# The MEME Suite

## Motif-based sequence analysis tools

## 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:

file scan charge spectrum precursor m/z spectrum neutral mass peptide mass delta_cn xcorr score xcorr rank distinct matches/spectrum sequence cleavage type protein id flanking aa demo.ms2 35 1 709.07 708.063 709.275 0.00361925 0.305444 1 17 S[79.9]LGIIGA trypsin-full-digest YFR053C(479) K- demo.ms2 35 1 709.07 708.063 710.245 0.061339 0.301825 2 17 QS[79.9]GLAR trypsin-full-digest YDL198C(8) KL demo.ms2 35 1 709.07 708.063 709.449 0.0103678 0.240486 3 17 SIHILK trypsin-full-digest YMR242C(126) RV

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
    ...