Hello Veit, Thank you for the report. We don't often follow the *mgf->mzML* workflow, so it took us a while to look into this. We have fixed this in the code, and will be included in our next release of TPP -- aiming for ASMS (early June).
In the meantime, here is a one-line perl command that you can use to fix your Comet pepXML files and run them through TPP. Just make sure you back-up any files in case something gets messed up. For each file "FILE.pep.xml", run the following (watch the quotes!) : perl -pi -e 's/index=(\d+)/"scan=".($1+1)/eg' FILE.pep.xml This should work in TPP 4.8.0 as well as 5.0.0. Hope this (still) helps! --Luis On Mon, Jan 30, 2017 at 11:03 PM, Veit Schwaemmle <[email protected]> wrote: > 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 [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
