Software:ProbID

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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).

Getting the software

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.

Installation

ProbID is a java program. 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...

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