Hi guys, When applying the pipeline *msconvert (mgf to mzML) -> comet -> peptideprophet + libra*, I get wrong assignment of the spectra. It looks that identifications are taken looking for *spectrum* while iTRAQ reporter ion intensities were retrieved by matching *spectrumNativeID*. As you can see in the example, the numbering is different (msconvert creates indexes starting by 0 while comet results start by 1) and I get wrong assignment. The results fantastic when correcting the number by increasing the indices by 1 :-).
<spectrum_query spectrum="outiTRAQ_fractionation_1-4-5.00022.00022.3" spectrumNativeID="index=21" start_scan="22" end_scan="22" precursor_neutral_mass="2166.082358" assumed_charge="3" index="2" retention_tme_sec="647.9"> I suggest that all modules in *xinteract* use the same IDs when looking for spectra/search results. Or is there an easy fix when using command line? Best regards Veit -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
