Software:ProbID

From SPCTools

1 Overview
2 Getting the software
- 2.1 Downloading the package
- 2.2 Source Code
3 Installation
4 Running ProbID
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.

[edit]

Getting the software

[edit]

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.

[edit]

Source Code

Source is accessible from Sashimi SVN (add svn link).

[edit]

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.

[edit]

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.

[edit]

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

[edit]

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.