Rich, Since no one else has responded, I'm staring at iTRAQ data I just processed through Libra today and the intensities reported in the pepXML file are exactly those that are in the corresponding mzXML. I have never seen data where this is not the case which means something went wrong somewhere for you.
Regarding your second point, Libra expects the reporter ions to be in the same spectrum/scan as was used to identify the peptide. So notions of HCD-CID pairs of spectra won't work directly with Libra as it knows nothing of that type of relationship within your spectral data. Folks here so the same analysis you're doing so we had to put together a simple little tool which merged these scans together and spit out merged mgf and mzXML files that we use to search and process through Libra. Someone in your lab is already using this but feel free to email Eva if you want to try the tool yourself; I'm sure she'll be happy to give you a quick tutorial if you want to stop by. https://proteomicsresource.washington.edu/MassSpecUtils.php On Mon, Feb 27, 2012 at 11:11 AM, greener <greener_98...@yahoo.com> wrote: > Hi everyone, I have two questions about the iTRAQ quantitation by > libra. > > (1) Why are the iTRAQ label intensities of peptides in the Libra > output files different from the intensities in the native ms/ms > spectrum? > (2) Suppose a single precursor ion triggers two MS/MS scans (two HCD- > CID pair). However only one out of the two HCD-CID scans enabled the > peptide and corresponding protein identification, then does Libra uses > that particular scan (HCD) for iTRAQ quantitation? > Since the Libra output file does not give any information about > retention time or scan # for the individual quantified peptides, it is > extremely difficult to know which HCD scan (out of many for a > precursor ion of a peptide) was used to do the measurement. > > Any thoughts folks have on this is appreciated. Thanks! > -Rich > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
