There is an ExPASy tool to merge CID/HCD spectra from a Mascot MGF format peaklist for this purpose. Can you go from RAW/MzXML/MzML into MGF, use this tool, and then convert to dta for SEQUEST? We've done iTRAQ on an XL, but only using PQD not mixed CID/HCD, so it's just a suggestion to try, can't say I've tried it.
http://expasy.org/tools/HCD_CID_merger.html Cheers, DT http://expasy.org/tools/HCD_CID_merger.html On Nov 4, 7:15 pm, parimal samir <parimal.sa...@gmail.com> wrote: > I am using LTQ Orbitrap XL for iTRAQ or TMT based quantitation. I > fragment the peptide using CID in ion trap to get the sequence > information. I use HCD fragmentation with high fragmentation energy to > get the reporter ion spectra. Since, the reporter ion spectra and > sequence spectra are in different scan events, I would assume that > once converted to .dta, these spectra will be in different .dta files. > So my question is there a way that SEQUEST can be used to identify the > peptides in such a way that downstream quantitation tool can use the > corresponding reporter ions information for quantitation in this case? > If not, can I somehow merge the two spectra so that I will have both > the information in the same .dta file? Then I can use Scaffold or > Libra for quantitation. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@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.
