---

• Some of the programs don't work with the Opera browser.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Multiply specified amino acids in MS-Comp are erroneously removed.
• The links to other searches from the MS-Fit detailed results don't work in Internet Explorer if there are too many (around 80) peaks. This doesn't seem to be a problem with Netscape.
• The applet graph doesn't always display in the MS-Fit detailed results with Netscape.
• 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.
• MS-Homology fails to calculate the correct score there is a match containing the amino acid U which is now used to denote selenocysteine. This problem could also occur if other amino acid codes such as B or Z don't appear in the relevant matrix in the mat_score.txt file.
• 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.

---

• 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.
• Some of the programs don't work with the Opera browser.
• 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.
• ICAT and IDEnT options don't filter the results for cysteine containing peptides.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Multiply specified amino acids in MS-Comp are erroneously removed.
• The links to other searches from the MS-Fit detailed results don't work in Internet Explorer if there are too many (around 80) peaks. This doesn't seem to be a problem with Netscape.
• The applet graph doesn't always display in the MS-Fit detailed results with Netscape.
• 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.
• MS-Homology fails to calculate the correct score there is a match containing the amino acid U which is now used to denote selenocysteine. This problem could also occur if other amino acid codes such as B or Z don't appear in the relevant matrix in the mat_score.txt file.
• 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.

---

• 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.
• Some of the programs don't work with the Opera browser.
• 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.
• The user defined amino acids u, v, w and x don't have their masses correctly initialised.
• ICAT and IDEnT options don't filter the results for cysteine containing peptides.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Multiply specified amino acids in MS-Comp are erroneously removed.
• The links to other searches from the MS-Fit detailed results don't work in Internet Explorer if there are too many (around 80) peaks. This doesn't seem to be a problem with Netscape.
• The applet graph doesn't always display in the MS-Fit detailed results with Netscape.
• 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.
• MS-Homology fails to calculate the correct score there is a match containing the amino acid U which is now used to denote selenocysteine. This problem could also occur if other amino acid codes such as B or Z don't appear in the relevant matrix in the mat_score.txt file.
• 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.

---

• 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.
• Some of the programs don't work with the Opera browser.
• 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.
• The user defined amino acids u, v, w and x don't have their masses correctly initialised.
• ICAT and IDEnT options don't filter the results for cysteine containing peptides.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Multiply specified amino acids in MS-Comp are erroneously removed.
• The links to other searches from the MS-Fit detailed results don't work in Internet Explorer if there are too many (around 80) peaks. This doesn't seem to be a problem with Netscape.
• The applet graph doesn't always display in the MS-Fit detailed results with Netscape.
• 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 masses.
• 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.
• Links to MS-Tag Unknome still available.
• MS-NonSpecific hits reported incorrectly. The peptides all have an extra amino acid at the end.
• 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.
• MS-Homology fails to calculate the correct score there is a match containing the amino acid U which is now used to denote selenocysteine. This problem could also occur if other amino acid codes such as B or Z don't appear in the relevant matrix in the mat_score.txt file.
• 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.

---

• 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.
• Some of the programs don't work with the Opera browser.
• 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.
• The user defined amino acids u, v, w and x don't have their masses correctly initialised.
• ICAT and IDEnT options don't filter the results for cysteine containing peptides.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Multiply specified amino acids in MS-Comp are erroneously removed.
• The links to other searches from the MS-Fit detailed results don't work in Internet Explorer if there are too many (around 80) peaks. This doesn't seem to be a problem with Netscape.
• The applet graph doesn't always display in the MS-Fit detailed results with Netscape.
• 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.
• 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 masses.
• 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.
• Links to MS-Tag Unknome still available.
• MS-NonSpecific hits reported incorrectly. The peptides all have an extra amino acid at the end.
• 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.
• MS-Homology fails to calculate the correct score there is a match containing the amino acid U which is now used to denote selenocysteine. This problem could also occur if other amino acid codes such as B or Z don't appear in the relevant matrix in the mat_score.txt file.
• 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.

---

• 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.
• Some of the programs don't work with the Opera browser.
• 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.
• ICAT and IDEnT options don't filter the results for cysteine containing peptides.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Multiply specified amino acids in MS-Comp are erroneously removed.
• 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.
• d, v and w ion exclude AA's incorrectly assigned.
• Composition search in MS-Tag checked by default.
• 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 are not possible in a database.
• Sometimes names/accession numbers/species aren't reported for Pdefault and Ddefault type databases.
• The applet graph doesn't always display in the MS-Fit detailed results with Netscape.
• w ion masses calculated incorrectly.
• In Netscape 4.7 and older browsers the links to other programs sometimes don't work because spaces in the URLs aren't escaped.
• 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.
• MS-Fit, MS-Bridge, MS-NonSpecific can't deal with average masses.
• 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.
• Links to MS-Tag Unknome still available.
• 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.
• MS-Homology fails to calculate the correct score there is a match containing the amino acid U which is now used to denote selenocysteine. This problem could also occur if other amino acid codes such as B or Z don't appear in the relevant matrix in the mat_score.txt file.
• 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.

---

• Some of the programs don't work with the Opera browser.
• Command line FA-Index instructions confusing.
• The NCBI ftp site used for most of the databases has now changed.
• 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).
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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.
• The delete DNA database option in FA-Index doesn't delete all the DNA database files.

---

• Some of the programs don't work with the Opera browser.
• Command line FA-Index instructions confusing.
• The NCBI ftp site used for most of the databases has now changed.
• 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.
• H3PO4 and SOCH4 losses are not reported in MS-Product if the instrument specific default ion types tick box is selected.
• 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.
• ICAT and IDEnT options don't filter the results for cysteine containing peptides.
• 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).
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of the database entries from various databases.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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.
• The delete DNA database option in FA-Index doesn't delete all the DNA database files.

---

• Some of the programs don't work with the Opera browser.
• Command line FA-Index instructions confusing.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
• H3PO4 and SOCH4 losses are not reported in MS-Product if the instrument specific default ion types tick box is selected.
• 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.
• 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.
• 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.
• 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).
• The hit information line in MS-Fit containing the percentage of hits, size, PI and protein name is separate 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.
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• Pdefault and Ddefault database prefixes incorrectly named in the manual (they were called PDefault and DDefault).
• The delete DNA database option in FA-Index doesn't delete all the DNA database files.

---

• Some of the programs don't work with the Opera browser.
• Command line FA-Index instructions confusing.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
• H3PO4 and SOCH4 losses are not reported in MS-Product if the instrument specific default ion types tick box is selected.
• 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.
• 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.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• The programs crash if the msparams/colors.txt file is missing.
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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-Edman 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.
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• The delete DNA database option in FA-Index doesn't delete all the DNA database files.

---

• Some of the programs don't work with the Opera browser.
• Command line FA-Index instructions confusing.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
• H3PO4 and SOCH4 losses are not reported in MS-Product if the instrument specific default ion types tick box is selected.
• 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.
• 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.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• The programs crash if the msparams/colors.txt file is missing.
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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-Edman 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.
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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.
• The delete DNA database option in FA-Index doesn't delete all the DNA database files.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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-Edman 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.
• MS-Product doesn't allow multiply charged ions.
• MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• The MS-Fit detailed report fails to report the m/z submitted if any of the data is multiply charged.
• MS-Comp doesn't work if Combination Type is set to Elemental.
• MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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 *.sp files for multiple and excluded species filters to work correctly.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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-Edman 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.
• Forward links in results pages don't work with the Internet Explorer browser version 3.
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
• MS-Product doesn't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• The MS-Fit detailed report fails to report the m/z submitted if any of the data is multiply charged.
• MS-Comp doesn't work if Combination Type is set to Elemental.
• MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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 *.sp files for multiple and excluded species filters to work correctly.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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-Edman 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.
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
• MS-Product doesn't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• The MS-Fit detailed report fails to report the m/z submitted if any of the data is multiply charged.
• MS-Comp doesn't work if Combination Type is set to Elemental.
• MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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 *.sp files for multiple and excluded species filters to work correctly.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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-Edman 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.
• DNA and open reading frame results don't line up with the headers in the MS-Tag output.
• MS-Isotope crashes if the monoisotopic peak abundance is too low.
• MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
• pI calculation in error under certain conditions.
• MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
• MS-Product doesn't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• MS-Comp doesn't work if Combination Type is set to Elemental.
• MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
• MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on your browser preferences to get MS-Isotope to run without displaying the graph.
• 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 *.sp files for multiple and excluded species filters to work correctly.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Edman and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• The list of sequences resulting from an MS-Tag unknome search cannot easily be supplied to MS-Edman for a homology search.
• MS-Digest and MS-Product don't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• 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.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Edman and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• The list of sequences resulting from an MS-Tag unknome search cannot easily be supplied to MS-Edman for a homology search.
• MS-Digest and MS-Product don't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Faulty species alias lists cause database search programs to crash rather than generate error.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• 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.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Edman and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• The list of sequences resulting from an MS-Tag unknome search cannot easily be supplied to MS-Edman for a homology search.
• MS-Digest and MS-Product don't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Faulty species alias lists cause database search programs to crash rather than generate error.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• 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.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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-Edman 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Edman and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• Bug in MS-Tag where automated immonium ion assignment alters multiply charged ion assignments.
• Cosmetic bug in MS-Fit multiply charged output. Charges displayed above table in Detailed Results, instead of as subscripts on input masses.
• The list of sequences resulting from an MS-Tag unknome search cannot easily be supplied to MS-Edman for a homology search.
• MS-Digest and MS-Product don't allow multiply charged ions.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Complement strand DNA translation incorrect, frames 4,5,6 are incorrect.
• Faulty species alias lists cause database search programs to crash rather than generate error.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
• 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.

---

• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• 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-Comp doesn't work if the full amino acid composition of the ion is specified.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• 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.
• 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).
• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Edman and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• MS-Tag allow errors mode does not match star ions unless at least one N-terminal ion type AND at least one C-terminal ion type are designated.
• Unix version of MS-Digest does not work from html input form. Changing the line
  !--Unix version--
  form method="POST" action="../cgi-bin/msdigest"
  to
  form method="GET" action="../cgi-bin/msdigest"
  Will allow MS-Digest to work, however, user supplied protein sequences are tolerated only up to length ~200.
• All Programs are unable to extract species information from the comment line of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a species name of UNREADABLE. The protein name is assigned as the complete Fasta comment line.
• Complement strand DNA translation incorrect, frames 4,5,6 are incorrect.
• Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.

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• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• Every 50th peak in MS-Digest doesn't get reported.
• 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.
• mmu tolerance calculations incorrect.
• 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Edman and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• MS-Tag allow errors mode does not match star ions unless at least one N-terminal ion type AND at least one C-terminal ion type are designated.
• MS-Product incorrectly calculates c ions, off by 2 Hydrogens.
• Non-uniform input variable names across htm files for all programs hinders automated input bypassing of html forms.
• HTML output for all programs contains no line breaks, thus hindering automated output parsing of search results.
• Global error handling display, repeats footer line.
• When searching the NCBInr database all programs, matches are made to proteins with MW outside the MW cutoffs. This is caused by combining sequences from multiple entries to make a single protein, and originates from inability to extract species information from the comment line of ~15% of entries (mostly originating in PIR).

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• Some of the programs don't work with the Opera browser.
• The NCBI ftp site used for most of the databases has now changed.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
• 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.
• 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).
• There is a limit to the size of the database that can be used of around 2 GBytes.
• Every 50th peak in MS-Digest doesn't get reported.
• 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.
• mmu tolerance calculations incorrect.
• 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.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• MS-Tag allow errors mode does not match star ions unless at least one N-terminal ion type AND at least one C-terminal ion type are designated.
• MS-Tag incorrectly labels star ion types in allow errors mode with position number from the wrong end of sequence.
• MS-Digest retrieval by accession number fails frequently.
• MS-Product incorrectly calculates c ions, off by 2 Hydrogens.
• HTML output for all programs contains no line breaks, thus hindering automated output parsing of search results.

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