Peptide-Spectrum Match (PSM) Format

Description

Some MEME Suite programs allow as input a file containing tab-delimited data from analysis of tandem mass spectrometry. Some popoular softwares that produce files that are supported by the MEME Suite include Crux's Tide and Percolator, Comet, and MS-GF+, and tab-delimited exports from TPP's PepXML Viewer.

Format Specification

The basic structure of a tab-delimited PSM File is where each such file consists of a single line containing the tab-separated names of fields, followed by one or more lines giving the corresponding field values. For example:

An example PSM file can be found here.

When specifying post-translational modifications, MoMo requires for the user to specify the name of a column where the modification is embedded inside the matched peptide. By default, MoMo assumes the column is named "sequence". MoMo allows three different methods of embedding the modifications:

Tide and Percolator
AAAS[79.9]AAA
...
Comet and TPP
A.AAAS[167]AAA.-
...
MS-GF+
AAAS+79.9AAA
...