From SPCTools

Jump to: navigation, search



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.
  • 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).
  • 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).


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 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


Note: should we recommend MzXML2Search instead of mzxml2other?

ProbID and the TPP

Please see the ProbID and the TPP page.


Coming soon...

Personal tools