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:
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 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 |