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.
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