Apologies to both Matt and Luis for my incredibly slow response ... for some reason this didn't show up in my inbox until today :( though I see you responded very quickly.
I have tried Luis's suggestion which solves my problems pretty nicely in the short term. I've updated my tpp source and rebuilt it to try Matt's new titleMaker filter. Unfortunately the new binray I built doesn't seem to recognise the new filter (it says it is ignoring it). I think the problem is that I don't seem to have the titleMaker code in my source .. I'm at Revision 5324 of the tpp. When I grep for 'titleMaker' in the source directory I get no results. Do I need to update the pwiz source separately to the tpp? Thanks again for your help. Ira On Mar 5, 5:52 am, Matthew Chambers <[email protected]> wrote: > Hi Ira, > > I checked this in. I've run some tests and it seems to be working ok. The new > filter is "titleMaker" > and the currently supported fields are: > > <RunId> - Run::id > <Index> - Spectrum::index > <Id> - Spectrum::id (nativeID) > <ScanNumber> - if the nativeID can be represented as a single number, that > number, else index+1 > <ActivationType> - for the first precursor, > Activation::cvParamChild("dissociation method") > <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation > target m/z") > <SelectedIonMz> - for the first selected ion of the first precursor, > SelectedIon::cvParam("selected > ion m/z") > <ChargeState> - for the first selected ion of the first precursor, > SelectedIon::cvParam("charge state") > <SpectrumType> - Spectrum::cvParamChild("spectrum type") > <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start > time") > <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start > time") > <BasePeakMz> - Spectrum::cvParam("base peak m/z") > <BasePeakIntensity> - Spectrum::cvParam("base peak intensity") > <TotalIonCurrent> - Spectrum::cvParam("total ion current") > > i.e. > msconvert data.raw --filter "titleMaker > <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState>" --mgf > > This should allow people to use msconvert's MGF output with TPP. It doesn't > have the zero padding > (yuck) but it's conceivable to add support for format flags that specify > padding and precision. > > -Matt > > On 3/1/2011 3:31 PM, Matthew Chambers wrote: > > > > > > > > > Hi Ira, > > > Without looking at the code, I recall that Mascot2XML depends on certain > > title formats. Msconvert > > preserved the Bruker nativeID of scan=xxx which is not one of those formats. > > > This is a good reason to have user-customizable MGF titles in pwiz (and > > thus msconvert). I think a > > TPP compatible format could be implemented quite easily as a spectrum list > > filter like: > > --filter "spectrumTitle <RunId>.<ScanNumber>.<ScanNumber>" > > > I may take a crack at it sometime this week since I think a basic > > implementation could be hacked out > > in an hour or so. I'm open to ideas about the field syntax. %RunId% > > $(RunId) $RunId, oh joy. > > > I'm copying Eva since she asked about this. An <ActivationType> field is > > right up your alley. :) > > > -Matt > > > On 2/27/2011 7:27 PM, Ira Cooke wrote: > >> Hi, > > >> I've been running some searches on bruker MALDI data. > > >> The overall processing is as follows; > > >> 1. Convert original raw data to mzML using CompassExport > > >> 2. Convert mzML file to mgf using msconvert > > >> 3. Submit mgf file for searching with Mascot > > >> 4. Attempt to convert mascot dat file to pep.xml > > >> This step fails with the following output (using latest development > >> version of tpp, or with latest > >> release ). (see bottom of email for output) > > >> The search seemed to succeed in mascot so it seems to be an error with > >> Mascot2XML. > > >> Any help would be much appreciated. I'd be happy to upload an example file > >> .... and in the interim > >> here is one of the entries from the file. > > >> Many thanks > > >> Ira > > >> --gc0p4Jq0M2Yt08jU534c0p > >> Content-Type: application/x-Mascot; name="query49" > > >> title=scan%3d465 > >> rtinseconds=2569.998 > >> index=356 > >> charge=1+ > >> mass_min=42.978138 > >> mass_max=942.880249 > >> int_min=22.03 > >> int_max=136.2 > >> num_vals=59 > >> num_used1=-1 > >> Ions1=85.891281:91.3,174.844437:57.05,311.813507:81.99,375.793213:101,450.7 > >> > >> 80975:69.69,632.835754:89.87,926.932861:136.2,128.844223:76.01,240.782654:5 > >> > >> 0.81,243.792587:48.49,356.814117:69.49,454.723877:69.17,591.914917:62.51,92 > >> > >> 9.205750:134.9,119.835655:50.81,146.810730:44.12,313.753174:46.04,432.69970 > >> > >> 7:66.65,490.830780:59.32,931.451904:119.3,69.872475:50.47,178.782593:43.7,2 > >> > >> 72.742065:43.81,408.824493:45.39,942.880249:115,117.840309:49.52,198.775986 > >> > >> :42.92,324.805359:42.99,344.773254:39.04,109.852356:47.57,187.770813:39.76, > >> > >> 133.594757:43.39,160.772324:39.08,56.943443:39.36,226.134232:38.81,67.87564 > >> > >> 1:38.61,171.799027:38.8,111.822693:35.59,176.832809:38.53,42.978138:23.79,5 > >> > >> 0.916721:27.19,52.566887:26.87,54.913723:22.46,72.841072:34.07,76.249527:23 > >> > >> .81,82.256073:22.03,93.497459:24.16,94.913765:31.94,96.887436:34.87,115.820 > >> > >> 259:35.2,157.781494:33.38,162.763641:32.95,180.753448:29.66,189.855454:30.0 > >> > >> 7,194.830963:27.97,196.772705:34.92,201.053894:36.89,216.776947:38.16,220.8 > >> 65006:34.84 > > >> Output from Mascot2XML > > >> Mascot2XML F019018.dat > >> -D/sharedData/TPP/Databases/OnMascot/SPHuman/sphuman_20101013_DECOY.fasta > >> filepath: /sharedData/TPP/Data/MALDI/1011/MT237/, extn: F019018 > >> A stored as 71.0779 > >> B stored as 114.595 > >> C stored as 160.194 > >> D stored as 115.087 > >> E stored as 129.114 > >> F stored as 147.174 > >> G stored as 57.0513 > >> H stored as 137.139 > >> I stored as 113.158 > >> J stored as 0 > >> K stored as 128.172 > >> L stored as 113.158 > >> M stored as 131.196 > >> N stored as 114.103 > >> O stored as 0 > >> P stored as 97.1152 > >> Q stored as 128.129 > >> R stored as 156.186 > >> S stored as 87.0773 > >> T stored as 101.104 > >> U stored as 150.038 > >> V stored as 99.1311 > >> W stored as 186.21 > >> X stored as 111 > >> Y stored as 163.173 > >> Z stored as 128.622 > >> c stored as 17.0073 > >> n stored as 1.00794 > >> variable modification 1, delta mass 0.9848 for Deamidated-N (N): > >> residues: N > >> nterm: 0 > >> cterm: 0 > >> protterm: 0 > > >> warning: cannot open "F019018.mzXML" for reading scan numbers. > >> Warning: could not find scan numbers of spectrum scan=637 > >> Set to 0000 > >> Warning: could not find scan numbers of spectrum scan=72 > > >> ...... lots of warnings like the one above > > >> Warning: could not find scan numbers of spectrum scan=284 > >> Set to 0000 > >> Warning: could not find scan numbers of spectrum scan=673 > >> Set to 0000 > >> Sample enzyme has not been specified, "Trypsin" from .dat file assumed > >> trypsin : cut(KR) nocuts(P) sense(C) > >> prev_aa and next_aa have already been read from .dat file. > >> Replacing 1913 protein id with full ids by parsing through the database... > >> searching > >> /sharedData/TPP/Databases/OnMascot/SPHuman/sphuman_20101013_DECOY.fasta.... > >> > >> .5%.....10%.....15%.....20%.....30%.....35%.....40%.....45%.....50%.....60% > >> .....65%.....70%.....75%.....80%.....90%.....95%...done > > >> 481. opening scan=671.out > >> warning: cannot open "F019018.mzXML" for reading MS instrument info. > >> error: only found 0 periods in scan=11 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
