PSM Format - MEME Suite

# 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 popular software applications that produce files that are supported by the MEME Suite include:

- Comet
- MS-GF+
- Tide (Crux)
- Percolator (Crux)

### 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.

The supported PSM formats each have a column containing modified peptides, where the modified amino acid (if any) is indicated by a number (weight) following it. The table below gives the appropriate column names and an example peptide containing a modified serine in different PSM formats.

PSM Program Name | Modified Peptide Column Name | Modified Peptide Format (Example)
--- | --- | ---
Comet | 'modified sequence' | A.AAAS[167]AAA.G
MS-GF+ | 'Peptide' | AAAS+79.9AAA
Tide | 'sequence' | AAAS[79.9]AAA
Percolator | 'sequence' | AAAS[79.9]AAA