I just wanted to add that I checked on previously analyzed samples, and that apparently, with the same settings and experimental conditions, I got the expected distribution of 2+ and 3+ peptides before. This sample was acquired on march of this year, probably with an earlier version of TPP. After that acquisition, I checked my results, and I have only identified 2+ OR 3+ peptides in the pep.shtml files (I didn't realize back then on this peculiar observation). Could someone check if this has happened in your set of results?
Thanks! Alex On Tuesday, 3 July 2012 17:03:05 UTC-3, Alex wrote: > > 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/-/g1RZVxHLCLsJ. 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.
