Please note; this documentation may be out of date. Please see the ProbID documentation on the SPCTools Wiki for up-to-date information.
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:
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.
This is the parameter file for doing peptide searches.
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.
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.
- for single MS/MS spectrum processing:
OR if you didn't set up the "CLASSPATH" variable
- java org.systemsbiology.dbsearch.ProbID your_file.dta
- Java -cp where_ProbIDALL.jar_is org.systemsbiology.dbsearch.ProbID your_file.dta
- for batch processing of many .dta files on one computer
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 runprobid.pl your_file.mzXML.
Both options, your have to have probid.param in the same directory where your data locate.