menu items such as HUMAN MOUSE or MICROORGANISMS.
  • Multiple entries can be selected from the taxonomy menu.
  • The Species Codes item has been replaced with a Taxonomy Names item. This overrides the Taxonomy menu and allows you to search taxonomies that aren't on the Taxonomy menu. The Remove Taxonomies checkbox now works with this item so you can also use it to remove taxonomies from the database search.
  • DB-Stat and MS-Pattern (with Pre-Search Only set) give a full report of the species identified by a taxonomy pre-search. The other database search programs just report the number of entries identified by the taxonomy pre-search.
  • The list of species classed as microorganisms has been updated.
  • All the taxonomy files have been updated.
  • Charge reduced fragmentation introduced for ECD and ETD data.
  • Batch-Tag, MS-Tag and MS-Product now support c-1 and z+1 ions.
  • Ion tables in MS-Tag and MS-Product redesigned.
  • The DB-Stat default parameters are now read from the file params/dbstat/default.xml.
  • The MS-Bridge default parameters are now read from the file params/msbridge/default.xml.
  • The MS-Comp default parameters are now read from the file params/mscomp/default.xml.
  • The MS-Fit Upload default parameters are now read from the file params/msfitupload/default.xml.
  • The MS-Isotope default parameters are now read from the file params/msisotope/default.xml.
  • The MS-NonSpecific default parameters are now read from the file params/msnonspecific/default.xml.
  • The MS-Product default parameters are now read from the file params/msproduct/default.xml.
  • The MS-Seq default parameters are now read from the file params/msseq/default.xml.
  • The MS-Tag default parameters are now read from the file params/mstag/default.xml.
  • a1 and b1 ions can now be reported for relevant N-terminus modifications.
  • Some minor changes to allow compilation on Debian LINUX release 5.
  • MS-Seq prints a warning if the precursor mass is less than the lowest fragment mass.
  • The databases files can now have a suffix such as .fasta which is defined in params/info.txt. If used this is not visible in the database menus.
  • Fixed the following bugs:
    • Some No enzyme matches were missed in Batch-Tag/MS-Tag searches if a large mass modification range was chosen.
    • Some hits can't be found by MS-NonSpecific if a very large mass tolerance is used.
    • If a Batch-Tag search is done with Expectation Cal Method set to None there is no way of getting rid of the expectation value columns in the Search Compare reports.
    • A message is now output if one of the spectra used in an MS-Fit search has less peaks than the minimum number of peaks required to match parameter.
    • MS-NonSpecific now has a maximum number of hits of 50000 to prevent it running out of memory.
    • In MS-Comp the mass of a user defined amino acid cannot now be less than that of Glycine as defining one of very low mass can cause the program to run out of memory
    • There was a call to the usleep command with a parameter greater than 1 sec. This was thought to be causing an intermittant problem with starting searches on the LINUX version.
    • Under certain circumstances it was possible to get an infinite MOWSE score in MS-Fit. This caused the Windows version to abort because of a division by zero error.
    • If FA-Index was run with no parameters it reported that Search Compare had no parameters passed to it.
    • MS-Fit could crash if it was passed an MGF peak list with an END IONS line which wasn't matched by a BEGIN IONS line.
  • Changed HTML files:
    • mshome.htm
    • html/print.css - corrected a syntax error
    • html/instruct/allman.htm
    • html/instruct/faman.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/dbest.spl.txt
    • params/disc_score.txt
    • params/disc_score2.txt
    • params/enzyme.txt - Corrected an error in one entry.
    • params/fragmentation.txt
    • params/info.txt
    • params/instrument.txt
    • params/quan.txt - Corrected an error in one entry.
    • params/usermod.txt - added Cys->Dha
    • params/batchtag/default.xml
    • params/msdigest/default.xml
    • params/msfit/default.xml
    • params/mshomology/default.xml
    • params/mspattern/default.xml
    • params/searchCompare/default.xml
    • params/taxonomy/citations.dmp
    • params/taxonomy/delnodes.dmp
    • params/taxonomy/division.dmp
    • params/taxonomy/gc.prt
    • params/taxonomy/gencode.dmp
    • params/taxonomy/merged.dmp
    • params/taxonomy/names.dmp
    • params/taxonomy/nodes.dmp
    • params/taxonomy/readme.txt
  • New param files:
    • params/b1.txt - Some N-terminus modifications now have a b1 directive.
    • params/taxonomy.txt - Entries for the Taxonomy menu.
    • params/taxonomy_groups.txt - More entries for the taxonomy menu.
    • params/dbstat/default.xml added
    • params/msbridge/default.xml added
    • params/mscomp/default.xml added
    • params/msfitupload/default.xml added
    • params/msisotope/default.xml added
    • params/msnonspecific/default.xml added
    • params/msproduct/default.xml added
    • params/msseq/default.xml added
    • params/mstag/default.xml added
    • A new file params/taxonomy/taxonomy_cache.txt is now created automatically by the system.
    • The basic version now needs the files in the params/taxonomy directory.
  • Deleted param files:
    • params/species.txt

V 5.1.8 12/10/2008 (2000/XP/XPx64/LINUX)
  • The is a new feature in MS-Product which can bypass counting the basic amino acids to determine the maximum charge. This is necessary because sometimes amino acid modifications themselves can hold one or more charges.
  • There is a new parameter in params/info.txt for limiting the value of the Maximum Reported Hits parameter in MS-Fit. The default is 500.
  • The MS-Pattern regular expression field can now accept J and O.
  • There is a new parameter in params/info.txt for limiting the number of peaks in an MS-Fit spectrum. The default is 1000.
  • The Add User feature for Batch MSMS searching now has a more helpful error message if the user enters an invalid user name.
  • Copper now available as an element.
  • Fixed the following bugs:
    • The case insensitivity of accession numbers wasn't working.
    • MS-Fit could crash if the user asked for too many reported hits.
    • MS-Fit could crash if there were too many peaks in a spectrum.
    • On some LINUX versions the daemon didn't react correctly to a terminate request.
    • Some things typed into the MS-Homology possible sequences box, such as full protein sequences, leaving it empty or certain characters, could make it crash.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • Changed param files:
    • params/elements.txt
    • params/info.txt

V 5.1.7 12/2/2008 (2000/XP/XPx64/LINUX)
  • The MS-Digest default parameters are now read from the file params/msdigest/default.xml.
  • The MS-Homology default parameters are now read from the file params/mshomology/default.xml.
  • The MS-Pattern default parameters are now read from the file params/mspattern/default.xml.
  • An error message is now output if the contaminant masses field incorrectly formatted.
  • An error message is now output if the temporary data file stored by MS-Tag to allow the MS-Product links to work has been deleted.
  • Messages are now output during the pre-search.
  • A message is now output when MS-Fit is collating the detailed results.
  • If commas are entered into an MS-Product peptide sequence they are ignored.
  • If '^' characters are entered into an MS-Digest protein sequence they are ignored.
  • If a user enters accession numbers in MS-Digest but set the Retrieve entry by field to Index Number a more informatative error message is output.
  • Fixed the following bugs:
    • MS-Pattern sometimes crashed if the maximum number of mismatched amino acids was set to zero. This didn't occur on the Windows version.
    • MS-Digest sometimes ran out of memory. To try to prevent this happening the maximum number of hits is now 50000. There is also a limit of 50000 different combinations of modifications on a single peptide.
    • MS-Digest had a memory leak that was apparent if there were a very large number of peptides in the report.
    • MS-Homology crashed if the possible sequences contained commas.
    • The error message is not very informative if users omit the precursor ion in MS-Seq.
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm
  • New param files:
    • params/msdigest/default.xml added
    • params/mshomology/default.xml added
    • params/mspattern/default.xml added

V 5.1.6 11/27/2008 (2000/XP/XPx64/LINUX)
  • Cosmetic changes to the links from the MS-Fit detailed report to search for unmatched masses.
  • Cosmetic changes to the MS-Digest form.
  • The MS-Fit default parameters are now read from the file params/msfit/default.xml. This does not apply to the MS-Fit Upload form.
  • There are more checks on the data files uploaded in MS-Fit Upload. This can now detect if binary files or mgf MSMS files are uploaded by mistake.
  • On the LINUX version the databases are now sorted into alphabetical order.
  • If there are only sequences relating to a single spectrum in MS-Homology then the first number in the Possible Sequences forms option can be left out. Also if the maximum errors number is left out then it is assumed to be zero.
  • If '\' or '&' characters are entered into an MS-Product peptide sequence they are ignored.
  • The default Max Mods parameter on MS-Fit has been changed from 2 to 1.
  • If the pre-search Protein High MW is less than or equal to the Protein Low MW an error message is printed.
  • If the pre-search Protein High pI is less than or equal to the Protein Low pI an error message is printed.
  • If no proteins are found in the pre-search then this is shown prominently in the results.
  • If additional sequences are used in an MS-Product report and there is a form in the MS-Product output then the additional sequences portion of that form is left open.
  • The possible sequences in MS-Homology have to be at least 4 amino acids long. Also there have to be at least 4 more amino acids in the sequence than the maximum number of errors.
  • Version number checking disabled for this release.
  • Fixed the following bugs:
    • If there was a very long stretch of amino acids with no cleavage site in a protein that was either an MS-Fit hit or chosen for MS-Digest/MS-Bridge/MS-NonSpecific then the program could hang. The problem occurred more often when more variable modifications were chosen.
    • If inappropriate homology parameters are selected for MS-Fit resulting in a very large number of hits then the program could hang.
    • The links from the MS-Fit detailed report to search for unmatched masses didn't work properly if the peak list was too long.
    • If the effective precursor mass (the precursor mass minus the masses of the known amino acids) is too large then MS-Comp could run out of memory. There is now a maximum effective precursor mass of 1600 Da.
    • If there were space characters before the masses in the MS-Fit/MS-Bridge Data Paste area the data wasn't read in properly.
    • MS-Bridge crashed if the Separate Proteins tick box was selected and there was more than one protein.
    • MS-Fit could run out of memory if a species pre-search of NOT HUMAN was used with a protein MW pre-search on the NCBInr database.
    • Entering species codes in lower case caused the search programs to crash.
    • MS-Homology now has a maximum number of peptide hits of 2000000 to prevent it running out of memory.
    • MS-Pattern now has a maximum number of hits of 100000 to prevent it running out of memory.
    • MS-Pattern pre-search only now has a maximum number of hits of 2000000 to prevent it running out of memory.
    • Some entries in the Possible Sequences box in MS-Homology can cause it to crash.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/homologyman.htm
    • html/misc/bughist.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • New param files:
    • params/msfit/default.xml added

V 5.1.5 11/17/2008 (2000/XP/XPx64/LINUX)
  • User Protein sequences in MS-Digest/MS-Bridge and MS-NonSpecific can now be in 3 letter amino acid code or lower case (but not mixed case).
  • User Protein sequences in MS-Digest/MS-Bridge and MS-NonSpecific can now be DNA sequences.
  • The available PSI modification names are now included on the MS-Product and MS-Isotope forms.
  • Some more form entries are checked for incorrect information on the client side.
  • There has been an attempt made to try to interpret what the user wanted to enter as a peptide or protein sequence in MS-Digest/MS-Bridge/MS-NonSpecific and MS-Product. For example certain characters such as numbers are now ignored.
  • MS-Product and MS-Isotope now have improved instructions on the form.
  • The version parameter can now be left blank.
  • Accession numbers are now case insensitive thus an accession number such as Q01205 can be entered as q01205.
  • MS-Product internal ions are only reported if the sequence is 200 amino acids or less in length.
  • MS-Product internal ions are only reported if the sequence is 4 amino acids or more in length.
  • The internal ion option in MS-Product is off by default.
  • Fixed the following bugs:
    • Code has been added to help limit the entry of illegal elemental formulae. Eg some users tried entering elemental formulae without spaces (eg. C2H6 rather than C2 H6) and these were being incorrectly interpreted.
    • Log files were incorrectly handled if a user closed the browser or pressed the browser stop button during a search on a LINUX server.
    • Log files were incorrectly handled if a user pressed the abort search button.
    • Accession number lists were incorrectly interpreted if the accession number had leading spaces.
    • There were problems if the user select the Auto option on MS-Fit/MS-Bridge/MS-NonSpecific. This option is no longer available.
    • In MS-Product the phosphorylation and methionine oxidation specific fragments were only output if the modification was entered in the correct case. Eg. S(Phospho) worked but not S(phospho).
    • Calibration was not possible in Search Compare.
    • Batch-Tag and MS-Tag sometimes crashed during a search that was in some way non-enzymatically specific. This seemed to happen particularly when searching for high mass modifications.
    • Very long sequences caused MS-Product to crash.
    • MS-Product calculated internal ion masses whether they were needed or not.
    • The MS-Product multiple losses option didn't work properly if PSI modifications were used in the sequence.
  • Changed param files:
    • params/usermod.txt - Some modifications now have the Uncleaved directive
  • Changed HTML files:
    • mshome.htm
    • html/instruct/allman.htm
    • html/instruct/isoman.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm

V 5.1.4 10/30/2008 (2000/XP/XPx64/LINUX)
  • Error messages are now printed if no parameters are passed to one of the programs. This can happen if a user presses return in the browser URL box.
  • Error messages are now printed if the form is from a different version number than the search program. This happens if the software has just been updated.
  • If logging is enabled and the program prints an error message then this also gets inserted into the log file.
  • Protein sequences can now be entered into MS-Digest with numbers and asterisks in them. This facilitates pasting of sequences from other sources.
  • Fixed the following bugs:
    • If logging is enabled and the program printed an error message then the log file wasn't correctly closed.
    • Links from MS-Fit and other programs to MS-Digest didn't work.
    • Some sets of parameters for MS-Fit/MS-Digest/MS-Bridge caused the program to run very slowly.
    • Sequences entered into MS-Product with trailing spaces led to an error message.
  • Changed param files:
    • params/idxlinks.txt
  • Changed HTML files:
    • mshome.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm

V 5.1.3 10/16/2008 (2000/XP/XPx64/LINUX)
  • The MS-Product error graph now has a key explaining the meaning of the colored dots.
  • MS-Product can now handle multiple sequences. These can either be alternative sequences such as different positions of modified amino acids or complementary sequences such as coeluting or crosslinked peptides.
  • MS-Product now has a vertical and a horizonal sequence report. The vertical report just shows the main ions.
  • MS-Product now prints statistics on the percentage intensity matched.
  • MS-Product no longer has a constant modification option.
  • The parameters required for quantitation methods which make use of MSMS reporter ions are now entered in parameter files. This means new methods can be supported without changing the source code.
  • Thermo tandem mass tag quantitation is now supported.
  • Species extraction from NCBInr database comment lines improved.
  • Support added for new UniProt comment line format.
  • Search Compare now reads its default form parameters from the file params/searchCompare/default.xml.
  • MS-Digest/MS-Bridge now use PSI notation. The options on the possible modifications menu are now covered by the variable modifications menu.
  • MS-Bridge now supports cross-links that have different amino acids at the ends of the crosslink.
  • Default maximum link molecules in MS-Bridge changed from 5 to 2.
  • Chem score feature removed from MS-Digest/MS-Fit.
  • End terminus parameters now in a hidden section of the MS-Digest form.
  • MS-Bridge user defined link parameters now in a hidden section of the MS-Digest form.
  • Variable modifications to amino acids can now called uncleaved. That means that they can't occur at digest cleavages.
  • MS-Bridge/MS-Digest end terminus and Present Amino Acids parameters now in hidden sections of the forms.
  • There are now variables in the parameter file info.txt to specify whether the MS-Batch-Tag expectation search is done before or after the main search and whether to join the results files together.
  • DB-Stat now has maximum missed cleavage and constant modification options.
  • More instructions have been added explaining how to run Batch-Tag/Search Compare from the command line.
  • Fixed the following bugs:
    • Hits from the same peptide sequence with different terminal groups or constant neutral losses weren't displayed in Search Compare unless the keep replicate peptides option was selected.
    • If the mail script mail.pl has the wrong permissions the Batch-Tag Daemon stops without reporting an error (only reported on the UNIX version).
    • The record_created field isn't filled in the search_jobs database table.
    • Programs run from HTML forms with method="POST" and enctype="multipart/form-data" don't work on a 64-bit UNIX platform.
    • Batch-Tag crashes if a database pre-search doesn't generate any entries. This could happen for example if someone pasted accession numbers in the species codes field.
    • The Search Compare composition column shows 1 rather than 0 if no composition items have been selected.
    • If modifications for MS-Digest are chosen from the Variable Mods menu then the terminal specifications aren't applied. This can be avoided for Gln->PyroGlu by selecting Peptide N-terminal Gln to pyroGlu from the Possible Modifications menu.
    • In MS-Digest if more than one modification from the Variable Mods is chosen to the same amino acid (eg Acetyl (K) and Methyl (K)) then the same amino acid can be modified more than once.
    • Quantitation ratios sometimes weren't calculated. This was because one of the peaks had more or less no intensity and the peak fitting algorithm wasn't working.
    • User defined amino acids weren't being correctly passed between MS-Digest/MS-Bridge and MS-Product.
    • The start number of the stripping range in the end-terminus parameters on MS-Digest/MS-Bridge can now be zero.
  • Changed param files:
    • params/usermod.txt
  • New param files:
    • params/acclinks.txt
    • params/info.txt
    • params/itraq.txt removed
    • params/itraq8.txt removed
    • params/iTRAQ4plex.txt added
    • params/iTRAQ8plex.txt added
    • params/links.txt
    • params/pr_graph.par.txt
    • params/quan.txt
    • params/quan_msms.txt added
    • params/usermod.txt
    • params/searchCompare/default.xml added
    • params/taxonomy/citations.dmp added
    • params/taxonomy/delnodes.dmp added
    • params/taxonomy/division.dmp added
    • params/taxonomy/gc.prt added
    • params/taxonomy/gencode.dmp added
    • params/taxonomy/merged.dmp added
    • params/taxonomy/names.dmp added
    • params/taxonomy/nodes.dmp added
    • params/taxonomy/readme.txt added
    • params/taxonomy/speclist.txt added
  • Changed HTML files:
    • mshome.htm
    • html/pform.css - code added for multiple MS-Product sequences
    • html/print.css - code added for multiple MS-Product sequences
    • html/images/cent_repos.jpg added
    • html/images/raw_repos.jpg added
    • html/instruct/allman.htm
    • html/instruct/bridgeman.htm
    • html/instruct/digestman.htm
    • html/instruct/fitman.htm
    • html/instruct/nonspecificman.htm
    • html/instruct/servadmn.htm
    • html/java/SpectrumGraph.jar
    • html/misc/bughist.htm
    • html/misc/invar.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
  • R Scripts:
    • msmsErrorScatter.R - key added to graph

V 5.0.1 5/19/2008 (2000/XP/XPx64/LINUX)
  • There is now an optional mass modification column in Search Compare. If this is selected for a peptide report a mass modification histogram is displayed near the top of the report.
  • Search Compare results can now be sorted by mass modification.
  • The Search Compare composition option now supports mass modifications.
  • A mass modification histogram is displayed in the Search Compare .
  • Search Compare results now have 2 sort levels.
  • Fixed the following bugs:
    • The feature in Search Compare whereby hits with known modifications were sorted above identically scoring hits with mass modifications didn't work properly for modifications containing stable isotopes.
  • Changed param files:
    • params/enzyme_comb.txt - CNBr/Trypsin/V8 DE and CNBr/Trypsin/V8 E added
  • New param files:
    • params/mmod_hist.par.txt
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/invar.htm
    • html/misc/revhist.htm

V 5.0.0 5/6/2008 (2000/XP/XPx64/LINUX)
  • Fixed the following bugs:
    • Hidden parts of the forms or output were displayed whilst they were loading.
    • The pre-search parameter which dealt with results from another search had menu items for batchtag and msmatch. These have now been removed.
    • Decoy accession numbers are now put in square brackets in Search Compare tab delimited output so they sensibly displayed in Excel. The word "decoy" is put in the gene name column for such entries in such reports.
    • Hit numbers are now put in square brackets in Search Compare tab delimited output so they sensibly displayed in Excel.
    • Usermod entries in the quan.txt file could not have non-isotopic elements in their delta formula.
  • Changed HTML files:
    • mshome.htm
    • html/peakSpotter.htm
    • html/wiffread.htm
    • html/images/fragtag.gif deleted
    • html/images/wznowsma.gif deleted
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/bridgeman.htm
    • html/instruct/compman.htm
    • html/instruct/dbstatman.htm
    • html/instruct/digestman.htm
    • html/instruct/faman.htm
    • html/instruct/fitman.htm
    • html/instruct/homologyman.htm
    • html/instruct/isoman.htm
    • html/instruct/nonspecificman.htm
    • html/instruct/patternman.htm
    • html/instruct/prodman.htm
    • html/instruct/seqman.htm
    • html/instruct/servadmn.htm
    • html/instruct/tagman.htm
    • html/js/info.js
    • html/misc/bughist.htm
    • html/misc/faq.htm
    • html/misc/invar.htm
    • html/misc/links.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm

V 5.0.0beta7 4/28/2008 (2000/XP/XPx64/LINUX)
  • Search form headings are now a link to the relevant manual.
  • Fixed the following bugs:
    • Quantitation in Search Compare/MS-Display didn't work if there was a mass modification. It now gives an answer. Any answers given should be checked manually.
    • FA-Index hung when sorting the accession numbers for the dbEST.human database.
    • Fixed the following problems with Search Compare tab delimited multi sample reports:
      • Sample number now a column in peptide reports.
      • Uniq pep column now available in peptide reports.
      • Header not printed if there were no results to report in the first sample.
      • Whether the Uniq Pep column is included in the report depends on whether any of the hits had homology hits. However this was previously done on a per fraction basis so the columns could potentially not line up. Now the column is included if any of the fractions have homology hits.
  • Changed param files:
    • params/dbest.spl.txt
  • Changed HTML files:
    • mshome.htm
    • html/images/unknome.gif deleted
    • html/instruct/faman.htm
    • html/instruct/servadmn.htm
    • html/instruct/tagman.htm
    • html/js/info.js
    • html/misc/revhist.htm

V 5.0.0beta6 4/19/2008 (2000/XP/XPx64/LINUX)
  • Fixed the following bugs:
    • Batch-Tag searching sometimes failed on LINUX versions. This was thought to be because some peaks in the centroid file had exactly the same M+H (not m/z) value. Replacing a sort with a stable_sort seemed to get rid of the problem.
    • FA-Index hung when sorting the accession numbers for the dbEST.others database.
    • The User Protein Sequence option on the Create or Append to User Database form on the FA-Index page had some instructions that needed correcting slightly.
    • The User Protein Sequence option on the Create or Append to User Database form on the FA-Index page accepted characters that weren't amino acids (eg numbers).
    • Search Compare crashed if the peptide sequences contained numbers. This shouldn't happen but see the bug above.
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/misc/bughist.htm
    • html/misc/revhist.htm

V 5.0.0beta5 4/15/2008 (2000/XP/XPx64/LINUX)
  • New Search Table program added which prints out details of all running and queued jobs. Users have links to the Job Status program to control their own jobs. Root users have extended information and can control all jobs.
  • MGF files created by Mascot Distiller for Water and Sciex Analyst files now supported. Raw data supported for the Sciex Analyst.
  • Parameter file links.txt, which is used by the Link Search Type menu on MS-Bridge, is now more PSI compliant.
  • DB-Stat additionally reports the number of theoretical enzyme fragments in the histogram range.
  • New variables added to html/js/info.js to control whether various links on mshome.htm are displayed.
  • feedback_email parameter removed from params/info.txt.
  • Fixed the following bugs:
    • There was a problem with Batch-Tag if Windows was used as the web server with LINUX compute nodes and an mgf file without a .mgf suffix was uploaded.
    • Incorrect font used for the error message if an invalid user modification is used.
  • Changed param files:
    • params/info.txt
    • params/links.txt
    • params/mgf.xml
    • params/usermod.txt
  • Changed HTML files:
    • mshome.htm
    • html/instruct/servadmn.htm
    • html/js/info.js
    • html/misc/bughist.htm
    • html/misc/revhist.htm

V 5.0.0beta4 4/1/2008 (2000/XP/XPx64/LINUX)
  • expectation.txt parameters min_used_spectra and max_used_spectra changed to min_used_peptides and max_used_peptides.
  • Score Matrix menu on MS-Homology page now created from params/mat_score.txt.
  • Display graph option added to MS-NonSpecific.
  • kill_button option removed from params/info.txt. The Kill button is now always displayed when appropriate.
  • params_dir option removed from params/info.txt.
  • user_repository_temp option in params/info.txt now changed to upload_temp.
  • Quantitation menu options on Search Compare form now based on PSI names. This involved changes to params/quan.txt.
  • Peptide count option added to Search Compare form.
  • params/info.txt file sorted into more logical order.
  • Some manuals updated.
  • dbEST.others species list updated.
  • params/disc_hist.par.txt deleted
  • params/immonium.txt deleted
  • params/novo_graph.par.txt deleted
  • Dehydrated (ST) added to usermod.txt
  • Fixed the following bugs:
    • Search Compare protein report Uniq Pep column sometimes had negative numbers if Keep Replicate Peptides was selected. This also meant too many homologous proteins were retained.
    • Search Compare Num Unique column gave incorrect values if Keep Replicate Peptides was selected.
    • Messages are now printed out during quantitation either every time a peptide is processed from the raw file or every 10 seconds, whichever is the longer time. This was to get around a problem with Apache timing out (which it does after 5 minutes of inactivity) when there was a problem with a slow wiff file. Occasionally wiff files are very slow to process when they are on a network drive. The cause of this presently unknown.
    • Link to Batch MSMS Searching manual missing.
  • Changed param files:
    • params/acclinks.txt
    • params/dbest.spl.txt
    • params/disc_hist.par.txt deleted
    • params/elements.txt
    • params/expectation.txt
    • params/immonium.txt deleted
    • params/indicies.txt
    • params/info.txt
    • params/itraq.txt
    • params/itraq8.txt
    • params/mat_score.txt
    • params/novo_graph.par.txt deleted
    • params/quan.txt
    • params/unimod.txt
    • params/usermod.txt
    • params/batchtag/default.xml
  • Changed HTML files:
    • mshome.htm
    • html/instruct/homologyman.htm
    • html/instruct/servadmn.htm
    • html/js/info.js
    • html/misc/revhist.htm

V 5.0.0beta3 3/17/2008 (2000/XP/XPx64/LINUX)
  • Logout facility added.
  • Some form text entries now checked for validity.
  • More comprehensive information is now saved to the database in the case of an aborted search.
  • Fixed the following bugs:
    • Batch-Tag searches that were aborted before they started weren't being properly cleaned up until the daemon tried to start them.
    • There were missing columns in Search Compare tab delimited reports if the previous and next amino acid were reported and more than one search were compared.
    • Search Compare comparisons peptide reports of quantitation data sometimes crashed.
    • The parameter max_btag_searches, defined in params/info.txt, had a default value of zero rather than one.
    • If Batch-Tag/MS-Tag mass modification searches were done with constant modifications set then the mass modification was reported relative to the constant modification rather than the unmodified amino acid. This also caused problems if the match was viewed in MS-Product

V 5.0.0beta2 3/7/2008 (2000/XP/XPx64/LINUX)
  • The default name for the Batch-Tag Daemon on the LINUX version is now btag-daemon.
  • The name for the Batch-Tag Daemon/Service can now be specified in params/info.txt. The idea of this is to allow multiple instances of Prospector to run on the same computer.
  • The time in days that entries in the sessions table controlling browser cookies is kept can now be specified in params/info.txt.
  • The time in days that details on aborted Batch-Tag jobs is kept for can now be specified in params/info.txt.
  • Simplified the email code. The default value of the virtual directory is now prospector.
  • Fixed the following bugs:
    • If the Batch-Tag Service on the Windows version was installed using btag_daemon rather than btag_daemon.exe on the command line it was installed with the wrong name.
    • If a Batch-Tag search fails for any reason the user isn't informed about the reason.
    • If a Search Compare report shows no results the search parameters aren't printed.
    • If a the Default search page is used on an existing project then the instrument is always set to ESI-Q-TOF.

V 5.0.0beta1 2/29/2008 (2000/XP/XPx64/LINUX)
  • A system may now consist of mixed LINUX and Windows computers with separate daemons running on the separate computers. To achieve this the host name of the running job is stored in the database.
  • Some daemon service parameters can now be redefined whilst the daemon is still running. On Windows systems the parameters are read if the info.txt last update time changes. On UNIX systems a HUP signal must be sent to the daemon process to get the parameters to be read. The parameters are updated after the daemon loop time so may not update immediately.
  • The amino acid statistics option in DB-Stat now dramatically faster.
  • Version number no longer part of the name of the Batch-Tag Daemon service. This makes updating the release easier as the service doesn't generally need to be deleted.
  • Some parameters for sending email are now defined in info.txt rather than as command lines to the server.
  • The repository date directories are now deleted if they become empty as a result of deleting results, etc.
  • The daemon loop time and job status update times can now be defined in info.txt.
  • Queued jobs are no longer deleted when a daemon is stopped.
  • To accomodate mixed UNIX and Windows systems all user directories are now in lower case.
  • Search Compare now prints out progress messages.
  • The FA-Index progress messages now generally overwrite each other.
  • On LINUX the date directories for log files now have a leading zero in the day of the month.
  • System error messages are no longer reported. These were usually confusing.
  • There is no longer an option for running searches without a daemon/service.
  • The version number has now been removed from most files.
  • Instrument name field added to the projects directory in the database. This isn't used as yet.
  • Fixed the following bugs:
    • Search Compare reports which took longer than 5 minutes to generate activated an Apache timeout. This has been solved by printing progress messages.
    • Performance problem with network drives due to flushing the output buffers too much when writing out Batch-Tag results files.
    • An error message is now printed if unknown elements are used in MS-Isotope.
    • There was a problem if both variable and constant N or C terminal modifications were used at the same time (eg iTRAQ N-terminus and Acetyl N-terminus).
    • There was a confusing error message given if command line arguments weren't properly specified (eg when running FA-Index from the command line).
    • There were some problems with CNBr searches.

V 4.27.2 1/9/2008 (2000/XP/XPx64/LINUX)
  • N termini-1=D option added to the Non-specific menu in MS-Tag and Batch-Tag.
  • Protein length option added to Search Compare.
  • Search Compare/MS-Display can now average the scans for a specified time range around the time of the MSMS spectrum. The time range doesn't have to be symmetical. This works for both Thermo RAW files and ABI wiff files and can improve quantitation.
  • Cations are now counted as positive charge bearing amino acids.
  • Neutral loss modifications can now be set in usermod.txt.
  • The Max MSMS Peaks option is now blank on the Search Compare form. If this option is left blank the default option is used from the instrument.txt file.
  • Search Compare now has an option for turning off the discriminant score graph. The program will use considerably less memory if this is deselected. This is helpful for large data sets particularly those involving quantitation.
  • The check box option is now only available on Search Compare if a single search is being compared.
  • There is now a Maximum Reported Hits option on Search Compare. The value set here is passed through to MS-Tag From File. For mass modification searches it is appropriate to set this to a higher value than used for a normal search.
  • There now have to be an even number of Dehydro modifications in a hit peptide.
  • Hits with known modifications are now sorted above identically scoring hits with mass modifications in the results files.
  • Quantitation ratios are no longer calculated for peptides where only some of the possible residues are labelled.
  • Some changes made to try to make the use of memory during quantitation calculations more efficient.
  • The theoretical isotope distibution calculation used during quantitation is now less accurate to improve speed.
  • A Print button has been added to the interactive graph applet. This allows the graph to be printed at high resolution via a dialog.
  • m/z and charge of precursor ion is now displayed as a title to the MS-Display report.
  • MS-Display now has an option for browsing the MS scans in a Thermo RAW file.
  • Fraction names are now listed in the parameters section of a Search Compare report.
  • Mercury can now be used in elemental formulae.
  • Logging facility added which can record some cgi environment variables, process IDs, start and end times and search parameters for some of the cgi-bin programs.
  • Import project feature added. This is chiefly for importing projects from previous releases.
  • Package is now generally installed in Program Files on a Windows platform. Version numbers are now longer in the URL.
  • Fixed the following bugs:
    • Neutral loss modifications couldn't be combined with other modifications.
    • The Batch Tag daemon isn't started the first time it is used.
    • There was no check to see if the same modification is set as a constant and a variable modification.
    • Carbamidomethyl C was set as both a constant and default modification on the default Batch-Tag form.
    • In MS-Product matched masses weren't shown in red in the immonium ion and theoretical spectrum tables.
    • If the precursor charge was reset in MS-Tag from File the new charge wasn't passed through to MS-Product.
    • The root user was able to create projects.
    • Quantitation ratios were not being calculated for peptide where the modification name had a dash character (eg. Gln->pyro-Glu).
    • Quantitation ratios were not being calculated for cases where one of the peaks had no data in the area where the peak was expected.
    • A lot of memory was being used up in the quantitation ratio calculate by using deque instead of vector. This appears to be a bug in the Visual C++ compiler.
    • The maximum MSMS peak setting on Search Compare wasn't being passed through to MS-Product and MS-Tag from File.
    • Some printing problems have been resolved.
    • Peptide hits with expectation values below the expectation value limit were being rejected as there was another peptide with an expectation value above the limit but with a better disciminant score. This generally occurs when both hits are correct due to coeluting peptides.
    • Problem with discriminant scoring for the ESI-FT-ICR-CID instrument.
  • Changed param files:
    • batchtag/default.xml, deleted variable mod Carbamidomethyl C.
    • disc_score.txt
    • disc_score2.txt
    • instrument.txt
    • elements.txt - Hg added.
    • instrument.txt
    • usermod.txt - Carboxy (W), Cation:N(1)H(4) (Neutral Loss), Delta:H(2)C(3) (K), Delta:H(4)C(3)O(1) (CHK), Delta:H(4)C(6) (K), Delta:H(6)C(6)O(1) (K), Delta:H(8)C(6)O(2) (K), Dioxidation (W), GluGlnIleGlyGly (K), HNE (CHKPRT), HNE+Delta:H(2) (CHKPRT), HNE-Delta:H(2)O (CHKPRT), Label:13C(6)15N(2)+GluGlnIleGlyGly (K) added.
  • Changed HTML files:
    • mshome.htm
    • default.htm
    • index.htm
    • missing.htm
    • html/pform.css
    • html/instruct/allman.htm
    • html/instruct/batchtagman.htm
    • html/instruct/bridgeman.htm
    • html/instruct/compman.htm
    • html/instruct/dbstatman.htm
    • html/instruct/digestman.htm
    • html/instruct/faman.htm
    • html/instruct/fitman.htm
    • html/instruct/homologyman.htm
    • html/instruct/isoman.htm
    • html/instruct/nonspecificman.htm
    • html/instruct/patternman.htm
    • html/instruct/prodman.htm
    • html/instruct/seqman.htm
    • html/instruct/servadmn.htm
    • html/instruct/tagman.htm
    • html/java/SpectrumGraph.jar
    • html/js/info.js
    • html/misc/bughist.htm
    • html/misc/dipep.htm
    • html/misc/faq.htm
    • html/misc/invar.htm
    • html/misc/links.htm
    • html/misc/mutation.htm
    • html/misc/publications.htm
    • html/misc/revhist.htm
    • html/misc/trypsin.htm
  • New HTML files:
    • html/print.css

V 4.27.1 9/28/2007 (2000/XP/XPx64/AIX/LINUX)
  • Database that controls users, projects and results from Batch-Tag/Search-Compare. Results are now owned sorted by user.
  • Modifications now follow the PSI standard. The same file is used to control constant and variable modification.
  • Search daemon that queues up searches and can limit the number of concurrent searches.
  • Mass modification searches can now deal with constant neutral loss and terminal groups.
  • An automatic installer has been written.
  • Constant modifications are shown in the sequences in Search-Compare.
  • Constant terminal modifications now listed with other constant modifications.
  • There is now a link to the Unimod site from MS-Product for peptides with a mass modification.
  • Data file formats are now much independent of instrument. Also the program automatically tries to determine the file format.
  • The user interface has been redesigned.
  • A Non-Specific at 2 termini option has been added. This is similar to a no enzyme search except that it considers missed cleavages.
  • Batch-Tag Web can now use multiple processors.
  • Batch-Tag Web can now upload archive (eg zip) files containing multiple centroid files and/or raw data. Off-site quantitation is thus now possible.
  • Batch-Tag Web now has the same options as the standard Batch-Tag form.
  • Search-Compare now has a missed cleavages column.
  • Batch-Tag can now deal with unspecified charges in centroid files.
  • There is a resolution option in the Search Compare raw data/quantitation section. This is to allow peak fitting of high resolution data.
  • There is a button to return you to the search form after an Abort Search button has been pressed.
  • q can no longer be used for pyroglutamic acid.
  • MS-Fit options removed from Batch-Tag form.
  • DB-Stat now only prints a second graph if there are less than 300000 data points.
  • MS-Product now has a tab delimited output option when called from Search-Compare.
  • New Uniprot comment format supported.
  • The MS-Digest XML output now has a peptide tag around each peptide.
  • Pre search results and search parameters are now in expandable blocks in some search results.
  • Composition options in Search-Compare now supports all modifications.
  • Time sort option removed from Search-Compare form.
  • Fixed the following bugs:
    • Quantitation doesn't work on high resolution data.
    • Some very intensive searches can run out of memory (eg No enzyme combined with mass modifications) can fail especially if the first protein in the list is a heavy one.
    • Average mass searches in MS-Fit don't work properly.

V 4.25.2 1/24/2007 (NT/2000/XP/XPx64 and LINUX)
  • Expectation values can now be reported with Batch-Tag search results.
  • Discriminant scoring is now based on expectation values where calculated.
  • MS-Tag from File can plot a survival curve of peptide scores for peptides passing the precursor filter.
  • There is now a mass modifications option in Batch-Tag and MS-Tag that can consider a range of integer mass shifts on any selected amino acid.
  • There is a new Allow Non-Specific Cleavage option in several of the programs.
  • Raw data from an LCQ can now be displayed or used for quantitation.
  • Search Compare can now have a gene name column with a link to an external database.
  • Search Compare now has a number of precursor matches option in the peptide report.
  • In the Search Compare results pressing the Batch-Tag of Listed Accession Numbers brings up a new browser window.
  • DB-Stat can now draw a density plot of enzymatic fragments over a given mass range and with a given bandwidth.
  • FA-Index now requires more passes through the database to create the index files. This is a temporary measure to extend the life of the public server.
  • Protein Prospector pages now have html tags and have a DOCTYPE directive .
  • Make project now displays folder icons for the Mozilla browser.
  • Abort search button now hidden after some programs have finished.
  • In MS-Product the sequence ion match table is in an expandable block. This is now only open by default if there is no spectrum to display.
  • The MS-Digest XML output now includes the charge of the potential fragment.
  • iTRAQ purity corrections are now defined in a file.
  • Protein level quantitation added. This includes a range of statistics in the protein report and scatter plots in the peptide report.
  • 8-plex iTRAQ is now supported.
  • Area and/or intensity thresholds can be specified for iTRAQ quantitation.
  • Search Compare peptide reports can now be sorted by retention time (independent of fraction).
  • Search Compare time reports can now be sorted by start amino acid.
  • Quantitation column headings have been changed in Search Compare reports.
  • The N and C-terminus can now be changed on the MS-Product results page form.
  • Search Compare can now do quantitation on peptides with residues that have been isotopically labelled and modified (eg ubiquitinated Lys).
  • In Search Compare it is now possible to eliminate selected peptides and save the processed results.
  • Search Compare now has an option for plotting the false positive rate against the expectation value threshold. This is possible for both decoy and concatenated databases.
  • Individual tolerance thresholds for different fractions in a data set no longer supported.
  • No enzyme searches speeded up.
  • PDF versions of R images are not now always available.
  • iTRAQ peaks are now filtered out of the peak lists used for BatchTag searches.
  • Retention times reported from mzXML files now use a period rather than a semi colon to separate minutes from seconds.
  • The first occurance of a peptide in a peptide report is shown in a bold font.
  • The full input and output paths of the files can now be specified in the WiffRead program.
  • MS-Product can now deal with multiply charged internal ions.
  • MS-Product can do an internal calibration based on ion matches.
  • MS-Product now has a raw data display option.
  • MS-Product now has an option to display the unprocessed peaks from the centroid file.
  • MS-Product now supports modifications specified as a mass shift.
  • Make Project now has a direct link to the Batch-Tag form with the instrument and project filled in.
  • New SwissProt/Uniprot database comment line supported.
  • Fixed the following bugs:
    • There was a problem processing multiple spectra with programs using MS data, such as MS-Fit and MS-Bridge.
    • There were sometimes problems when one of the peaks of a quantitation pair was so weak that the peak fitting failed. If the first guess of the intensity divided by the noise standard deviation is less than the signal to noise threshold or there are no samples in this area of the spectrum an intensity of zero is now assumed.
    • Error now printed if sample can't be extracted from a wiff file.
    • Error now printed if spectrum can't be extracted from a wiff file.
    • The code that deleted old temporary files didn't work properly in October. This led to temporary files not being deleted.
    • Uniprot comment lines weren't correctly written out when using the Create or Append to user database feature in FA-Index.
    • Font colour wasn't correctly specified in coverage maps, the abort search button and the coloured background used for multiply charge ions in MS-Product.
    • The amino acid N was erroneously listed as a protonation site for some instruments.
    • An error message is now printed if a time comparison report of two different projects is attempted.
    • The parent ion tolerance units can't be changed after a project has been calibrated.
    • Signal to noise ratio calculations wrong for TOFTOF iTRAQ data.
    • If an R image fails to draw for some reason the rest of the report is now generated.
    • The Search Compare links to MS-Product reports from mzXML results don't work.
    • Batch Tag no enzyme searches sometimes fail if the N-terminus is heavy (eg 8 plex iTRAQ).
    • There were sometimes problems doing quantitation on calibrated data.
    • Batch Tag/Search Compare don't work with DNA or EST databases.
    • MS-Digest doesn't work with Protein converted DNA databases.
    • It is possible to create a project with the same name using Batch-Tag and Batch-Tag Web. These projects interfere with each other.
    • In a multi-sample report the fractions are sorted alphabetically rather than numerically.
    • Search Compare can run out of memory when processing very large searches.
    • There are problems if the m/z values in an mgf file aren't sorted into m/z order.
    • In MS-Bridge hits which only contained a single unlinked peptide and which contained the link amino acid weren't displayed.
    • The Hide HTML links tick box didn't work in MS-Bridge and MS-NonSpecific.
  • Changed param files:
    • deleted batchtag/params_big.xml, batchtag/params_nuc.xml, batchtag/params_nucf1.xml, batchtag/params_pa.xml, batchtag/script.xml and batchtag/sprot_default.xml.
    • const_mod.txt - iTRAQ8 Lys, Acrolein56 Modified Cysteine and Dimethyl Acrylamide Modified Cysteine added.
    • disc_score.txt
    • enzyme.txt - CymostrypsinFWYMEDLN added.
    • enzyme_comb.txt - Trypsin DE-N, CNBr/Arg-C, CNBr/V8 E, CNBr/Arg-C/V8 E and CNBr/Lys-C/V8 E added.
    • homology.txt - Formyl N Terminus added.
    • imm.txt - masses in this file adjusted for electron rest mass.
    • info.txt.
    • instrument.txt - changes to positively charge bearing amino acids, some defunct calibration parameters removed.
    • n_terms.txt - Carbamidomthyl changed, Formyl and iTRAQ8 added.
    • quan.txt - 'SILAC NC of L and SILAC R' and iTRAQ8 added.
    • usermod.txt - Oxidation of M, Carbamidomethylation of MHK, Carmbamylation of SILAC_NC K, Acetyl-met1 of K, Acetyl-met2 of K, Ubiquitination of SILAC K, Ubiquitination of SILAC_NC K, Ubiquitination2 of K, Carbamidomethylation of KHMED, Methylation of E, Dioxidation of M, Oxidation of W, Nedd8_LysC of K, Ubiq_LysC of K, Lysine Formylation and Tyrosine oxidation to 2-aminotyrosine added.
  • New param files:
    • batchtag/default.xml.
    • disc_score2.txt.
    • expectation.txt.
    • expectation.xml.
    • genelinks.txt.
    • itraq.txt.
    • itraq8.txt.
  • Changed HTML files:
    • mshome.htm
    • default.htm
    • index.htm
    • html/wiffread.htm
    • html/instruct/allman.htm
    • html/instruct/dbstatman.htm
    • html/instruct/faman.htm
    • html/instruct/homologyman.htm
    • html/instruct/instaix.htm
    • html/instruct/instnti.htm
    • html/instruct/instunix.htm
    • html/instruct/servadmn.htm
    • html/js/info.js
    • html/misc/invar.htm
    • html/misc/revhist.htm
  • New HTML files:
    • html/images/folder.gif
  • R Scripts in cgi-bin:
    • Script init.R split into two files, initargs.R and initgraph.R.
    • New R scripts expectationDensity.R, peptideDensity.R, scatterSurvival.R and quan.R.
    • Modified R script msmsErrorScatter.R.
  • Perl Scripts in cgi-bin:
    • Modified Perl script mssearch.pl.

V 4.21.4 7/3/2006 (NT/2000/XP and LINUX)
  • It is possible to make a concatenated database in FA-Index. This is a reverse or random database appended to the end of a normal database.
  • Amino acid modifications in MS-Product can now be entered as a mass in brackets eg. M(15.9949).
  • In MS-Tag from File it is now possible to override the charge in the centroid file using the Precursor Charge option.
  • The is a new MS-Product results page format with the following features:
    • Sequence and charge displayed at the top of the page.
    • Small form allowing the sequence to be resubmitted with a modified sequence, a different fragment ion tolerance, more peaks or a modified maximum fragment charge. This is useful for helping to locate the position of post translational modifications.
    • Parts of report are now contained in expandable blocks.
    • Font smaller in report.
    • Error plot slightly smaller
  • Less confusing interface to choose results name on Search Compare form.
  • Batch-Tag processes (but not Batch-Tag Web processes) are now run at a lower priority than other programs in the package.
  • The Java applet now uses an absolute rather than a relative path which should allow results to be saved.
  • The default minimum protein score in Search Compare has been changed to 22.0.
  • Slow scoring options removed in MS-Tag/Batch-Tag.
  • Fixed the following bugs:
    • Min digest fragment length option didn't work properly on MS-Digest/MS-Bridge.
    • For some instruments (eg Q-STAR) MS-Bridge/MS-NonSpecific/MS-Seq/MS-Tag didn't allow pasted peak lists with a small number of peaks as there was a mimimum number of peaks specified for different instruments. Now the peak filtering options have been disabled for pasted peak lists for both MS and MSMS data.
    • Maximum hits default in Batch-Tag and MS-Tag changed from 20000 to 2000000. The old value sometimes caused problems with Batch-Tag searches.
    • The code that deleted old temporary files didn't work properly in July. This caused a problem with MS-Product as for this reason it wasn't able to display the error graph.
  • Changed param files:
    • elements.txt - lithium added.
    • instrument.txt - high energy ion types removed from TOFTOF settings.
    • species.txt - added GLYCINE MAX and HUMAN ADENOVIRUS 5.
    • usermod.txt - added Tyrosine oxidation, DiMethylation of R, Methylation of H, Formaldehyde adduct and Hydroxymethyl.
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm
  • R Scripts in cgi-bin:
    • msmsErrorScatter.R
    • init.R

V 4.21.3 4/21/2006 (NT/2000/XP and LINUX)
  • There is an option to relocate the params directory. Thus parameter files can be shared by different installations via a network drive.
  • Search Compare prints out the original search parameters.
  • MS-Isotope has an option for printing isotope profiles with incomplete heavy isotope incorporation.
  • MS-Product has a scatterplot showing fragment ion mass errors against mass. Different ion types are given different colour code. The R statisitics package is required for this option.
  • Correction for incomplete heavy isotope labelling in Search Compare/MS-Display (eg you can specify a %C13 such as 98% for SILAC).
  • There is a link to MS-Isotope from the MS-Display results to help set the incomplete heavy isotope incorporation percentage.
  • Correction for overlapping of light and heavy isotope profiles in Search Compare/MS-Display.
  • Replacement of high and low designation in the reporting of quantitation rations in Search Compare/MS-Display by > and <. If there is no evidence of one of the peaks then the high/low designation is retained.
  • Better peak fitting for quantitation for heavy peptides where the monoisotopic peak previously didn't fit.
  • Correction for iTRAQ peak purity now possible.
  • Correction for incomplete single O18 conversion.
  • The accession number is now printed when Search Compare has problems setting a coverage map. Also only one such message is printed per protein.
  • Default minimum signal to noise ratio for quantitation changed from 20 to 10.
  • When Q-STAR quantitation is done the data is got is wiff file/retention time order rather than protein order. This can speed the calculations up as peptides which occur in multiple proteins are only processed once.
  • MS-Display now has a menu making it possible to select any retention time in the file for the display of MS Precursor, MS Full Scan and Quantitation report.
  • Min Best Descriminant Score options on Search Compare form now only listed for the relevant instruments.
  • Peptide Composition options on Search Compare form now hidden.
  • Probability option on Search Compare form removed.
  • Amino acid composition removed from MS-Product output.
  • Changes to Peak Spotter program:
    • There is now a link to Peak Spotter from the home Prospector page.
    • Most of database queries changed over to SELECT queries so there is no need to change the database installation now. Also it is moderately faster.
    • MSMS and PSD spectra now identified as MSMS.
    • All JOB_RUN_ITEMS are processed not just ones with an ACQUISITION flag.
    • Diagnostics tick box to help resolve problems. PEAK_LIST_ID is listed in the diagnostics.
    • Correct calibration equation used for all MSMS spectra.
    • Precursor mass no longer used to resolve MS/MSMS.
    • Correct instrument serial number written to calibration file.
    • Run numbers should be correct.
    • Spot set templates are no longer listed in the spot set list.
    • Raw data is only written out if the acquisition status is 10.
  • Fixed the following bugs:
    • Corrected some problems with electron rest mass corrections in the MS-Product fragment ion list.
    • Fixed a problem with quantitation where sometimes the raw data was truncated before the end of the high mass profile.
    • Fixed a problem with the public server whereby report headers weren't included in MS-Tag from File.
    • Links to files in the prospector temp directory sometimes had \ rather than / in the address. Eg: /prospector/4.21.3/temp\Apr_13_2006\graph1.txt
    • Incorrect year in copyright notices in results pages.
    • Peptides # in database column in Search Compare peptide report gave incorrect values when different modifications to the same peptide were alternative possibilities in the stored hits for a given spectrum.
  • Changed param files:
    • info.txt - new parameter for R installation binary and relocated parameter directory.
    • usermod.txt - SILAC L modifications
  • Changed HTML files:
    • mshome.htm
    • html/misc/revhist.htm
  • Changed cgi-bin files:
    • mssearch.pl - version number now just in one place.
  • R Scripts:
    • New R scripts msmsErrorScatter.R and init.R in cgi-bin

V 4.21.2 3/8/2006 (NT/2000/XP and LINUX)
  • The search programs now print out the time elapsed since the start of the search and the time remaining until the end of the search.
  • Search Compare Peptide and Time reports can now be sorted by Mass Error.
  • Quantitation reports in Search Compare involving lots of wiff files sometimes are now quicker if only the results from a single protein are displayed.
  • Narrow scan iTRAQ scans can be combined with MSMS scans for Q-STAR data.
  • Temporary files more than 2 days old are automatically deleted at the time a new temporary file is created.
  • The search progress information is updated more often if there are less proteins in the search.
  • Doubly charged ions can now have a separate score coefficients defined in the instrument.txt file.
  • A quantitation tolerance directive (quan_tolerance) is now available in the instrument.txt file. Its only current use is to define the window for Q-STAR iTRAQ quantitation (current default +/- 0.2 Da).
  • The following columns are no long available in quantitation reports:
    • Measured Light/Heavy Intensity Ratio
    • Measured Light/Heavy Area Ratio
    • Actual Heavy/Light Intensity Ratio
    • Actual Heavy/Light Area Ratio
  • On the search Compare form Min PP Protein Score and Min PP Peptide Score have been replaced by Min Protein Score and Min Peptide Score.
  • Empty table cells now have a <td> rather than <th> html code.
  • It is now possible to look for internal disulfide bridges.
  • Fixed Following Bugs:
    • If the results name has a certain characters in it (one example is the + character). Then the link to Full Search Compare Options from the Batch-Tag results page doesn't produce the Search Compare form.
    • If the Search Compare remove (accession number) tick box is ticked then the links to the single protein peptide reports from the protein report don't give a report for a single protein.
    • Accession number limited searches of large databases (eg Uniprot) where the search gets split up into a lot of different sections can fail or run very slowly because of a memory leak.
    • Quantitation reports in Search Compare involving lots of wiff files sometimes don't work.
    • There are problems with quantitation and the MS-Display program if user modifications contain a dash (-) character.
    • The <nobr> directive has been removed for cells containing quantitation ratios.
  • Changed param files:
    • acclinks.txt - new Swiss Prot accession number link
    • enzyme_com.txt
    • homology.txt
    • instrument.txt
    • n_terms.txt
    • usermod.txt
  • Changed HTML files:
    • mshome.htm

V 4.21.1 1/6/2006 (NT/2000/XP and LINUX)
  • There is a menu offering the choice of what raw data you want to see when you click on the m/z column. The choices are MS Precursor, MS Full Scan, MS/MS or Quantitation. The should work with TOF-TOF or Q-STAR data.
  • MS-Display has a facility for switching the mode of raw data display as given in point 1.
  • The Make Project program will allow directories to contain centroid files. This is probably only relevant to TOFTOF data.
  • Centroid, raw MS and MSMS can be extracted from a 4700 database into a repository using Peak Spotter. A new Oracle procedure is used. There is no link to this page from the package as this is an administrative feature. The web page is:

    http://server_name/prospector/4.21.1/html/peakSpotter.htm

  • Multiply charged parent with and without water and ammonium losses can be labelled in MS-Product. This requires a change to instrument.txt.
  • There will be several extra options for sorting time reports:
    • RT with and without fraction being taken into account (so you can see if a peptide occurs in different fragments).
    • m/z
    • M+H so you can look for common contamonant peaks for example.
    • Charge then M+H.
    • Centroid intensity (only relevant for the LCQ).
    • Peptide score.
    • Discriminant score.
  • Time intersection reports won't include unmatched peaks.
  • Number of database entries searched will be in the output.
  • DB-Stat output now includes a histogram showing the distribution of peptide masses.
  • Better rules are used for selecting the histogram bin width when there are more data points.
  • a-SOCH4 is now an ion type that can be selected in instrument.txt.
  • Acetylations can now be specified for N terminal peptides where the database entry doesn't start with M. This required a change to the code so that if a '-' was specified in the homology.txt file then it also possible to specify 'n' as the terminal specificity.
  • The libraries have been repackaged to make it easier to make versions without MPI and/or Analyst. mssearch.cgi now doesn't include mpi so can be used for single process searches. Separate version can be made for searchCompare and msdisplay for versions with and without Analyst. This is now a simple matter.
  • The quan.txt file format has been simplified. Also it is now possible to specify more than one usermod in a quantitation experiment. This has been doen to allow SILAC_K and SILAC_R to be quantified in the same run.
  • Fixed the following bugs:
    • Fixed an bug with multi-sample peptide reports with MS data links.
    • Fixes the heavy use of memory for searches with a lot of modifications/No Enzyme. Some searches of this type will now run a lot faster.
    • Protein names in the peptide report are now "wrapped" if they are too long.
    • Fixed some bugs in the intinsic ratio quantitation calculations.
    • Lan's quantitation usermods added.
  • New param files:
    • dbstat_hist.par.txt
  • Changed param files:
    • homology.txt - changed rules for acetylation
    • instrument.txt - added new intact loss ion types
    • quan.txt
      • previous line 4 (contains a string for the modification along with the amino acid) now no longer required.
      • previous line 5, new line 4 - more than one amino acid can be specified here.
  • Changed HTML files:
    • mshome.htm
    • peakSpotter.htm
  • Others:
    • TOFTOF database needs new Oracle procedure.

V 4.21.0 12/15/2005 (NT/2000/XP and LINUX)
  • The number of significant figures printed for numbers printed with in the mantissa/exponent format has been reduced by 1.
  • Amended printing of large and small numbers so the scientific format is printed say 7.4e-7 rather than 7.4e-007. Numbers less than 1x10-3 are printed like this. Previously it was less than 1x10-4.
  • Mass error histograms aren't now done for Time reports in Search Compare just Peptide reports.
  • Fixed the following bugs:
    • Some of the strings used to identify the scans to sum together for Q-STAR iTRAQ quantitiation were being incorrectly written out to the results file. Eg:

      1998,:2009,3

      rather than

      1998,2:2009,3

    • The software can now correctly handle the situation of having no peaks in a spectrum in an mgf file.
    • The name field option on the FA-Index page mistakenly had the same CGI name as the database field. The correct name is now included.
    • Histogram of peptide m/z errors now only counts peptides from homologous proteins once.
    • Fixed error whereby Start AA and End AA contained random characters in time report if there is no peptide hit for a given spectrum.
    • The spectrum applet has been amended so it leaves less blank space at the top of the graph.
    • An error is printed if there is insufficient information in an mgf file to allow extraction of the raw data from a wiff file. This can happen if an mgf file created by an old version of the Mascot.dll is used.

V 4.20.3 12/15/2005 (NT/2000/XP and LINUX)
  • The number of MS scans in a data file is now also written to the project file.
  • CHARGE=, TITLE= and PEPMASS= can be in any order in an mgf file.
  • In an mgf file the spot number defaults to the numerical spectrum number in the file unless this is overriden by what's in the TITLE line.
  • Score no longer printed in MS-Product.
  • Phosphorylation fragmentation mask changed from sty to st.
  • Facility to automatically centroid Q-STAR runs in Batch-Tag removed.
  • Link added so MS-Tag from File can use new style form on public server.
  • Fractions only printed if more than one fraction.
  • Fixed the following bugs:
    • Deisotoping added to the instrument file for LTQ on the public server.
    • Random characters are sometimes printed at the end of error messages. This was because the message sent with the error message wasn't null terminated.
    • There was a problem dealing with mgf files with less spectra than processors.
    • An error message is now printed if there are no spectra in the data file.
    • A couple of changes have been made to stop the program halting or hanging if a Gaussian can't be fitted to a discriminant score distribution.
    • MS links only available if there is MS data in the centroid files.

V 4.0.8 1/2007 (LINUX, AIX, NT/2000/XP/XPx64)
  • New SwissProt/Uniprot database comment line supported.
  • The search programs now print out the time elapsed since the start of the search and the time remaining until the end of the search.
  • MS-Product has a scatterplot showing fragment ion mass errors against mass. Different ion types are given different colour code. The R statisitics package is required for this option.
  • Fixed the following bugs:
    • The amino acid N was erroneously listed as a protonation site for some instruments.
    • DB-Stat sometimes runs out of memory when used against a very large database. This problem was caused by the histogram feature introduced in 4.0.7.
    • Mass tolerances in programs such as MS-Fit, MS-Bridge and MS-NonSpecific were handled incorrectly for multiply charged peaks.
    • In MS-Bridge hits which only contained a single unlinked peptide and which contained the link amino acid weren't displayed.
    • The Hide HTML links tick box didn't work in MS-Bridge and MS-NonSpecific.

V 4.0.7 9/2006 (LINUX, AIX, NT/2000/XP/XPx64)
  • FA-Index can now create a random, reverse or concatenated database.
  • Some changes to Javascript code for displaying database and species items on forms.
  • Sequence database directory now defined in a parameter file rather than a Javascript file.
  • Change to distribution directory structure.
  • Errors are now printed in bold red.
  • Amended printing of large and small numbers so the scientific format is printed say 7.4e-7 rather than 7.4e-007. Numbers less than 1x10-3 are printed like this. Previously it was less than 1x10-4.
  • A completely new browser page is now generated when pressing links in Prospector results.
  • Results can now be saved and the Java graphs will still work.
  • Protein sequence printed in a more compressed format in MS-Digest/MS-Bridge/MS-NonSpecific.
  • The XML output now includes a complete set of the parameters used for the search.
  • Lithium added to the elements file.
  • DB-Stat output now includes a histogram showing the distribution of peptide masses.
  • MS-Isotope has an option for printing isotope profiles with incomplete heavy isotope incorporation.
  • The spectrum graph is MS-Product/MS-Tag can now selectively label particular ion types.
  • Some part of the MS-Product report are now in expandable blocks.
  • The MS-Product report font has been reduced.
  • Matching peaks are now shown in red in MS-Product.
  • Abort search button now hidden after searches have finished.
  • Default MS-Bridge report now works.
  • Phosphorylation fragmentation mask changed from sty to st.
  • Amino acid composition removed from MS-Product and MS-Isotope output.
  • Multiple proteins can now be separated in MS-Digest and MS-Bridge.
  • Fixed the following bugs:
    • MS-Homology crashes if a mass is specified in a sequence and no amino acid combination correspond to it.
    • The electron mass isn't currently subtracted when calculating the exact mass which could lead to a significant discrepancy at low mass (around 5 ppm at 100 amu).
    • CNBr peptides incorrectly handled by MS-Product.

V 4.0.6 11/2005 (LINUX) 3/2006 (AIX)
  • Added support for IPI and Uniprot databases.
  • New Swiss Prot format now supported.
  • Some work has been done to make the forms and results pages XHTML compliant to the xhtml1-transitional standard.
  • MS-Product maximum charge increased to 25.
  • MS-Isotope maximum sequence length increased to 60.
  • Less NCBI entries now have unreadable species.
  • Fixed the following bugs:
    • The delete DNA database option in FA-Index doesn't delete all the DNA database files.
    • MS-Homology fails to calculate the correct score if two or more of the sequences entered have different lengths and match the same bit of database sequence with the same number of errors. Only the shorter matching sequence is now retained.
    • y type ions are off by 2 Da in MS-Comp.
    • A HTML break code is printed at the top of the report if XML output is chosen. This problem doesn't occur if the results are saved to a file.

V 4.0.5 11/2002 (AIX and NT/2000)
  • MS-Bridge now has a user defined link option.
  • New forms MS-Bridge Upload and MS-Product Upload which are used when the user wants to upload data from file. This prevents the problem with "security precautions" preventing browsing backwards and forwards from the results page to the form. If you now use the standard MS-Product and MS-Bridge forms you will no longer get this problem.
  • Abort search button removed from MS-Digest and MS-Product.
  • Multiple losses flag no longer reported if not set.
  • Program links now come up in a new browser page.
  • MS-Isotope works to higher masses.
  • Elements of the form 13C or 2H can now be used in the elements.txt file.
  • MS-Product spectrum showing match (after following link from MS-Tag) now shown at top of the results page.
  • B and Z now considered as Unknown Amino Acids for MS-Tag search mode.
  • Fixed the following bugs:
    • MS-Fit and MS-Tag batch searches have a write text file option which doesn't do anything.
    • MS-Fit and MS-Tag crash if no data is entered.
    • MS-Seq composition exclude option doesn't work.
    • Command line FA-Index instructions confusing.
    • The first fragment ion peak is not passed to MS-Product when a peptide sequence link is from the MS-Tag results.
    • The NCBI ftp site used for most of the databases has now changed.

V 4.0.4 05/2002 (NT/2000 only)
  • Fixed the following bugs:
    • The user defined amino acids u, v, w and x don't have their masses correctly initialised.

V 4.0.3 04/2002 (NT/2000 only)
  • New summary report added to protein summary report in MS-Tag batch programs.
  • Identical peptides now count as a single hit in MS-Tag. For example if you specify the maximum reported hits as 5 then the first 5 distinct hits are reported.
  • Graph display option added to MS-Bridge.
  • Fixed the following bugs:
    • Sometimes MS-Product doesn't display product ions when accessed via a link due to there being no specified instrument parameter. This problem is apparent, for example, when going from MS-Tag to MS-Digest and then to MS-Product.
    • Link to MS-NonSpecific from home page incorrectly specified.
    • MS-Fit, MS-Bridge, MS-NonSpecific can't deal with average mass.
    • In the MS-Fit results hits containing two cysteines are reported twice.
    • MS-Product calculate the internal ions masses incorrectly if the N-terminus is modified.
    • MS-NonSpecific hits reported incorrectly. The peptides all have an extra amino acid at the end.
    • Links to MS-Tag Unknome still available.

V 4.0.2 03/2002 (NT/2000 only)
  • Mascot generic format now available as a data format in MS-Tag.
  • Fixed the following bugs:
    • In Netscape 4.7 and older browsers the links to other programs sometimes don't work because spaces in the URLs aren't escaped.
    • Detailed report flag not passed on when doing mixture searches from MS-Fit.

V 4.0.1 03/2002 (NT/2000 only)
  • New program MS-NonSpecific which can look for non-specific cleavage hits in one or more specified proteins. There is a link to this program from the MS-Fit results page.
  • Four user defined amino acids are now available (u, v, w and x).
  • Maximum peptide length in MS-Product increased to 100 amino acids.
  • Protein summary report not displayed in MS-Tag if only one data set.
  • Protein summary report in MS-Tag now optional.
  • Protein summary report in MS-Tag num contains the number of peaks in the spectrum.
  • Graphs in MS-Fit/MS-Tag now optional.
  • Errors no longer reported on MS-Tag graphs.
  • HPLC and Bull Breese indicies now optional in MS-Digest report.
  • Chem score now available for MS-Fit/MS-Bridge/MS-Digest.
  • Parameter for link type in MS-Bridge are now defined in a file.
  • MS-Bridge/MS-Digest can now display results for multiple proteins.
  • There can be multiple user defined proteins in MS-Digest/MS-Bridge.
  • No link option now available in MS-Bridge.
  • Table in MS-Fit summary showing which peaks match which hits.
  • Rank removed from MS-Fit Report.
  • Peptide composition option added to MS-Bridge/MS-Digest.
  • Separate batch and web batch forms for MS-Fit/MS-Tag.
  • Contaminant masses option added to MS-Bridge.
  • Detailed report now optional in MS-Fit/MS-Tag.
  • Fixed the following bugs:
    • Multiple charges don't work in MS-Digest.
    • Multiply charged peaks aren't found in MS-Tag.
    • Mixed digests don't work.
    • User protein field needs to be cleared before MS-Digest works.
    • MS-Fit homology search doesn't work.
    • HPLC Index incorrectly reported in MS-Digest XML output.
    • Some programs don't work with older versions of Netscape/Internet Explorer.
    • Pdefault and Ddefault database prefixes incorrectly named in the manual (they were called PDefault and DDefault).
    • Empty protein/DNA entry not possible in a database.
    • Sometimes names/accession numbers/species aren't reported for Pdefault and Ddefault type databases.
    • W-ion masses calculated incorrectly.

V 4.0.0 01/2002 (NT/2000 only)
  • New program MS-Homology for doing remote homology searches.
  • New program MS-Bridge. This program does an MS-Fit style search on a single protein and can find disulphide or DSS linked peptides and peptides with an unlimited number of user defined modifications.
  • Batch search facility added to MS-Fit and MS-Tag. The data can be upload from a file on the user's local disk.
  • MS-Fit and MS-Tag can display the input data showing matched and unmatched peaks.
  • MS-Tag and MS-Product can handle high energy fragment ions.
  • MS-Fit has a systematic error parameter.
  • MS-Tag has a regular expression parameter.
  • Immonium and other low mass ions are now defined by elemental formula and the exact mass is displayed.
  • The programs can now give XML output.
  • Option to treat composition ions as normal ions in MS-Tag.
  • MS-Digest can now have an unlimited number of user defined modifications.
  • Facilities for reading extra comment line information added to FA-Index/MS-Digest.
  • MS-Bridge search can be invoked from MS-Fit.
  • MS-Product can accept a data set and show matching peaks.
  • MS-Product can display ions with multiple neutral losses.
  • MS-Tag Unknome program removed.
  • Pre search only option added to MS-Pattern.
  • Species codes option added to MS-Pattern and DB-Stat.
  • pI search option added to MS-Pattern.
  • Search mode option removed from MS-Pattern.
  • If a database entry has multiple comment lines then all of them are searched during accession number, species or name pre-searches.
  • Combinatorial peptide output option removed from MS-Pattern.
  • MS-Isotope now plots peak profiles and can plot a profile of an averagine mass. An averagine is an average amino acid and is one of the concept used in automatic centroiding.
  • The MS-Isotope elemental composition input item can now accept all defined elements.
  • Max. % Unmatched Ions, Max. Num Unmatched Ions and Min. Num Matched Ions in MS-Tag merged into a single parameter. Min. % Matched Ions added.
  • Maximum fragment mass parameter added to MS-Digest.
  • The FA-Index database summary report now display protein molecular weights and pIs.
  • The FA-Index database summary report now has MS-Digest index number links and accession number links. If there are multiple comment lines they are all shown.
  • The displayed precision for masses, masses errors and intensities can be defined in the instrument.txt file.
  • Fixed the following bugs:
    • No fragment ions are reported in MS-Product if you click on a peptide sequence link in MS-Digest.
    • Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
    • Accession number link in results pages doesn't work for Ludwignr database.
    • Some NCBInr entries are reported as having UNREADABLE species which are in fact reference entries with more than one comment line. Such entries sometimes have more than one species.
    • Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
    • MS-Tag save hits to file doesn't work properly.
    • H3PO4 and SOCH4 losses are not reported in MS-Product if the instrument specific default ion types tick box is selected.
    • MS-Digest should print an error message if invalid amino acids are used in a user protein (eg, if the user uses lower case letter by mistake).

V 3.4.1 10/2000 (NT/2000 only)
  • MS-Fit can now accept a list of contaminant masses as a parameter. Data peaks which are within the tolerance of the contaminant peaks will be deleted from the data set before the search takes place. All charge states are considered.
  • The facility to list search parameters at the end of the report, rather than the beginning, has been removed.
  • Phosphorylation of tyrosine is now considered in MS-Product and MS-Tag.
  • Support added for Ludwig non-redundant database.
  • In MS-Tag there is now a choice between maximum % unmatched ions, maximum number of unmatched ions or minimum number of matched ions.
  • Fixed the following bugs:
    • MS-Comp doesn't work if the full amino acid composition of the ion is specified.
    • DB-Stat crashes if the pre-searches select no entries.
    • If a selected accession number is not present in the database the program either prints an incorrect error message or crashes.
    • If the instrument specific default ion types are selected in MS-Product or MS-Tag then the default lists of amino acids which are defined in instrument.txt for MSMS fragmentation are not initialised properly.
    • If the pre-searches select no entries it is still possible for the search programs to get a hit.
    • The name and species pre-searches don't work properly it one of the names/species contains spaces.
    • When a subsequent MS-Fit search is invoked from the MS-Fit results page to find mixture components an obselete name is used to describe the data format. This is not known to cause any problems at present.
    • The coverage count in MS-Fit is out by 1 if the last amino acid in the protein is included in one of the hits.

V 3.4.0 8/2000 (NT/2000 only)
  • The search programs can now search databases containing the sequence of an entire genome.
  • There is a new maximum hits parameter on MS-Tag which controls when a search is aborted.
  • The DB-Stat program can now do a pre-search based on a list of species names. The species names used are the ones contained in the database comment lines. These vary from database to database. The species name list can also be used as a pre-search parameter in FA-Index. Licensees could add this pre-filter to the other search programs if required.
  • The programs can now be operated directly from the command line with the search parameters specified via command line arguments. HTML style escape characters can be used to deal with newline characters and spaces, etc.
  • MS-Digest now has an open reading frame parameter when used with DNA databases and only gives results for that reading frame. This allows it to be used with single entry genome databases.
  • In MS-Tag/MS-Seq the parent error is reported in the tolerance units.
  • The elements file has been updated. The masses were taken from Audi, G., Wapstra, A. H., Nucl. Phys. A, Vol. 595, pp. 409-480 (1995).
  • Element definitions have been added for Deuterium, Chlorine, Fluorine, Sodium, Potassium, Zinc, Selenium, Bromine and Iodine.
  • MS-Fit can be now used as a pre-filter for MS-Seq or MS-Tag.
  • The MS-Tag matching ion table now has 12 ions per row.
  • The size of the memory map used by the programs can now be controlled. This leads to faster operation in some circumstances.
  • MS-Tag now uses percent unmatched ions rather than number of unmatched ions.
  • There is an option on the MS-Fit results page to submit the unmatched masses to another MS-Fit search and thus search for subsequent components.
  • There is an option on the MS-Fit results page to submit a single unmatched mass to a No enzyme MS-Tag search on the hit protein. This will find peptides with non-specific cleavages.
  • Some additional tags in the form of html comments have been added to the MS-Fit results to facilitate cooperation with automation programs. Also the text version of the MS-Fit report has been tidied up.
  • ICAT-light, ICAT-heavy and IDEnT have been added to cysteine modification file. However the results are not currently filtered so that they only contain cysteine containing peptides.
  • The species.js file can now be updated automatically from the FA-Index page. This means that only the msparams/species.txt file needs to be edited when adding species definitions.
  • There has been a comprehensive rewrite of the software which extracts species, accession numbers and names from database comment lines.
  • There is now a new Protein Propsector email address.
  • The percent TIC, mean error, data tolerance and mean number of missed cleavages are printed after an MS-Fit hit. If intensities aren't specified then the percent TIC value will be the same as the percent masses matched. The mean error is useful for diagnosing systematic errors in the results - indicating a calibration problem. The data tolerance is twice the standard deviation of the results and is the number that should be used as a tolerance parameter in the absence of systematic errors. This number is more reliable if there are a reasonable number of matching peaks (say 10). Also the number is only valid if all the matched peptides are real hits.
  • The species, accession number and name searches have been removed from MS-Pattern.
  • The molecular weight and pI pre-searches are no longer available for DNA databases.
  • Species collections can now contain other species collections (eg MAMMALS could contain RODENTS).
  • Fixed the following bugs:
    • There is a limit to the size of the database that can be used of around 2 GBytes.
    • The hit information line in MS-Fit containing the percentage of hits, size, PI and protein name now makes up the first line of the detailed result table. Netscape and IE display the results fine but when they are copied from IE into Word the first column of the table is formatted to the width of the information line. This pushes everything else together resulting in a messy table that has to be reformatted by hand.
    • The column header is MH+ in MS-Digest when the data in multiply charged.
    • Every 50th peak in MS-Digest doesn't get reported.
    • If there is only a single base on the last line of an entry in a DNA database then frames 5 and 6 come out the same. This only affects a small proportion of the entries.
    • The protein sequence is erroneously appended to the name for a few NCBI entries (eg. Accession no:464430).
    • MS-Tag crashes if there are more than 400 internal ions in a potential hit. This only affects very high mass peptides.
    • The Genpept accession number link doesn't work.
    • The Owl accession number link doesn't work.
    • MS-Tag in homology mode sometimes fails to find hits that it should find if the number (or %) of unmatched ions is too low.
    • The lowest mass peptide is not reported in MS-Digest. This isn't normally a problem as masses below 500 Da aren't displayed by default.

V 3.2.2 12/1999 (NT only - not released)
  • Name of MS-Edman program changed to MS-Pattern.
  • Pre-searches based on the name field and a list of accession numbers are now possible in MS-Fit, MS-Tag, MS-Pattern and MS-Seq.
  • The name field can be used as an additional parameter in FA-Index and DB-Stat.
  • A list of accession numbers can be used as an additional parameter in FA-Index.
  • End terminus digesting has been added to MS-Digest.
  • MS-Fit can now have zero peaks entered. This allows searches of just pI, MW, etc.
  • MS-Fit results can be sorted based on pI or intact protein molecular weight.
  • A default database type has been added. This allows Prospector to be used with FASTA format databases with any comment line format. Prospector assigns the accession number to the numerical position of the entry in the database the species as UNREADABLE and the name as the entire comment line.
  • A more meaningful error message is printed if the database is not present on the server.
  • The procedures for adding Cysteine modifications have been simplified.
  • Web server users can now control the minimum peptide mass and the minimum peptide length in MS-Digest.
  • Multipart form data is now supported in addition to get and post.
  • The absence of an immonium ion can be used to denote absence of an amino acid in MS-Tag.
  • Accession numbers are now saved when hits are saved to a file.
  • DB-Stat prints out the total number of amino acids in the entries matching the search conditions.
  • The mass and ion type columns have been swapped in the final MS-Product table.
  • A column listing the number of missed cleavages has been added to the MS-Digest report.
  • More than one of a given amino acid can be specified as a partial composition in MS-Comp.
  • In MS-Tag/MS-Seq the fragment error is reported in the tolerance units.
  • Fixed the following bugs:
    • IUPAC ambiguity codes not supported in DNA to protein conversions.
    • mmu tolerance calculations incorrect.
    • The programs crash if the msparams/colors.txt file is missing.
    • MS-Fit MOWSE scores can be incorrectly ranked if the score overflows what can be stored in a 4 byte integer number.
    • The format of the OWL database has changed. This means that most of the time the link from accession number in the reports doesn't work.
    • After the MS-Pattern list of sequences option has found a hit in a protein it only starts looking for new hits at the end of the peptide it has just found whereas it should start looking at the next amino acid.
    • Pepsin enzyme rules incorrect.
    • Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
    • The delta mass column in the MS-Pattern and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
    • Next 20 entries button on the FA-Index Database Summary Report doesn't work if seqdb directory or msparams directory has been relocated.

V 3.2.1 3/1999
  • The mutation/modification feature in MS-Tag/MS-Fit now has more options. The options can also be programmed by licencees.
  • The form entries for the Max. # of mismatched AA's in MS-Edman, the Min. # matches with NO AA substitutions in MS-Fit and the Max. # unmatched ions in MS-Tag have been changed to allow any number to be entered.
  • Fixed the following bugs:
    • There are sometimes problems with inputs of lists of text strings (eg. list of sequences in MS-Edman) if the cursor does not end up at the start of the line underneath the last text string. There are problems both when the cursor ends up directly at the end of the last text string (with no carriage return) and when there are lines after the last text string containing only space or tab characters.
    • Setting the ion types in MS-Comp to include anything except MH+, y or b+H2O and the combination type to elemental caused the peptide mass and mass error columns in the report to show incorrect results.
    • There are sometimes problems with inputs of lists of text strings (eg. list of sequences in MS-Edman) if the cursor does not end up at the start of the line underneath the last text string. There are problems both when the cursor ends up directly at the end of the last text string (with no carriage return) and when there are lines after the last text string containing only space or tab characters.
    • Excluded species entries have to be placed after multiple species entries in the species.txt file for multiple and excluded species filters to work correctly.

V 3.2.0 2/1999
  • MS-Seq introduced. This is our implementation of the Mann and Wilm sequence tag algorithm.
  • Database statistics program DB-Stat added.
  • MS-Product now works with multiply charged ions.
  • MS-Product now displays a list of the theoretical fragment ions in mass/charge order.
  • One of the MS-Fit/MS-Digest Considered Modification is now user programmable. This replaces the Phosphorylation of S, T and Y option.
  • An instrument parameter has been added to some of the programs. This currently defines mass accuracies for reports, ammonia loss aas, water loss aas, positive charge bearing aas, maximum internal ion masses and fragmentation ion types.
  • Now no support for non-JavaScript aware browsers.
  • One release supports both the Internet Explorer 4 and Netscape Navigator 4 browsers.
  • Licencees can now control the minimum peptide mass and the minimum peptide length in MS-Digest.
  • Licencees can now enter a mixture of monoisotopic and average data into MS-Fit.
  • Licencees can now control whether the search parameters in MS-Fit, MS-Edman, MS-Tag and MS-Seq appear at the top or bottom of the output.
  • Licencees can now define the number of hits which cause an MS-Tag or MS-Seq search to abort.
  • FA-Index can now deal with the SwissProt database supplied by NCBI.
  • MS-Comp now works with a range of fragment ion types.
  • There is now only one species alias file which is used for all the databases.
  • SwissProt URL changed.
  • FA-Index now has an option to convert DNA databases to a protein format. This makes the searches somewhat faster but doubles the database size.
  • Licencees may now change the page colors.
  • MS-Tag users can now specify a-H2O, y-H2O and c ions.
  • The JavaScript files have been simplified.
  • The msparams files now have .txt on the end of the file names.
  • The dbEST.spl.txt file has been updated.
  • The links to similar programs by other groups have been checked.
  • The database summary report on FA-Index can now display protein sequences. The sequences can be pasted into the MS-Digest user supplied protein sequence box.
  • s, t and y can now be used in the MS-Digest User Protein.
  • MS-Isotope now works with peptide or elemental formulae containing phosphorus.
  • MS-Comp now works if Combination Type is set to Elemental.
  • MS-Fit now has a column reporting the m/z submitted if any of the data is multiply charged.
  • Fixed bug which caused MS-Tag to sometimes give false positives with the CNBr digest in which the parent ion didn't match.

V 3.1.1ie 8/1998
  • A version of 3.1.1 intended for use with Internet Explorer 4. It only contains Javascript which is compatible with Internet Explorer 4.
  • The next and previous amino acids are now always displayed on the same line as the peptide sequence.

V 3.1.1njs 8/1998
  • A version of 3.1.1 intended for use with older browsers. It contains no Javascript.
  • Fixed bug in MS-Fit which causes first column of the detailed report to be too wide when using the Internet Explorer browser.

V 3.1.1 7/1998
  • In MS-Edman sequence and mass mode the results have to match the sequence when the .* wildcard used.
  • MS-Fit, MS-Tag and MS-Edman search conditions now at the end of the report. They can be accessed via a link from the top of the report.
  • MS-Digest report gives protein amino acid composition.
  • MS-Isotope prints an error message rather than crashing if the monoisotopic peak abundance is too low.
  • MS-Isotope limit on the length of the peptide sequence removed.
  • MS-Tag reports fragment ion m/z's to two decimal places.
  • Fixed bug in the MS-Tag output which caused the DNA and open reading frame results not to line up with the headers.
  • Fixed bug which caused an error in the pI calculation under certain conditions.
  • Copyright notices updated.
  • msparams, seqdb and results directories can now have their locations defined in ucsfhtml/js/info.js.
  • In the msparams3.1/*.sp files the species specified in a species collection don't have to be in the same order as the single species specifications.

V 3.1 4/1998
  • MS-Fit has an optional MOWSE style scoring system (Pappin et al, Current Biology, 1993, Vol 3, No 6, pp. 327-332).
  • MS-Fit results contain a link to a coverage map displayed in MS-Digest.
  • MS-Fit searches can be constrained by pI range; MS-Edman, MS-Digest, MS-Fit and MS-Tag report the pI of the intact protein in the search results.
  • MS-Isotope introduced, as a tool for calculating and visualizing isotope patterns of peptides and organic molecules.
  • MS-Fit can search the hits saved by MS-Fit or MS-Edman.
  • MS-Tag can search the hits saved by MS-Fit, MS-Edman, or MS-Tag.
  • MS-Edman can search the hits saved by MS-Fit, MS-Tag, MS-Tag Unknome, or MS-Edman.
  • MS-Tag has an option of specifying an average parent mass along with monoisotopic fragment masses.
  • MS-Fit, MS-Tag, and MS-Edman report hits up to the specified maximum reported hits when this value is exceeded instead of generating an error.
  • MS-Digest calculates masses of multiply-charged ions.
  • MS-Comp has an elemental composition search option which includes nitrogen rule and valency checks.
  • MS-Edman has options for searching lists of names, species and accession numbers. This option would typically be used in conjunction with FA-Index to create subset databases.
  • Mixtures of 2 or more digests are possible; you can mix N and C terminal digests and any digest with CNBr.
  • MS-Fit and MS-Digest have the option of looking for fragments containing either acrylamide modified cysteines or another form of cysteine.
  • The species filtering mechanism has been expanded to allow searches limited to a collections of species and searches which exclude certain species.
  • PTC added as an N terminal group option.
  • Additional options added to the DNA frame translation parameter.
  • The digest cleavage rules are defined in a file. Licensees can thus add new digests or modify existing ones.
  • The list of available options for the database, terminal groups, cysteine modification, digest and species parameters are defined in one place for all the programs, for easier updating by licensees.
  • The programs can handle database files with carriage return and line feed at the end of the line as well as just line feed (ie. both DOS and UNIX ASCII).
  • Licensees can now run FA-Index from a browser page. It also has options for creating subset databases based on species/molecular weight filters and from saved results files. Also new entries can be added to existing databases and databases can be created from scratch. A database summary report has also been added.
  • A new file (suffix .sl) is created by the FA-Index program when it is makes the index files for a database. The file contains an alphabetic listing of the species aliases which occur more than ten times in a given database, for easier creation of species collections by licensees.

V 3.0.4 4/1998
  • Changed the way in which databases with the same accession number links and/or species alias files can be grouped.
  • Fixed bug for printing error message with faulty species alias lists.

V 3.0.3 4/1998
  • Limit removed on the number of allowed user databases.
  • Fixed bug whereby alphanumeric accession numbers in DA.. databases didn't work.
  • The software can now deal with changes to the Owl comment line introduced after revision 30.
  • Minor bug in the MS-Tag abort facility fixed.
  • Updated Owl.sp file implementing improved species searching.

V 3.0.2 3/1998
  • Cosmetic changes to the MS-Fit output including addition of comment tags.
  • Pressing stop on client browser aborts MS-Tag and MS-Edman searches on server.
  • Fixed bug in MS-Tag where automated immonium assignement altered multiply charged ion assignments.
  • Fixed complement strand DNA translation so frames 4,5,6 are correct.

V 3.0.1 9/1997
  • MS-Fit searches can be terminated by pressing the browser STOP button.
  • Fixed cosmetic bug in MS-Fit multiply charged output. Charges were displayed above table in Detailed Results, instead of as subscripts on input masses.

V 3.0 7/1997
  • Extensive overhaul of instructions for most programs,installation and administration.
  • Multiply charged ions for electrospray allowed.
  • Dynamic memory allocation eliminates the restriction on maximum number of masses that can be input to MS-Fit and MS-Tag.
  • Intact Protein MW pre-filter can be bypassed in MS-Fit, MS-Tag, and MS-Edman.
  • MS-Fit Homology mode implemented by adding mutation matrix routines from MS-Tag.
  • MS-Fit results can be saved to a file.
  • MS-Tag can search the hits saved from MS-Fit.
  • MS-Tag no errors and allow error modes renamed identical and homology modes.
  • MS-Tag results split into summary and detail reports.
  • MS-Tag output shows mass error on fragment ion masses.
  • MS-Tag allows use of monoisotopic parent mass and average fragment masses.
  • MS-Tag, MS-Edman, and MS-Comp allow for modified peptide termini to be designated.
  • MS-Tag allows for immonium and related ion masses to be entered directly.
  • MS-Tag b+H2O ion type modified to allow occurence when ion contains K.
  • Maximum internal ion mass in MS-Tag increased from 500 to 800 Da.
  • Improved implementation of de novo sequencing in MS-Tag (searching Unknome), particularly with display of results in degenerate peptide form.
  • MS-Edman modified to accept a list of sequences (expected to come from MS-Tag Unknome mode results).
  • MS-Edman modified for better homology searching by allowing mismatched amino acids.
  • Results now display the version number of the program in the footer.
  • All input variables internally assigned default values so that automated bypassing of the HTML input form doesn't crash the program if some input variables are not supplied.
  • The URL's linked to from the peptide sequence and the MS-Digest index number are now externally modifiable by a server administrator.
  • Prospector logo first used.
  • DN1, DN2, DA1, DA2, PN1, PN2, PA1, and PA2 prefixes for generic FASTA formatted databases introduced.
  • Fixed bug in MS-Tag homology mode so star ions are matched when only N-terminal ion types OR only C-terminal ion types are designated.

V 2.0 2/1997
  • Whole package of programs now called Protein Prospector.
  • 6-frame translation added to handle dbEST.
  • MS-Fit, MS-Tag output contains html comment tags to facilitate possible automated parsing of redirected output.
  • Input variable names unified across htm files for all programs to facilitate possible automated input bypassing of HTML forms.
  • MS-Comp introduced.
  • Preliminary implementation of de novo sequencing in MS-Tag (searching Unknome).
  • MS-Tag allow errors mode control of mutation matrix added.
  • MS-Tag allow errors mode searches speed increased.
  • Fixed bug in global error handling display.
  • MS-Fit, MS-Tag, MS-Edman have variable maximum number of hits displayed.
  • MS-Fit calculates % of protein covered by matched peptides.
  • MS-Fit, MS-Tag, MS-Edman allows for a sample ID (comment) input field.
  • MS-Digest allows user specified protein sequence.
  • MS-Digest, MS-Product allows user specified amino acid.
  • Fixed bug pertaining to unreadable species in NCBInr database.
  • faindex creates database_name.usp file for unreadable species entries.
  • MS-Product; added b+H2O; a,b,y-H3PO4; b,y-SOCH4; Y; and N,C-term ladder ion types.
  • MS-Product modified to display both monoisotopic and average parent masses.
  • MS-Product prints fragment masses to 2 decimal places.
  • MS-Product fixed so c ions are correctly calculated.
  • Changed suffix on forms from html to htm.
  • Made source code portable to Windows NT.
  • Shifted software development environment to PC.

V 1.1 8/1996
  • Added MS-Edman program.
  • Added NCBInr database usage.
  • Implemented global error handling.
  • Fixed bug in MS-Tag associated with incorrect labeling of star ion types in allow errors mode.
  • Fixed bug in MS-Digest retrieval by accession number.
  • Added elemental composition and amino acid composition calculation to MS-Product.
  • Cosmetic revisions to output display in MS-Fit and MS-Tag.
  • Allowed comments in msparams/database.sp files.
  • Separated source code libraries.

V 1.0 6/1996
  • Programs available for use only on the world wide web prior to 6/1996 (starting 10/1995), and not distributed to licensees for use locally. Work on Protein Prospector started in 04/1995.