Software:ProbID
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| ==Overview== | ==Overview== | ||
| - | ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence database. It computes z scores for the identifications and output the results in pepXML format, which subsequently can be analyzed by the TPP (trans-proteomic pipeline). | + | ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence database. It computes z scores for the identifications and output the results in pepXML format, which subsequently can be analyzed by the [[Software:TPP|TPP]] (Trans-Proteomic Pipeline). ProbID is written in Java. |
| ==Getting the software== | ==Getting the software== | ||
| + | ===Downloading the package=== | ||
| You can download from the [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=156703 Sashimi File Release page on SourceForge]. The package includes | You can download from the [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=156703 Sashimi File Release page on SourceForge]. The package includes | ||
| *ProbIDALL.jar This is the main package of software to identify peptides from MS/MS spectra using protein sequence database (FASTA format). This jar file includes both the source code and binary class files. | *ProbIDALL.jar This is the main package of software to identify peptides from MS/MS spectra using protein sequence database (FASTA format). This jar file includes both the source code and binary class files. | ||
| Line 10: | Line 11: | ||
| * runprobiddta.pl This is a script that batch processes all your .dta files in a directory. | * runprobiddta.pl This is a script that batch processes all your .dta files in a directory. | ||
| * README basic information. | * README basic information. | ||
| + | |||
| + | ===Source Code=== | ||
| + | Source is accessible from [http://sashimi.cvs.sourceforge.net/sashimi/ProbID/ Sashimi CVS]. | ||
| ==Installation== | ==Installation== | ||
| - | ProbID is a java program. First, | + | Assuming you've downloaded the package, first unzip ProbID.tgz: |
| - | unzip ProbID.tgz: | + | |
| tar -xzf ProbID.tgz | tar -xzf ProbID.tgz | ||
| * set up "CLASSPATH" environment variable for ProbIDALL.jar | * set up "CLASSPATH" environment variable for ProbIDALL.jar | ||
Revision as of 23:08, 6 July 2007
Contents |
Overview
ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence database. It computes z scores for the identifications and output the results in pepXML format, which subsequently can be analyzed by the TPP (Trans-Proteomic Pipeline). ProbID is written in Java.
Getting the software
Downloading the package
You can download from the Sashimi File Release page on SourceForge. The package includes
- ProbIDALL.jar This is the main package of software to identify peptides from MS/MS spectra using protein sequence database (FASTA format). This jar file includes both the source code and binary class files.
- probid.param This is the parameter file for doing peptide searches.
- example.dta This is the file format of MS/MS spectra that ProbID takes.
- runprobid.pl This is the script that takes a your_file.mzXML and returns a your_file.xml which can be analyzed by TPP (Trans-Proteomic Pipeline).
- runprobiddta.pl This is a script that batch processes all your .dta files in a directory.
- README basic information.
Source Code
Source is accessible from Sashimi CVS.
Installation
Assuming you've downloaded the package, first unzip ProbID.tgz:
tar -xzf ProbID.tgz
- set up "CLASSPATH" environment variable for ProbIDALL.jar
- you need either jre1.4 (or above) or j2sdk1.4 (or above) installed on your machine.
- ProbID was written in java and can be run on almost any OS.
Running ProbID
ProbID may be run in single-spectrum or batch processing modes. Both options require you to have probid.param in the same directory where your data is located.
single MS/MS spectrum processing
java org.systemsbiology.dbsearch.ProbID your_file.dta
OR if you didn't set up the "CLASSPATH" variable
Java -cp where_ProbIDALL.jar_is org.systemsbiology.dbsearch.ProbID your_file.dta
batch processing of many .dta files on one computer
perl runprobid.pl your_file.mzXML.
You do need "mzxml2other" installed on your machine to start from your_file.mzXML. If you already have all .dta files in current directory, use runprobiddta.pl.
perl runprobiddta.pl
Reference
Coming soon...
