Diagnostic ions/neutral losses for modifications

[lewotre]

Dear MSFragger team,

Thanks for developing this nice piece of software! I'm looking into two modifications in the same LC-MS/MS run and I know they have specific diagnostic ions and neutral losses that can be assigned to them. Is there a way to search with these specifically for the modifications, or could this be implemented?

Also, I have searched for diagnostic ions/ neutral losses, using the labile search option, however, after looking viewer to the spectra, they weren't annotated, is this how it's supposed to be or am I doing something wrong?

Thanks in advance, Wouter

[dpolasky]

Hi Wouter, We are planning to implement specific diagnostic ion <-> modification pairs soon but have not done so yet, so currently all modifications are considered when diagnostic ions are found, and searched with the same neutral losses. A possible workaround in the meantime is to run two separate searches and combine the results (with iProphet, for example), depending on how differently the modifications behave.

You're right that the visualization tool does not show custom diagnostic ions yet, but that's another thing we'd like to add soon. You can show neutral losses (fragment remainder ions) using the "change modification" option in the Tools menu. If you set the modification mass to whatever mass remains on the peptide (or a negative value if part of the side chain is lost with the modification), it will show all fragment ions with that mass/neutral loss.

Best, Dan