Hi Luis, Thank you for the update and the fix! I already corrected the index numbers with another one-liner :-)
Best regards Veit 2017-04-13 20:53 GMT+02:00 Luis Mendoza <luis.mend...@systemsbiology.org>: > 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 <veitv...@gmail.com> > 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 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. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/mdMIkYzJ9I4/unsubscribe. > To unsubscribe from this group and all its topics, 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. > -- \|||/ (o o) ----ooO-(_)-Ooo---- Don't worry about life; you're not going to survive it anyway. http://computproteomics.bmb.sdu.dk -- 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.
