Parallel Tandem:  A Program for Parallel Processing of Tandem Mass Spectra Using PVM or MPI and X!Tandem

Abstract

A method for the rapid correlation of tandem mass spectra to a list of protein sequences in a database has been developed. The combination of the fast and accurate computational search algorithm, X!Tandem, and a Linux cluster parallel computing environment with PVM or MPI, significantly reduces the time required to perform the correlation of tandem mass spectra to protein sequences in a database. A file of tandem mass spectra is divided into a specified number of files, each containing an equal number of the spectra from the larger file. These files are then searched in parallel against a protein sequence database. The results of each parallel output file are collated into one file for viewing through a web interface. Thousands of spectra can be searched in an accurate, practical, and time effective manner. The source code for running Parallel Tandem utilizing either PVM or MPI on Linux operating system is available from http://www.thegpm.org. This source code is made available under Artistic License from the authors.