We have worked on merging PQD and CID spectra for iTRAQ before. Raw could be converted to mgf using extract_msn.exe packed in Sequest/Bioworks. I can provide a script to merge spectra with reporter peaks if you need. You may find some description of the method in JPR.7:4831. Now I have also developed some script to extract spectra with reporters from mzXML directly, which I think is more convenient. I have not tried HCD with my script, but I think it won't be too difficult to take a try if you provide some example data.
cheers, Tiannan On Sat, Nov 6, 2010 at 12:23 AM, dctrud <[email protected]>wrote: > 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 <[email protected]> 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 [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > 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 [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.
