Protein Prospector Automation Guidance
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 .....
Peak Spotter
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
- The raw directory needs to exist before running peakSpotter.
- 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.
- 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.
- Peaklists for both the MS and MSMS spectra are stored in the one centroid file.
- If you extract the raw data then the program will typically take a lot longer to run.
Wiff To Centroid
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.
Parameters for Other Protein Prospector Programs
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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/species.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 |
| enzyme | Trypsin | valid text strings from params/enzyme.txt or params/enzyme_comb.txt |
| missed_cleavages | 1 | integer |
| 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) |
| parent_mass_tolerance | 0.5 | double |
| tolerance_units | Da | Da, %, ppm, mmu |
| 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 |
| chem_score | 0 | 0, 1 |
| met_ox_factor | 1.0 | 0.2-5.0 |
| 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 | ||
|---|---|---|
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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/species.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 |
| missed_cleavages | 1 | integer |
| comment | "" | text |
| 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 |
| protein_report | 0 | 0,1 |
| detailed_report | 0 | 0,1 |
| display_graph | 0 | 0,1 |
| 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 |
| 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. |
| 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+,c,B,n,h,P,S,I,N,C |
| ion_unmatched_type | Max. % Unmatched Ions | Max. % Unmatched Ions Min. % Matched Ions Max. Num Unmatched Ions Min. Num Matched Ions |
| unused_ions | 10 | double or integer |
| fragment_mass_tolerance | 1.0 | double |
| 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 |
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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/species.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 |
| missed_cleavages | 1 | integer |
| 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 |
| protein_report | 0 | 0,1 |
| detailed_report | 0 | 0,1 |
| display_graph | 0 | 0,1 |
| 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 |
| 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 | ||
|---|---|---|
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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/species.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 | ||
|---|---|---|
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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/species.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 | 0.5 | double |
| tolerance_units | Da | Da, %, ppm, mmu |
| min_matches | 5 | integer |
| possible_sequences | NULL | list of peptides |
| score_matrix | 0 | integer |
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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 |
| 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 | Peptide N-terminal Gln to pyroGlu Oxidation of M Protein N-terminus Acetylated User Defined 1 Acrylamide Modified Cys |
| chem_score | 0 | 0, 1 |
| met_ox_factor | 1.0 | 0.2-5.0 |
| 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 | ||
|---|---|---|
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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 |
| 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) |
| parent_mass_tolerance | 0.5 | double |
| tolerance_units | Da | Da, %, ppm, mmu |
| parent_contaminant_masses | NULL | list of singly charged masses |
| mod_AA | None Defined | Peptide N-terminal Gln to pyroGlu Oxidation of M Protein N-terminus Acetylated User Defined 1 Acrylamide Modified Cys |
| link_search_type | Xlink:Dehydro (C) | valid text strings defined in links.txt |
| max_link_molecules | 5 | integer |
| chem_score | 0 | 0, 1 |
| met_ox_factor | 1.0 | 0.2-5.0 |
| 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 | ||
|---|---|---|
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault. |
| 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_msnonspecific | text |
| output_filename | "" | text |
| 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 |
| 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 or XML |
| 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 |
| nterm | "" | N-termini defined in params/usermod.txt or "" |
| cterm | "" | C-termini defined in params/usermod.txt or "" |
| parent_mass_convert | monoisotopic | monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi) |
| tolerance_units | Da | Da, %, ppm, mmu |
| 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+,c,B,n,h,P,S,I,N,C |
| multiple_losses | 0 | 0,1 |
| fragment_masses_tolerance | 1.0 | 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. |
| use_instrument_ion_types | 0 | 0,1 |
| max_charge | 1 | positive integer or No Limit |
| 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 |
| 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 |
| 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 | ||
|---|---|---|
| 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, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, 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 |
| indicies | "" | list of database indicies (integers) |
| accession_numbers | "" | list of database accession numbers |
| species | All | valid text strings from params/species.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 |
| 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 | ||
|---|---|---|
| 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 or XML |
| 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 |
| nterm | "" | N-termini defined in params/usermod.txt or "" |
| cterm | "" | C-termini defined in params/usermod.txt or "" |
| parent_charge | 1 | integer |
| 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. |
| 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 |
| distribution_type | Peptide Sequence | Peptide Sequence, Elemental Composition |
| profile_type | Peptide Sequence | Stick, Gaussian, Lorentzian |
| resolution | 10000.0 | double |
| averagine_mass | 1000.0 | double |
| percent_C13 | 100.0 | 0.0-100.0 |
| percent_N15 | 100.0 | 0.0-100.0 |
| percent_O18 | 100.0 | 0.0-100.0 |
| 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. |
| detailed_report | 0 | 0, 1 |
| FA-Index | ||
|---|---|---|
| name | Default Value | Valid Values |
| report_title | "" | text |
| output_type | HTML | HTML or XML |
| script | "" | text |
| script_type | "" | text |
| database | "" | valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, 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 |
| indicies | "" | list of database indicies (integers) |
| accession_numbers | "" | list of database accession numbers |
| species | All | valid text strings from params/species.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 |
| dna_reading_frame | 1 | 1, 2, 3, 4, 5, 6 |
| user_protein_sequence | "" | protein as a text string |
| hide_protein_sequence | 0 | 0, 1 |
| accession_num | L39370 | text |
| create_database_indicies | 0 | 0, 1 |
| create_sub_database | 0 | 0, 1 |
| sub_database_id | .sub | text |
| name_field | "" | text |
| create_user_database | 0 | 0, 1 |
| start_index_number | 0 | integer |
| end_index_number | 1 | integer |
| all_indicies | 0 | 0, 1 |
| 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 |