What is an MS/MS format analysis?
An MS/MS type analysis is an analysis of motifs from the peptides returned by a tandem mass spectrometry experiment. For example, if you did an MS/MS experiment where you enriched for tryptic phospho-peptides using SCX chromatography or IMAC resin and you searched your data using the SEQUEST algorithm, then you could upload your data directly to motif-x and search for phosphorylation motifs. SEQUEST output will often label phosphorylated residues as S* or S#, but you can use this data directly with motif-x. Just make sure you specify your central residue as S* or S# (or whatever it actually is). Note that indicating S* as a central residue, when you don’t have any “S*” characters in your data will return no motifs.
