Peptide-Spectrum Match (PSM) Format


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:

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.

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 NameModified Peptide Column NameModified Peptide Format (Example)
Comet'modified sequence'A.AAAS[167]AAA.G