---

• Introduction
• Automating Batch-Tag Searching
• Making Projects
• Batch-Tag
• Search Compare
• Job Status
• Results Management
• Batch-Tag Daemon
• Automation of Centroiding
  • Peak Spotter
  • Wiff To Centroid
• Parameters for Other Protein Prospector Programs
  • MS-Fit
  • MS-Tag
  • MS-Seq
  • MS-Pattern
  • MS-Homology
  • MS-Digest
  • MS-Bridge
  • MS-NonSpecific
  • MS-Product
  • MS-Comp
  • DB-Stat
  • MS-Isotope
  • FA-Index - Create Indicies for New Database
  • FA-Index - Database Summary Report
  • FA-Index - Create Subset Database
  • FA-Index - Create Subset Database with Indices from Saved Hits
  • FA-Index - Create or Append to User Database

---

Most of the programs in the Protein Prospector package are implemented according to the Common Gateway Interface (CGI) standard. The parameters for the programs are thus a set of name-value pairs. These can either be provided from a HTML form, a script that mimics the CGI format or from the command line.

A detailed description of the CGI format is beyond the scope of this document. Protein Prospector should be able to recognize forms where the method is either GET or POST. If the method is POST then the enctype attribute can either be multipart/form-data or text/plain. A useful book on CGI Programming is:

CGI Programming on the World Wide Web, Shishir Gundavaram, O'Reilly, 1996

The programs can be run from the command line by two different methods either as a long list of name value pairs:

$ programName - name1=value1 name2=value2 ............... nameN=valueN

or with the parameters are stored in an XML file:

$ programName -f params.xml name1=value1 name2=value2 ..... nameN=valueN

For example to index a database using FA-Index on a Windows system:

faindex.cgi - create_database_indicies=1 database=SwissProt.11.02

On a UNIX system you should use a command of the following form (run from the directory):

./faindex.cgi - create_database_indicies=1 database=SwissProt.11.02 

Note that the first argument has to be a dash character.

For the case where the parameters are stored in an XML file any parameters submitted on the command line will override those in the file. The format of the xml file should be as follows:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<name1>value1</name1>
<name2>value2</name2>
.....
<nameN>valueN</nameN>
</parameters>

The second version may be preferred if there are a lot of parameters or the environment you submit the command from imposes a maximum length for a command. A second alternative in this case would be to use a Perl script:

$c = "programName";
$c .= " - ";
$c .= "name1=value1";
$c .= " ";
$c .= "name2=value2";
$c .= " ";
........
$c .= "nameN=valueN";
$c .= " ";
system "$c";

Certain characters need to be escaped when included in a value. These are uppercase hexadecimal ASCII values preceded by a percent sign. If the parameters are stored in an XML file they don't strictly need to be escaped like this but can be. Some commonly used escape codes are listed in the table below:

space	%20
line end	%0D%0A
comma	%2C

Some parameters such as would appear as multiple choice menus or tick boxes on a HTML form may be specified multiple times with different values. Eg in an XML parameter file context:

.....
<mod_AA>Peptide%20N-terminal%20Gln%20to%20pyroGlu</mod_AA>
<mod_AA>Oxidation%20of%20M</mod_AA>
<mod_AA>Protein%20N-terminus%20Acetylated</mod_AA>
.....

or in a command line context:

$ command.cgi - it=a it=b it=y ...................

If the parameter is entered via a text box on a HTML form then its value can extend over several lines.

In an XML parameter file this could be specified thus:

<accession_nums>P40069
P15180
P11484</accession_nums>

Or thus:

<accession_nums>P40069%0D%0AP15180%0D%0AP11484</accession_nums>

In a list of command line arguments it would be specified as follows:

$ command.cgi - accession_nums=P40069%0D%0AP15180%0D%0AP11484 .....

To make a project you need to use the msform.cgi binary. The parameters used are shown below.

name	Default Value	Valid Values
data_file_list	None Defined	Paths to centroid data files in the centroid data repository.
project_name	""	text
form	""	needs to be set to makeproject
instrument_name	""	valid text strings from params/instrument.txt
user	""	valid user from the database
write_file	false	needs to be set to true

For example you could put the following into a file called test.xml:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<data_file_list>Q-STAR1/2008/06/F3.mgf</data_file_list>
<data_file_list>Q-STAR1/2008/06/F4.mgf</data_file_list>
<project_name>test</project_name>
<form>makeproject</form>
<instrument_name>ESI-Q-TOF</instrument_name>
<user>pp</user>
<write_file>1</write_file>
</parameters>

and run the command as follows:

$ msform.cgi -f test.xml

To run a Batch-Tag search you need to use the msbatch.cgi binary. The parameters used are shown below.

name	Default Value	Valid Values
search_name	""	needs to be set to batchtag
report_title	""	text
database	Non selected	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
dna_frame_translation	3	6, 3, -3, 1, -1
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
output_filename	""	text
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
allow_non_specific	at 0 termini	at 0 termini, at 1 termini, at 2 termini, at N termini, at C termini, N termini-1=D
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
msms_prot_low_mass	1000	integer
msms_prot_high_mass	100000	integer
msms_full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
species_names	None Defined	list of text strings
species_remove	0	0, 1
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
add_accession_numbers	None Defined	list of text strings
expect_calc_method	None	None, Linear Tail Fit
msms_precursor_charge_range	""	List of charges required separated by spaces
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
msms_parent_mass_tolerance	0.5	double
msms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
msms_parent_mass_systematic_error	0.0	double
fragment_masses_tolerance	0.5	double
fragment_masses_tolerance_units	Da	Da, %, ppm, mmu
msms_mod_AA	None defined	valid text strings formed from the information in params/usermod.txt.
msms_max_modifications	1	integer
msms_max_peptide_permutations	""	Left blank or non zero positive integer
mod_start_nominal	0	integer
mod_end_nominal	0	integer
mod_defect	0.0	double
mod_comp_ion	None defined	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
mod_n_term	0	0, 1
mod_c_term	0	0, 1
mod_neutral_loss	0	0, 1
mod_uncleaved	0	0, 1
msms_pk_filter	Max MSMS Pks	Max MSMS Pks or Max MSMS Pks / 100 Da
msms_max_peaks	""	integer
msms_search_type	None defined	valid text strings formed from the file params/homology.txt.
data_source	Data Paste Area	need to be set to "List of Files".
instrument_name	""	valid text strings from params/instrument.txt
project_name	""	text
user	""	valid user from the database
comment	""	text
max_hits	200	integer
msms_max_reported_hits	50	integer
script_filename	""	text
use_instrument_ion_types	0	0 or 1
save_params	0	0 or 1

For example you could put the following into a file called test.xml:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<allow_non_specific>at 0 termini</allow_non_specific>
<const_mod>Carbamidomethyl (C)</const_mod>
<data_source>List of Files</data_source>
<database>SwissProt.2008.08.20</database>
<dna_frame_translation>3</dna_frame_translation>
<enzyme>Trypsin</enzyme>
<expect_calc_method>Linear Tail Fit</expect_calc_method>
<fragment_masses_tolerance>300</fragment_masses_tolerance>
<fragment_masses_tolerance_units>ppm</fragment_masses_tolerance_units>
<full_pi_range>1</full_pi_range>
<high_pi>10.0</high_pi>
<instrument_name>ESI-Q-TOF</instrument_name>
<low_pi>3.0</low_pi>
<max_hits>9999999</max_hits>
<missed_cleavages>1</missed_cleavages>
<msms_full_mw_range>1</msms_full_mw_range>
<msms_max_modifications>2</msms_max_modifications>
<msms_max_reported_hits>5</msms_max_reported_hits>
<msms_mod_AA>Acetyl (Protein N-term)</msms_mod_AA>
<msms_mod_AA>Gln->pyro-Glu (N-term Q)</msms_mod_AA>
<msms_mod_AA>Met-loss (Protein N-term M)</msms_mod_AA>
<msms_mod_AA>Oxidation (M)</msms_mod_AA>
<msms_parent_mass_systematic_error>0</msms_parent_mass_systematic_error>
<msms_parent_mass_tolerance>200</msms_parent_mass_tolerance>
<msms_parent_mass_tolerance_units>ppm</msms_parent_mass_tolerance_units>
<msms_precursor_charge_range>2 3</msms_precursor_charge_range>
<msms_prot_high_mass>125000</msms_prot_high_mass>
<msms_prot_low_mass>1000</msms_prot_low_mass>
<output_filename>results</output_filename>
<parent_mass_convert>monoisotopic</parent_mass_convert>
<project_name>test</project_name>
<report_title>BatchTag</report_title>
<search_name>batchtag</search_name>
<species>SACCHAROMYCES CEREVISIAE</species>
<use_instrument_ion_types>1</use_instrument_ion_types>
<user>pbaker</user>
</parameters>

and run the command as follows:

$ msbatch.cgi -f test.xml

To run Search Compare you need to use the searchCompare.cgi binary. The parameters used are shown below.

name	Default Value	Valid Values
save_format	HTML	HTML, Tab delimited text, Filtered Peak Lists, pepXML
accession_nums	None Defined	list of text strings
remove	0	0 or 1
multi_sample	0	0 or 1
id_filter_list	None Defined	List of integers
preferred_species	None Defined	List of text strings
min_best_disc_score_ESI_Q_TOF	0.0	double
min_best_disc_score_ESI-ION-TRAP-low-res	0.0	double
min_best_disc_score_ESI-FT-ICR-CID	0.0	double
min_best_disc_score_ESI-FT-ICR-ECD	0.0	double
min_best_disc_score_MALDI-Q-TOF	0.0	double
min_best_disc_score_MALDI-TOFTOF	0.0	double
min_pp_protein_score	0.0	double
min_pp_peptide_score	0.0	double
max_protein_evalue	0.01	double
max_peptide_evalue	0.01	double
keep_replicates	0	0 or 1
best_disc_only	0	0 or 1
disc_score_graph	0	0 or 1
comp_mask_type	AND	OR, AND
comp_ion	None defined	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y and valid text strings formed from the information in params/usermod.txt.
mass_comp_list	None defined	List of doubles
report_m_plus_h	0	0 or 1
report_m_over_z	0	0 or 1
report_charge	0	0 or 1
report_m_plus_h_calc	0	0 or 1
report_m_over_z_calc	0	0 or 1
report_intensity	0	0 or 1
report_error	0	0 or 1
report_unmatched	0	0 or 1
report_num_pks	0	0 or 1
report_rank	0	0 or 1
report_score	0	0 or 1
report_score_diff	0	0 or 1
report_expectation	0	0 or 1
report_p_value	0	0 or 1
report_nlog_p_value	0	0 or 1
report_num_precursor	0	0 or 1
report_gradient	0	0 or 1
report_offset	0	0 or 1
report_disc_score	0	0 or 1
report_repeats	0	0 or 1
report_prot_score	0	0 or 1
report_num_unique	0	0 or 1
report_peptide_count	0	0 or 1
report_best_score	0	0 or 1
report_best_expect	0	0 or 1
report_coverage	0	0 or 1
report_best_disc_score	0	0 or 1
report_peptide	0	0 or 1
peptide_mod_type	Variable Mods Only	Off, Mods In Peptide, Variable Mods Only, Constant Mods Only, All Mods (1 column), All Mods (2 columns)
report_var_mod	0	0 or 1
report_protein_mod	0	0 or 1
slip_threshold	0.0	double
report_length	0	0 or 1
report_composition	0	0 or 1
report_start_aa	0	0 or 1
report_end_aa	0	0 or 1
report_previous_aa	0	integer
report_next_aa	0	integer
report_missed_cleavages	0	0 or 1
report_mass_mod	0	0 or 1
report_time	0	0 or 1
report_number	0	0 or 1
report_accession	0	0 or 1
report_uniprot_id	0	0 or 1
report_gene_name	0	0 or 1
report_prot_len	0	0 or 1
report_mw	0	0 or 1
report_pi	0	0 or 1
report_species	0	0 or 1
report_name	0	0 or 1
report_links	0	0 or 1
raw_type	""	MS Precursor, MS Full Scan, MS/MS, Quantitation
quan_type	""	valid text strings formed from the information in params/quan.xml and params/quan_msms.xml.
rep_q_median	0	0 or 1
rep_q_iqr	0	0 or 1
rep_q_mean	0	0 or 1
rep_q_n_sdv	2.0	double
rep_q_stdev	0	0 or 1
rep_q_num	0	0 or 1
rep_intensity	0	0 or 1
intensity_threshold	0.0	double
rep_resolution	0	0 or 1
rep_a_lh_int	0	0 or 1
rep_area	0	0 or 1
area_threshold	0.0	double
rep_a_lh_area	0	0 or 1
rep_snr	0	0 or 1
snr_threshold	0.0	double
rep_n_mean	0	0 or 1
rep_n_stdev	0	0 or 1
rt_int_start	0.0	double
rt_int_end	0.0	double
resolution	10000.0	double
percent_C13	100.0	double
percent_N15	100.0	double
percent_O18	100.0	double
purity_correction	0	From formulae, Default, No correction and options from purity files.
database_type	None defined	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.
report_type	Protein	Protein, Peptide, Time, False Positive Rate
report_homologous_proteins	Interesting	All, Interesting, None
report_hits_type	""	Union, Intersection, Difference
sort_type	""	Discriminant Score, Peptide Score, Expectation Value, Start Residue, Fraction/RT, RT, m/z, M+H, Intensity, Error, Time, Charge/M+H, Mass Mod
sort_type2	""	"", Discriminant Score, Peptide Score, Expectation Value, Start Residue, Fraction/RT, RT, m/z, M+H, Intensity, Error, Time, Charge/M+H, Mass Mod
msms_pk_filter	Max MSMS Pks	Max MSMS Pks, Max MSMS Pks / 100 Da or Unprocessed MSMS
unmatched_spectra	0	0 or 1
msms_max_peaks	""	integer
msms_max_reported_hits	50	integer
data	None defined	List of search job keys from mySQL database for searches that you want to compare. The relevant database field is search_jobs.search_job_key
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
run_msproduct	0	0 or 1
save_params	0	0 or 1

For example you could put the following into a file called test.xml:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<save_format>Tab delimited text</save_format>
<min_best_disc_score_ESI_Q_TOF>0.0</min_best_disc_score_ESI_Q_TOF>
<min_pp_protein_score>22.0</min_pp_protein_score>
<min_pp_peptide_score>15.0</min_pp_peptide_score>
<max_protein_evalue>0.01</max_protein_evalue>
<max_peptide_evalue>0.01</max_peptide_evalue>
<keep_replicates>0</keep_replicates>
<best_disc_only>1</best_disc_only>
<disc_score_graph>0</disc_score_graph>
<report_m_plus_h>0</report_m_plus_h>
<report_m_over_z>1</report_m_over_z>
<report_charge>1</report_charge>
<report_m_plus_h_calc>0</report_m_plus_h_calc>
<report_m_over_z_calc>0</report_m_over_z_calc>
<report_intensity>0</report_intensity>
<report_error>1</report_error>
<report_unmatched>0</report_unmatched>
<report_num_pks>0</report_num_pks>
<report_rank>0</report_rank>
<report_score>1</report_score>
<report_score_diff>0</report_score_diff>
<report_expectation>1</report_expectation>
<report_num_precursor>0</report_num_precursor>
<report_disc_score>0</report_disc_score>
<report_repeats>1</report_repeats>
<report_prot_score>0</report_prot_score>
<report_num_unique>1</report_num_unique>
<report_peptide_count>0</report_peptide_count>
<report_best_score>0</report_best_score>
<report_best_expect>1</report_best_expect>
<report_coverage>1</report_coverage>
<report_best_disc_score>1</report_best_disc_score>
<report_peptide>1</report_peptide>
<peptide_mod_type>Variable Mods Only</peptide_mod_type>
<report_protein_mod>1</report_protein_mod>
<slip_threshold>6</slip_threshold>
<report_length>0</report_length>
<report_composition>0</report_composition>
<report_start_aa>0</report_start_aa>
<report_end_aa>0</report_end_aa>
<report_previous_aa>1</report_previous_aa>
<report_next_aa>1</report_next_aa>
<report_missed_cleavages>0</report_missed_cleavages>
<report_mass_mod>0</report_mass_mod>
<report_time>1</report_time>
<report_number>1</report_number>
<report_accession>1</report_accession>
<report_gene_name>0</report_gene_name>
<report_prot_len>0</report_prot_len>
<report_mw>1</report_mw>
<report_pi>0</report_pi>
<report_species>1</report_species>
<report_name>1</report_name>
<report_links>1</report_links>
<database_type>SwissProt</database_type>
<report_type>Peptide</report_type>
<report_homologous_proteins>Interesting</report_homologous_proteins>
<report_hits_type>Union</report_hits_type>
<sort_type>Expectation Value</sort_type>
<sort_type_2></sort_type_2>
<data>VzTrrrtteaD7HySm</data>
<parent_mass_convert>monoisotopic</parent_mass_convert>
</parameters>

and run the command as follows:

$ searchCompare.cgi -f test.xml > temp.txt

The jobStatus.cgi binary can be used to control or output job status. The parameters for the program are shown below:

name	Default Value	Valid Values
abort	0	0 or 1
search_key	""	search keys stored in the mySQL database

For example to output the job status of a given job enter the following command:

$ jobStatus.cgi - search_key=VzTrrrtteaD7HySm

To abort a given job:

$ jobStatus.cgi - search_key=VzTrrrtteaD7HySm abort=1

The msform.cgi binary can be used to delete projects and results.

name	Default Value	Valid Values
form	""	needs to be set to results_management
user	""	valid user from the database
project_name	None defined	List of projects to delete.
results_file	None defined	List of results files to delete. These need to be specified in the form results/project

For example to delete some of the pp's projects from the database put the following commands into a file called test.xml:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<project_name>test</project_name>
<project_name>test2</project_name>
<form>results_management</form>
<user>pp</user>
</parameters>

and run the command as follows:

$ msform.cgi -f test.xml

If you delete a project then all the results for that project are also deleted.

If you just want to delete a set of results then the parameter file might look as follows:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<results_file>test/results1</results_file>
<form>results_management</form>
<user>pp</user>
</parameters>

The Batch-Tag Daemon is the program that controls the running of Batch-Tag searches in a Protein Prospector system. It runs as a service on a Windows computer (btag_daemon.exe) or as a daemon on a LINUX computer (btag-daemon). Multiple computers can run Batch-Tag Daemons at the same time. Its setup parameters are contained in the file info.txt which it reads on startup or on receipt of a HUP signal (LINUX only). It periodically checks a mySQL database for newly submitted or aborted searches. It will start a search if there are sufficient resources; otherwise the searches are queued or run by another Batch-Tag Daemon. On LINUX systems searches are run using a Perl script (mssearchmpi.pl or mssearch.pl) whereas on Windows systems the executable program is called directly (mssearchmpi.cgi or mssearch.cgi). Whether mssearchmpi or mssearch is used depends on whether the system is configured to run searches using multiple processes via MPICH2. If searches are aborted or finish unexpectedly the Batch-Tag Daemon is responsible for cleaning up the files in the user repository. It is possible to configure the daemon to send email to users when searches have finished via the Perl script mail.pl. It is also capable of preloading indexed protein databases into memory. It logs its activity to the file logs/btagd.log.

Peak Spotter is used to extract data from an ABI 4700/4800 TOF-TOF Oracle database (version 3). It doesn't require the rest of the Protein Prospector installation to work. However the Oracle client software needs to be installed to allow the database to be accessed. The program can work on UNIX type platforms as well as Windows ones. The program parameters are as follows:

Parameter	Default Value	Valid Values
server_name	""	text
username	TSQUARED	text
password	TS	text
spot_set_list	0	0 or 1
run_number	0	integer
all_runs	0	0 or 1
write_raw_ms	0	0 or 1
write_raw_msms	0	0 or 1
retain_isotopes	0	0 or 1
minimum_area	100.0	floating point number
intensity_type	Height	Height, Area, Cluster Area, Signal to Noise
spot_set_names	None defined	Spot sets names from the database
centroid_dir	""	valid directory name
centroid_filename	output.txt	valid filename
raw_dir	""	valid directory name

If the parameter is set to the default value then it does not need to be specified.

server_name

This is the server name as defined in the Oracle client file tnsname.org. This parameter is always required.

username

A username to log in to the database. This parameter is always required.

password

A password for the given username. This parameter is always required.

spot_set_list

This parameter is only required if you want to get a list of spot sets in the database. If you set this parameter to 1 then all the parameters below should not be used.

run_number

The run number can be specified if you just want to extract the data for a given run.

all_runs

This parameter should be set unless you just want to extract the data for a single run.

write_raw_ms

If you set this parameter the raw MS data is also extracted from the database. A separate T2D file is extracted for each spectrum. You need to extract this if you want to do quantitation, such as SILAC, that uses the MS data. You should also extract it if you want to include columns in the Search Compare report, such as intensity, which are calculated from the raw data or to be able to see the parent ion raw data by clicking on the m/z column in the Search Compare peptide report. These files are not used by the database search program.

write_raw_msms

If you set this parameter the raw MSMS data is also extracted from the database. A separate T2D file is extracted for each spectrum. You need to extract this if you want to do quantitation, such as iTRAQ, that uses the MSMS data. You should also extract it if you want to be able to look at the raw data from the Search Compare report. These files are not used by the database search program.

retain_isotopes

If you set this parameter then the isotope peaks are retained in the centroid file. Note that the default setting is for Prospector to allow the ABI software to do the deisotoping. If you want Protein Prospector to do the deisotoping then the Prospector instrument file will need to be set up accordingly.

minimum_area

The minimum area for a peak before it is included in the centroid file. Sometimes the peak lists can be very large if this value isn't set appropriately.

intensity_type

The units for the intensities stored in the centroid file. The possible values for the intensity type are:

• Intensity - The peak intensity of the monoisotopic peak.
• Area - The peak area of the monoisotopic peak.
• Cluster Area - The summed areas of all the peaks in the isotope cluster.
• Signal to Noise - The signal to noise ratio of the monoisotopic peak.

spot_set_names

A list of the names of the spot sets (one per line) to extract from the database. Generally only a single spot set is extracted at one time.

centroid_dir

The directory where you want the centroid file to be created. This directory should exist before running the program. A full path should be given for the directory.

centroid_filename

The name for the centroid file created.

raw_dir

The directory where you want the raw files to be created. This directory should exist before running the program. A full path should be given for the directory.

Examples

To get a list of spot sets from the database:

$ peakSpotter.cgi - server_name=server username=n password=p spot_set_list=1

Alternatively the following could be stored in a file called p.xml:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<server_name>server</server_name>
<username>n</username >
<password>p</password>
<spot_set_list>1</spot_set_list>
</parameters>

and the command run as follows:

$ peakSpotter.cgi -f p.xml

To extract a spot set from the database into a Protein Prospector data repository:

Create a file (say p.xml) containing the following:

<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<server_name>server</server_name>
<username>n</username>
<password>p</password>
<all_runs>1</all_runs>
<write_raw_ms>1</write_raw_ms>
<write_raw_msms>1</write_raw_msms>
<retain_isotopes>0</retain_isotopes>
<minimum_area>100.0</minimum_area>
<intensity_type>Height</intensity_type>
<spot_set_names>User Project 1\test</spot_set_names>
<centroid_dir>R:\peaklists\TOFTOF1\2005\11</centroid_dir>
<centroid_filename>User Project 1$test.txt</centroid_filename>
<raw_dir>R:\raw\TOFTOF1\2005\11\User Project 1$test</raw_dir>
</parameters>

and run the command as follows:

$ peakSpotter.cgi -f p.xml

Note that

1. The raw directory needs to exist before running peakSpotter.
2. Once several spot sets have been extracted you can combine them together to make a Protein Prospector project using the Make Project program. However for this to work the directory where the raw files are going to be stored needs to have the same name as the centroid file (without the .txt suffix). The name doesn't have to correspond to the name of the spot set in the database. The .txt suffix for the centroid file is also currently mandatory.
3. The \ character in the original spot set name has been replaced by a $ character so it isn't mistaken for part of the raw directory path.
4. Peaklists for both the MS and MSMS spectra are stored in the one centroid file.
5. If you extract the raw data then the program will typically take a lot longer to run.

The program wiffToCentroid.exe is a simple command line program to extract mgf (Mascot Generic Format) peak lists from ABI Sciex wiff files. It is compatible with Analyst QS 2.0 and Mascot.dll version 1.1446.0.20. An example use of the program is:

$ wiffToCentroid.cgi C:\wiffs\example.wiff C:\mgfs\example.mgf

The full paths to the wiff file and the mgf file must be specified.

The Analyst service must be running on the computer on which wiffToCentroid is running. The Analyst centroiding parameters stored in the registry are used to do the centroiding.

This program can only run on a Windows computer and does not support a CGI or XML parameter file interface.

MS-Fit is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/msfit/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt, fit_graph.par.txt, homology.txt, idxlinks.txt, instrument.txt, taxonomy.txt and taxonomy_groups.txt (taxonomy searches only) and usermod.txt. The program also requires an indexed protein database produced by the FA-Index program. Possible output formats are HTML or XML. HTML reports makes use of the Java applet html/java/SpectrumGraph.jar, the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Product, MS-Digest, MS-Bridge, MS-NonSpecific and MS-Fit programs and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/mstag. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Fit
name	Default Value	Valid Values
search_name	""	needs to be set to msfit
report_title	""	text
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
instrument_name	""	valid text strings from params/instrument.txt
dna_frame_translation	3	6, 3, -3, 1, -1
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
indicies	""	list of database indicies (integers)
accession_numbers	""	list of database accession numbers
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
species_names	None Defined	list of text strings
species_remove	0	0, 1
add_accession_numbers	None Defined	list of text strings
ms_prot_low_mass	1000	integer
ms_prot_high_mass	100000	integer
ms_full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
sort_type	Score Sort	Score Sort MW Sort pI Sort
ms_report_homologous_proteins	Interesting	All, Interesting, None
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
comment	""	text
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_msfit	text
output_filename	""	text
max_reported_hits	50	integer
detailed_report	0	0,1
display_graph	0	0,1
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
ms_parent_mass_tolerance	0.5	double
ms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
ms_parent_mass_systematic_error	0.0	double
parent_contaminant_masses	NULL	list of singly charged masses
average_to_mono_convert	NULL	list of 0's and 1's 0 = monoisotopic 1 = average
mod_AA	None Defined	Peptide N-terminal Gln to pyroGlu Oxidation of M Protein N-terminus Acetylated User Defined 1 Acrylamide Modified Cys
user1_name	""	valid text strings defined in usermod.txt
min_parent_ion_matches	1	integer
min_matches	5	integer
mowse_on	0	0, 1
mowse_pfactor	0.4	double
data_source	Data Paste Area	List of Files, Upload Data From File, Data Paste Area
upload_data	""	file name
data_directory	""	directory name
data_files	NULL	list of file names
data_format	""	M/Z Charge, M/Z Intensity Charge
data	NULL	See the data_format parameter.
ms_search_type	None Defined	valid text strings defined in params/homology.txt

MS-Tag is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/mstag/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt (not required for No enzyme searches), expectation.txt, fragmentation.txt, homology.txt, idxlinks.txt, imm.txt, instrument.txt, mgf.xml, taxonomy.txt and taxonomy_groups.txt (taxonomy searches only) and usermod.txt. The program also requires an indexed protein database produced by the FA-Index program. Possible output formats are HTML or XML. HTML reports use the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Digest and MS-Product programs and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/mstag. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Tag
name	Default Value	Valid Values
search_name	""	needs to be set to mstag
report_title	""	text
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
instrument_name	""	valid text strings from params/instrument.txt
dna_frame_translation	3	6, 3, -3, 1, -1
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern
input_filename	""	text
indicies	""	list of database indicies (integers)
accession_numbers	""	list of database accession numbers
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
species_names	None Defined	list of text strings
species_remove	0	0, 1
add_accession_numbers	None Defined	list of text strings
msms_prot_low_mass	1000	integer
msms_prot_high_mass	100000	integer
msms_full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
allow_non_specific	at 0 termini	at 0 termini, at 1 termini, at 2 termini, at N termini, at C termini, N termini-1=D
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
msms_mod_AA	None defined	valid text strings formed from the information in params/usermod.txt.
msms_max_modifications	1	integer
msms_max_peptide_permutations	""	Left blank or non zero positive integer
comment	""	text
expect_calc_method	None	None, Linear Tail Fit
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_mstag	text
output_filename	""	text
max_reported_hits	50	integer
max_hits	200	integer
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
ms_parent_mass_tolerance	0.5	double
ms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
ms_parent_mass_systematic_error	0.0	double
data_source	Data Paste Area	List of Files, Upload Data From File, Data Paste Area
upload_data	""	file name
data_directory	""	directory name
data_files	NULL	list of file names
data_format	""	M/Z Charge, M/Z Intensity Charge
data	NULL	See the data_format parameter. For MS-Tag the first line contains the m/z and optionally the charge of the parent ion.
mod_start_nominal	0	integer
mod_end_nominal	0	integer
mod_defect	0.0	double
mod_comp_ion	None defined	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
mod_n_term	0	0, 1
mod_c_term	0	0, 1
mod_neutral_loss	0	0, 1
mod_uncleaved	0	0, 1
msms_pk_filter	Max MSMS Pks	Max MSMS Pks, Max MSMS Pks / 100 Da or Unprocessed MSMS
msms_search_type	None Defined	valid text strings defined in params/homology.txt
it	None Defined	a,a-H2O,a-NH3,a-H3PO4, b,b-H2O,b-NH3,b+H2O, b-H3PO4,b-SOCH4, y,y-H2O,y-NH3,y-H3PO4,y-SOCH4, MH+,B,c-1,c,c+1,c+2,x,Y,z,z+1,z+2,z+3,n,h,P,S,I,N,C
fragment_masses_tolerance	1.0	double
fragment_masses_tolerance_units	Da	Da, %, ppm, mmu
comp_ion	None Defined	regular expression
composition_search	0	0, 1
exclude_flag	0	0, 1
aa_exclude	""	text string containing the following characters A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
aa_add	""	m,q,h,s,t,y,u
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
regular_expression	.	regular expression
use_instrument_ion_types	0	0,1
score_histogram_only	0	0,1. The option is not currently available on the form but could be set in the mstag/default.xml file. If set then MS-Tag will just produce a score histogram rather than the standard report.

MS-Seq is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/msseq/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt (not required for No enzyme searches), fragmentation.txt, idxlinks.txt, imm.txt, instrument.txt, taxonomy.txt and taxonomy_groups.txt (taxonomy searches only) and usermod.txt. The program also requires an indexed protein database produced by the FA-Index program. Possible output formats are HTML or XML. HTML reports use the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Digest and MS-Product programs and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/msseq. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Seq
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to msseq
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
instrument_name	""	valid text strings from params/instrument.txt
dna_frame_translation	3	6, 3, -3, 1, -1
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
indicies	""	list of database indicies (integers)
accession_numbers	""	list of database accession numbers
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
species_names	None Defined	list of text strings
species_remove	0	0, 1
add_accession_numbers	None Defined	list of text strings
msms_prot_low_mass	1000	integer
msms_prot_high_mass	100000	integer
msms_full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
allow_non_specific	at 0 termini	at 0 termini, at 1 termini, at 2 termini, at N termini, at C termini, N termini-1=D
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
comment	""	text
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_msseq	text
output_filename	""	text
max_reported_hits	50	integer
max_hits	200	integer
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
ms_parent_mass_tolerance	0.5	double
ms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
ms_parent_mass_systematic_error	0.0	double
fragment_masses_tolerance	1.0	double
fragment_masses_tolerance_units	Da	Da, %, ppm, mmu
data_format	""	M/Z Charge, M/Z Intensity Charge
data	NULL	See the data_format parameter. For MS-Tag the first line contains the m/z and optionally the charge of the parent ion.
msms_search_type	None Defined	no errors, high mass error, low mass error, middle masses error, parent mass
ion_type	b	a,b,c,y
fragment_mass_tolerance	1.0	double
comp_ion	None Defined	regular expression
composition_search	0	0, 1
composition_exclude	""	ACDEFGHIKLMNPQRSTVWY
regular_expression	.	regular expression

MS-Pattern is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/mspattern/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt (not required for No enzyme searches), idxlinks.txt and taxonomy.txt and taxonomy_groups.txt (taxonomy searches only). The program also requires an indexed protein database produced by the FA-Index program. Possible output formats are HTML or XML. HTML reports use the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Digest program and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/mspattern. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Pattern
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to mspattern
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
dna_frame_translation	3	6, 3, -3, 1, -1
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
indicies	""	list of database indicies (integers)
accession_numbers	""	list of database accession numbers
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
species_names	None Defined	list of text strings
species_remove	0	0, 1
add_accession_numbers	None Defined	list of text strings
prot_low_mass	1000	integer
prot_high_mass	100000	integer
full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
comment	""	text
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_mspattern	text
output_filename	""	text
max_reported_hits	50	integer
pre_search_only	0	0,1
regular_expression	.	regular expression
possible_sequences	NULL	list of peptides
max_aa_substitutions	0	integer

MS-Homology is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/mshomology/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt (not required for No enzyme searches), idxlinks.txt, mat_score.txt and taxonomy.txt and taxonomy_groups.txt (taxonomy searches only). The program also requires an indexed protein database produced by the FA-Index program. Possible output formats are HTML or XML. HTML reports use the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Digest program and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/mshomology. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Homology
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to mshomology
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
dna_frame_translation	3	6, 3, -3, 1, -1
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
indicies	""	list of database indicies (integers)
accession_numbers	""	list of database accession numbers
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
species_names	None Defined	list of text strings
species_remove	0	0, 1
add_accession_numbers	None Defined	list of text strings
prot_low_mass	1000	integer
prot_high_mass	100000	integer
full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
comment	""	text
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_mshomology	text
output_filename	""	text
max_reported_hits	50	integer
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
fragment_masses_tolerance	1.0	double
fragment_masses_tolerance_units	Da	Da, %, ppm, mmu
min_matches	5	integer
possible_sequences	NULL	list of peptides
score_matrix	0	integer

MS-Digest is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/msdigest/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt, indicies.txt, instrument.txt and usermod.txt. The program can either use entries from an indexed protein database produced by the FA-Index program or protein sequences entered as one of the program parameters. Possible output formats are HTML or XML. HTML reports makes use of the the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Product program and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/msdigest. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Digest
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to msdigest
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection.
instrument_name	""	valid text strings from params/instrument.txt
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
end_terminus	0	0, 1
stripping_terminus	N	N, C
start_strip	2	integer
end_strip	4	integer
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_msdigest	text
output_filename	""	text
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
mod_AA	None defined	valid text strings formed from the information in params/usermod.txt.
bull_breese	0	0,1
hplc_index	0	0,1
comp_ion	None Defined	regular expression
comp_mask_type	AND	AND or OR
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
dna_reading_frame	1	1, 2, 3, 4, 5, 6
open_reading_frame	1	non-zero positive integer
user_protein_sequence	""	protein as a text string
report_mult_charge	0	0, 1
hide_html_links	0	0, 1
separate_proteins	0	0, 1
hide_protein_sequence	0	0, 1
access_method	Index Number	Index Number Accession Number
entry_data	""	See manual
index_num	80707	integer
accession_num	L39370	text
min_digest_fragment_mass	500.0	double
max_digest_fragment_mass	4000.0	double
min_digest_fragment_length	5	integer

MS-Bridge is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/msbridge/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, enzyme.txt and enzyme_comb.txt, fit_graph.par.txt, instrument.txt, link_aa.txt, links.txt and usermod.txt. The program can either use entries from an indexed protein database produced by the FA-Index program or protein sequences entered as one of the program parameters. Possible output formats are HTML or XML. HTML reports makes use of the Java applet html/java/SpectrumGraph.jar, the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Product and MS-Isotope programs and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/mstag. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Bridge
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to msbridge
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection.
instrument_name	""	valid text strings from params/instrument.txt
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
end_terminus	0	0, 1
stripping_terminus	N	N, C
start_strip	2	integer
end_strip	4	integer
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_msbridge	text
output_filename	""	text
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
ms_parent_mass_tolerance	0.5	double
ms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
ms_parent_mass_systematic_error	0.0	double
parent_contaminant_masses	NULL	list of singly charged masses
mod_AA	None defined	valid text strings formed from the information in params/usermod.txt.
link_search_type	Xlink:Dehydro (C)	valid text strings defined in links.txt
max_link_molecules	5	integer
link_aa	""	string of the form C->C where the amino acids on each side of the cross-link are separated by ->. If there are multiple possibilities they should be separated by commas (eg. K,R->K,R). If one possibility is the protein N or C-terminus use this notation: K,Protein N-term->Q.
bridge_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
mod_1_label	""	string
aa_modified_1	""	An amino acid code or string such as Protein N-term.
mod_1_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
mod_2_label	""	string
aa_modified_2	""	An amino acid code or string such as Protein N-term.
mod_2_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
mod_3_label	""	string
aa_modified_3	""	An amino acid code or string such as Protein N-term.
mod_3_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
mod_4_label	""	string
aa_modified_4	""	An amino acid code or string such as Protein N-term.
mod_4_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
mod_5_label	""	string
aa_modified_5	""	An amino acid code or string such as Protein N-term.
mod_5_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
mod_6_label	""	string
aa_modified_6	""	An amino acid code or string such as Protein N-term.
mod_6_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
data_source	Data Paste Area	List of Files, Upload Data From File, Data Paste Area
upload_data	""	file name
data_format	""	M/Z Charge, M/Z Intensity Charge
data	NULL	See the data_format parameter.
comp_ion	None Defined	regular expression
comp_mask_type	AND	AND or OR
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
dna_reading_frame	1	1, 2, 3, 4, 5, 6
open_reading_frame	1	non-zero positive integer
user_protein_sequence	""	protein as a text string
separate_proteins	0	0, 1
hide_protein_sequence	0	0, 1
access_method	Index Number	Index Number Accession Number
entry_data	""	See manual
index_num	80707	integer
accession_num	L39370	text
min_digest_fragment_mass	500.0	double
max_digest_fragment_mass	4000.0	double
min_digest_fragment_length	5	integer

MS-NonSpecific is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/msnonspecific/default.xml. The relevant parameter files are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), elements.txt, fit_graph.par.txt, instrument.txt and usermod.txt. The program can either use entries from an indexed protein database produced by the FA-Index program or protein sequences entered as one of the program parameters. Possible output formats are HTML or XML. HTML reports makes use of the Java applet html/java/SpectrumGraph.jar, the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Product program and to external web sites which give more information about the proteins found in the search. If the output is written to a file rather than to the standard output then the file is stored in the directory results/msnonspecific. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-NonSpecific
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to msnonspecific
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection.
instrument_name	""	valid text strings from params/instrument.txt
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_msnonspecific	text
output_filename	""	text
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
ms_parent_mass_tolerance	0.5	double
ms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
ms_parent_mass_systematic_error	0.0	double
parent_contaminant_masses	NULL	list of singly charged masses
data_source	Data Paste Area	List of Files, Upload Data From File, Data Paste Area
upload_data	""	file name
data_format	""	M/Z Charge, M/Z Intensity Charge
data	NULL	See the data_format parameter.
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
dna_reading_frame	1	1, 2, 3, 4, 5, 6
open_reading_frame	1	non-zero positive integer
user_protein_sequence	""	protein as a text string
hide_protein_sequence	0	0, 1
access_method	Index Number	Index Number Accession Number
entry_data	""	See manual
index_num	80707	integer
accession_num	L39370	text

MS-Product
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to msproduct
output_type	HTML	HTML, XML or Tab Delimited Text
script	""	text
script_type	""	text
instrument_name	""	valid text strings from params/instrument.txt
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_msproduct	text
output_filename	""	text
s	1	0, 1
sequence	SAMPLER	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y m - Oxidized Methionine h - Homoserine lactone U - Selenocysteine s,t,y - Phosphorylated S,T,Y u, v, w, x - user specified amino acids Modified amino acids may be entered using PSI notation - eg. M(Oxidation), S(Phospho) An amino acid can also be followed by an exact mass - eg. P(-27.9949) or N(0.9840)
nterm	""	N-terminus defined in params/usermod.txt, an exact mass or ""
cterm	""	C-terminus defined in params/usermod.txt, an exact mass or ""
nloss	""	Neutral loss defined in params/usermod.txt, an exact mass or ""
mods	""	If there are multiple peptides it is possible either to specify each peptide individually (say a set of modification permutations) or to specify a value for the mods variable that describes the modifications and any ambiguity. The mods variable should be a combination of the const mod and variable mod columns in the Search Compare output. N-term, C-term and Neutral-loss are specified here.
s2	1	0, 1
sequence2	""	see instructions for sequence above
nterm2	""	see instructions for n_term above
cterm2	""	see instructions for c_term above
nloss2	""	see instructions for n_loss above
s3	1	0, 1
sequence3	""	see instructions for sequence above
nterm3	""	see instructions for n_term above
cterm3	""	see instructions for c_term above
nloss3	""	see instructions for n_loss above
s4	1	0, 1
sequence4	""	see instructions for sequence above
nterm4	""	see instructions for n_term above
cterm4	""	see instructions for c_term above
nloss4	""	see instructions for n_loss above
s5	1	0, 1
sequence5	""	see instructions for sequence above
nterm5	""	see instructions for n_term above
cterm5	""	see instructions for c_term above
nloss5	""	see instructions for n_loss above
s6	1	0, 1
sequence6	""	see instructions for sequence above
nterm6	""	see instructions for n_term above
cterm6	""	see instructions for c_term above
nloss6	""	see instructions for n_loss above
alternative	0	0 or 1
discriminating	0	0 or 1
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
data_source	Data Paste Area	List of Files, Upload Data From File, Data Paste Area
upload_data	""	file name
data_format	""	M/Z Charge, M/Z Intensity Charge
data	NULL	See the data_format parameter. For MS-Tag the first line contains the m/z and optionally the charge of the parent ion.
it	None Defined	a,a-H2O,a-NH3,a-H3PO4, b,b-H2O,b-NH3,b+H2O, b-H3PO4,b-SOCH4, y,y-H2O,y-NH3,y-H3PO4,y-SOCH4, MH+,B,c-1,c,c+1,c+2,x,Y,z,z+1,z+2,z+3,n,h,P,S,I,N,C
max_losses	1	1,2,3 or All
max_internal_len	200	integer
msms_parent_mass_tolerance	0.5	double
msms_parent_mass_tolerance_units	Da	Da, %, ppm, mmu
fragment_masses_tolerance	1.0	double
fragment_masses_tolerance_units	Da	Da, %, ppm, mmu
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
use_instrument_ion_types	0	0,1
max_charge	1	positive integer or No Limit
count_pos_z	Count Basic AA	Count Basic AA, Ignore Basic AA
msms_max_peaks	""	integer
multi_z_internal	0	0,1
calibrate	0	0,1
cal_tolerance	0.0	double
data_plotted	Centroid	Centroid, Raw and Centroid, Raw
msms_pk_filter	Max MSMS Pks	Max MSMS Pks, Max MSMS Pks / 100 Da or Unprocessed MSMS
display_graph	0	0,1
search_key	""	string
fraction	-1	integer
spot_number	"1"	string
run	1	integer
spectrum_number	1	integer
msms_info	""	string

MS-Comp is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/mscomp/default.xml. The relevant parameter files are info.txt, aa.txt, elements.txt, imm.txt, instrument.txt and usermod.txt. Possible output formats are HTML or XML. The HTML report makes use of the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The HTML report contains URL links to the MS-Isotope program. If the output is written to a file rather than to the standard output then the file is stored in the directory results/mscomp. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

MS-Comp
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to mscomp
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
instrument_name	""	valid text strings from params/instrument.txt
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_mscomp	text
output_filename	""	text
max_reported_hits	50	integer
parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)
parent_mass_tolerance	0.5	double
tolerance_units	Da	Da, %, ppm, mmu
it	None Defined	a,a-H2O,a-NH3,a-H3PO4, b,b-H2O,b-NH3,b+H2O, b-H3PO4,b-SOCH4, y,y-H2O,y-NH3,y-H3PO4,y-SOCH4, MH+,c,B,n,h,P,S,I,N,C
comp_ion	None Defined	regular expression
parent_mass	1000.0	double
parent_charge	1	integer
composition_search	0	0, 1
aa_exclude	""	text string containing the following characters A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
aa_add	""	m,q,h,s,t,y,u
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
combination_type	Amino Acid	Amino Acid Peptide Elemental Elemental

DB-Stat is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/dbstat/default.xml. The relevant parameter files are info.txt, aa.txt, computer.txt, dbEST.spl.txt (dbEST database searches only), dbstat_hist.par.txt (HTML reports only), elements.txt, enzyme.txt, enzyme_comb.txt, taxonomy.txt and taxonomy_groups.txt (taxonomy searches only), and usermod.txt. The program also requires an indexed protein database produced by the FA-Index program. Possible output formats are HTML or XML. The HTML report makes use of either the Java applet html/java/SpectrumGraph.jar or the R script cgi-bin/peptideDensity.R dependent on the number of points in the graph. The data for the graph is temporarily written to a file in the directory temp/mmm_dd_yyyy. HTML reports also use the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. If the output is written to a file rather than to the standard output then the file is stored in the directory results/dbstat. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

DB-Stat
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to dbstat
output_type	HTML	HTML or XML
script	""	text
script_type	""	text
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. User Protein is another possible selection. Multiple databases may be specified.
user_protein_sequence	""	protein as a text string
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
indicies	""	list of database indicies (integers)
accession_numbers	""	list of database accession numbers
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
species_names	None Defined	list of text strings
species_remove	0	0, 1
add_accession_numbers	None Defined	list of text strings
prot_low_mass	1000	integer
prot_high_mass	100000	integer
full_mw_range	0	0, 1
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
enzyme	Trypsin	valid text strings from params/enzyme.txt or params/enzyme_comb.txt
missed_cleavages	1	integer
const_mod	None defined	valid text strings formed from the information in params/usermod.txt.
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter ie: results_dbstat	text
output_filename	""	text
dna_reading_frame	1	1, 2, 3, 4, 5, 6
show_aa_statistics	0	0, 1

MS-Isotope is run using the exectuable file cgi-bin/mssearch.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are stored in the file params/msisotope/default.xml. The relevant parameter files are info.txt, aa.txt, elements.txt, sp_graph.par.txt and usermod.txt. Possible output formats are HTML, XML or Tab delimited text. The HTML report makes use of the Java applet html/java/SpectrumGraph.jar, the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. If the output is written to a file rather than to the standard output then the file is stored in the directory results/msisotope. The mssearch.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

Note that the web version of MS-Isotope supports up to 6 isotope profiles using the parameters parent_charge, parent_intensity, distribution_type, nterm, sequence, cterm, elemental_composition and averagine_mass. For the second and subsequent profiles the parameter names are followed by an integer (eg. parent_charge2). For the command line version there is no limit on the number of profiles that can be used.

MS-Isotope
name	Default Value	Valid Values
search_name	""	text which can be part of a filename.
report_title	""	needs to be set to msisotope
output_type	HTML	HTML, XML or Tab delimited text
script	""	text
script_type	""	text
results_to_file	0	0, 1
output_dir	"results_" + value of search_name parameter eg: results_msisotope	text
output_filename	""	text
parent_charge	1	integer
parent_intensity	1	double
distribution_type	Peptide Sequence	Peptide Sequence, Elemental Composition
nterm	""	N-termini defined in params/usermod.txt or ""
sequence	SAMPLER	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,m,q,h,s,t,y,u
cterm	""	C-termini defined in params/usermod.txt or ""
elemental_composition	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
averagine_mass	1000.0	double
parent_charge2	1	integer
parent_intensity2	1	double
distribution_type2	Off	Peptide Sequence, Elemental Composition
nterm2	""	N-termini defined in params/usermod.txt or ""
sequence2	""	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,m,q,h,s,t,y,u
cterm2	""	C-termini defined in params/usermod.txt or ""
elemental_composition2	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
averagine_mass2	0.0	double
parent_charge3	1	integer
parent_intensity3	1	double
distribution_type3	Off	Peptide Sequence, Elemental Composition
nterm3	""	N-termini defined in params/usermod.txt or ""
sequence3	""	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,m,q,h,s,t,y,u
cterm3	""	C-termini defined in params/usermod.txt or ""
elemental_composition3	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
averagine_mass3	0.0	double
parent_charge4	1	integer
parent_intensity4	1	double
distribution_type4	Off	Peptide Sequence, Elemental Composition
nterm4	""	N-termini defined in params/usermod.txt or ""
sequence4	""	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,m,q,h,s,t,y,u
cterm4	""	C-termini defined in params/usermod.txt or ""
elemental_composition4	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
averagine_mass4	0.0	double
parent_charge5	1	integer
parent_intensity5	1	double
distribution_type5	Off	Peptide Sequence, Elemental Composition
nterm5	""	N-termini defined in params/usermod.txt or ""
sequence5	""	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,m,q,h,s,t,y,u
cterm5	""	C-termini defined in params/usermod.txt or ""
elemental_composition5	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
averagine_mass5	0.0	double
parent_charge6	1	integer
parent_intensity6	1	double
distribution_type6	Off	Peptide Sequence, Elemental Composition
nterm6	""	N-termini defined in params/usermod.txt or ""
sequence6	""	A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,m,q,h,s,t,y,u
cterm6	""	C-termini defined in params/usermod.txt or ""
elemental_composition6	""	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
averagine_mass6	0.0	double
user_aa_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_2_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_3_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
user_aa_4_composition	C2 H3 N1 O1	Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in params/elements.txt can be used.
profile_type	Peptide Sequence	Stick, Gaussian, Lorentzian
resolution	10000.0	double
display_graph	0	0, 1
detailed_report	0	0, 1
percent_C13	100.0	0.0-100.0
percent_N15	100.0	0.0-100.0
percent_O18	100.0	0.0-100.0

FA-Index is run using the exectuable file cgi-bin/faindex.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are built in. The relevant parameter files when creating indicies for a new database are info.txt, aa.txt, computer.txt, dbEST.spl.txt (dbEST databases only) and elements.txt. The program also requires a FASTA format protein database. The outputs are a HTML report and an indexed protein database for use by the Protein Prospector database search programs. HTML reports use the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The faindex.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

FA-Index - Create Indicies for New Database
name	Default Value	Valid Values
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.
dna_to_protein	0	0, 1
delete_dna_database	0	0, 1
random_database	0	0, 1
reverse_database	0	0, 1
concat_database	0	0, 1
create_database_indicies	0	set this to 1

FA-Index is run using the exectuable file cgi-bin/faindex.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are built in. The relevant parameter files for a database summary report are info.txt, aa.txt, acclinks.txt, computer.txt, dbEST.spl.txt (dbEST databases only) and elements.txt and idxlinks.txt. The output is a HTML report. The HTML report uses the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The faindex.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

FA-Index - Database Summary Report
name	Default Value	Valid Values
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.
dna_reading_frame	1	1, 2, 3, 4, 5, 6
start_index_number	1	integer
end_index_number	1	integer
all_indicies	0	0, 1
hide_protein_sequence	0	0, 1

FA-Index is run using the exectuable file cgi-bin/faindex.cgi. The program can either be run from the command line or via a HTML form. The HTML form for running it is generated by the program cgi-bin/msform.cgi. The default form settings are built in. The relevant parameter files when creating a subset database are info.txt, aa.txt, computer.txt, dbEST.spl.txt (dbEST databases only), elements.txt, taxonomy.txt and taxonomy_groups.txt (taxonomy searches only). The program also requires a FASTA formatted protein database that has already been indexed. The outputs are a HTML report and an indexed subset protein database for use by the Protein Prospector database search programs. The HTML report uses the cascade stylesheet files html/pform.css and html/print.css and the image file html/images/bannerblack.gif. The faindex.cgi and msform.cgi programs can optionally write log files that are written to the directory logs/yyyy_mm_dd.

FA-Index - Create Subset Database
name	Default Value	Valid Values
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.
sub_database_id	sub	text
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
species_remove	0	0, 1 - Must be set to 1 for a DNA database
species_names	None Defined	list of text strings
prot_low_mass	1000	integer
prot_high_mass	100000	integer
full_mw_range	0	0, 1 - Must be set to 1 for a DNA database
low_pi	3.0	double
high_pi	10.0	double
full_pi_range	0	0, 1
names	None Defined	list of text strings
accession_nums	None Defined	list of text strings
add_accession_numbers	None Defined	list of text strings
create_sub_database	0	set this to 1
create_database_indicies	0	set this to 1

FA-Index - Create Subset Database with Indices from Saved Hits
name	Default Value	Valid Values
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.
results_from_file	0	0, 1
results_input_dir	results_" + value of input_program_name parameter eg: results_msfit	directory name
input_program_name	msfit	msfit, mstag, mspattern, mshomology, msseq
input_filename	""	text
sub_database_id	.sub	text
create_database_indicies	0	set this to 1
create_sub_database	0	set this to 1

FA-Index - Create or Append to User Database
name	Default Value	Valid Values
database	""	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, UniProt, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, IPI, ipi, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.
name_field	""	text
species	All	valid text strings from params/taxonomy.txt, params/taxonomy_groups.txt or All
accession_num	L39370	text
user_protein_sequence	""	protein as a text string
create_database_indicies	0	set this to 1
create_user_database	0	set this to 1

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