software
MS/MS Interpretation
ProbID
Please note; this documentation may be out of date. Please see the ProbID documentation on the SPCTools Wiki for up-to-date information.
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 TPP (trans-proteomic pipeline).
Components of downloadable package:
-
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.
Installation
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
- for 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
- for 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.
Both options, your have to have probid.param in the same directory where your data locate.
