Software:ProbID

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Revision as of 23:05, 6 July 2007 Jtasman (Talk | contribs) ← Previous diff		Current revision Jtasman (Talk | contribs) (svn)
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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.
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	* 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 Sashimi SVN ('''add svn link''').
	==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
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	perl runprobiddta.pl		perl runprobiddta.pl
		+	'''Note: should we recommend MzXML2Search instead of mzxml2other?'''
		+
		+	===ProbID and the TPP===
		+	Please see the [[TPP:ProbID and the TPP|ProbID and the TPP]] page.
	==Reference==		==Reference==
	Coming soon...		Coming soon...

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Current revision

Contents 1 Overview 2 Getting the software 2.1 Downloading the package 2.2 Source Code 3 Installation 4 Running ProbID 4.1 single MS/MS spectrum processing 4.2 batch processing of many .dta files on one computer 4.3 ProbID and the TPP 5 Reference

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 SVN (add svn link).

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

Note: should we recommend MzXML2Search instead of mzxml2other?

ProbID and the TPP

Please see the ProbID and the TPP page.

Reference

Coming soon...