Hi TPP community! I have an interesting puzzle that I can not figure out!!! I'm running a 2D-LC-MS/MS experiment of a yeast lysate (peptides labeled by dimethylation) on a QqLIT (QTrap 3000) instrument acquiring on IDA mode. I'm analyzing the data on the TPP using X!Tandem search engine with the params file attached, and interestingly, ALL the peptides identified on the pep.shtml file are derived from triply charged precursors!!! (ALL of them). When I check the prot.shtml file all the identified peptides have the 3_SEQUENCE nomenclature (my understanding is that the 3 identifies the charge on the precursor, right?). When I look at the raw data (.wiff) file on Analyst software, I can easily estimate that most (probably a little more than half) of the MS/MS was actually performed on CLEARLY doubly charged precursors, according the the ER-MS (enhanced resolution MS acquired on the LIT)... so it seem very weird that I dont find a single peptide to spectrum match (PSM) from a doubly charged precursor. Just wondering if I might have accidentally changed a parameter on the params file (.xml).
Has anybody crossed upon this observation before??? Anybody can help me??? Thanks!!! Alex -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/aeQNiykJwWcJ. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
isb_default_input_kscore_DML-MEDIUM_CysCAM_MetOX.xml
Description: XML document
isb_default_input_kscore_DML-LIGHT_CysCAM_MetOX.xml
Description: XML document
