Thanks Matt, I've tried this out ... and now it works perfectly.
Thanks Ira On Mar 8, 2:46 am, Matthew Chambers <[email protected]> wrote: > Hi Ira, > > The TPP source is manually sync'd to the pwiz source whenever there's a > significant TPP update. The > pwiz binaries are always available from the latest source though. You can > download them and put them > in your tpp-bin directory: > Windows:http://teamcity.labkey.org:8080/repository/download/bt36/27487:id/pwi... > Linux:http://teamcity.labkey.org:8080/repository/download/bt17/27488:id/pwi... > > You can also download the pwiz source and build it yourself of course. > > Hope this helps, > -Matt > > On 3/6/2011 8:29 PM, ira cooke wrote: > > > > > > > > > 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 > >>>> 7,194.830963:27.97,196.772705:34.92,201.053894:36.89,216.776947:38.16,22 > 0.8 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. 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