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.
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.AAASAAA.- ... MS-GF+ AAAS+79.9AAA ...