Hi- I'm processing data with both Sequest and X!Tandem followed by peptide & protein prophet. I've used TPP v4.6.3 and v7 and am seeing same issue for both versions and for both search engines. I did include a reduction/alkylation step during sample prep and I am using C57 as a fixed modification during the search, but yet in the results, most of the peptides that contain a C are not modified. I'm confused as I thought 'fixed' meant it would be required to be present in order for the peptide to be identified. When searching the same data with Morpheus, it is in general finding a lot more peptides with the carbamidomethlyation for the same protein than I"m getting in my current processing for Sequest & Tandem.
This is how my X!Tandem params file is setup: <note>residue modification parameters</note> <note type="input" label="residue, modification mass">57.021464@C</note> Can anyone clarify whether 'fixed' really means that the modification is required to be present if that amino acid is present in the sequence? Any suggestions on where to start looking for my error in the setup? Thanks! Rebekah -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
