Dear Eric Thanks for your analysis
1. I found that mzXML worked better with SpectraST and the mzML file did not work at all: $ spectrast -sLtestLib.splib spectra.mzML SpectraST started at Fri Oct 20 18:06:18 2017. Library File loaded: "testLib.splib". Total Number of Searches Performed = 0; Run Time per Search = inf seconds. Total Run Time = 2 seconds. SpectraST finished at Fri Oct 20 18:06:20 2017 without error. $ spectrast -sLtestLib.splib spectra.mzXML SpectraST started at Fri Oct 20 18:07:06 2017. Library File loaded: "testLib.splib". Sorting query spectra in all mzXML files by precursor m/z before searching...DONE! Searching...10%...20%...30%...DONE! Finished searching "spectra.mzXML" (3 spectra searched.) Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml". Total Number of Searches Performed = 3; Run Time per Search = 0.6667 seconds. Total Run Time = 2 seconds. SpectraST finished at Fri Oct 20 18:07:08 2017 without error. 2. Yes there are only two as comet did only find matches for 2 spectra. However, searching a library of 2 spectra against a file of 3 spectra should still work? 3. These are "MaxQuant compatible CR". I have removed those but without any change in result. Unfortunately. Hannes On Friday, October 20, 2017 at 5:57:45 PM UTC-4, Eric Deutsch wrote: > > Hi Hannes, I had a quick peek at your file and while I didn’t do any > testing a few things come to mind. > > > > 1) It could be that because you’re using mzXML (you meant to use mzML, > didn’t you? ;-) SpectraST might not be not detecting that these are HCD > spectra when building the library? The peptides are labeled (CID) when I > they should be labeled (HCD) I assume? When creating the library, maybe > -cIHCD would help? Just guessing > > > > 2) Unless I mis-count, there are only 2 spectra in the sptxt? > > > > 3) The mzML has some unusual carriage returns in the third spectrum. It > could be causing some problem possibly.. > > > > I would investigate those first, but maybe it’s something else.. > > > > Eric > > > > > > > > > > *From:* [email protected] <javascript:> [mailto: > [email protected] <javascript:>] *On Behalf Of *Hannes Roest > *Sent:* Friday, October 20, 2017 1:58 PM > *To:* spctools-discuss <[email protected] <javascript:>> > *Subject:* [spctools-discuss] spectrast produces empty output file > > > > Dear Henry > > I am trying to set up a minimal example for a spectral library search, but > I cannot get it to work. I have a spectral library and a corresponding > mzXML file: > > $ spectrast -sLtestLib.splib spectra.mzXML > SpectraST started at Fri Oct 20 16:43:54 2017. > Library File loaded: "testLib.splib". > Sorting query spectra in all mzXML files by precursor m/z before > searching...DONE! > Searching...10%...20%...30%...DONE! > Finished searching "spectra.mzXML" (3 spectra searched.) > Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml". > Total Number of Searches Performed = 3; Run Time per Search = 1 seconds. > Total Run Time = 3 seconds. > SpectraST finished at Fri Oct 20 16:43:57 2017 without error. > > however, the resulting file spectra.pep.xml appears to be empty. Is there > any reason for this or any parameter I can change to make this example > work? Note that I generated the spectral library from that same mzXML file > (searched with comet) and I expect that the spectra match perfectly, so I > find an empty result file an unexpected outcome. > > Thanks > > Hannes > > -- > 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] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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.
