Hi Luis, Thanks very much .. converting to mzXML and then using mzXML2Search works perfectly. (Also thanks for the file renaming tip).
I think it would be nice if this could be made to work without having to go through an mzXML step (I'm trying to stick with mzML). So I'll try to use Matt's titleFilter as that seems like a better long term solution for me. Cheers Ira On Mar 2, 9:13 am, Luis Mendoza <[email protected]> wrote: > Thanks for the reply, Matt. > > Ira: in the meantime, you can either write a script that will insert > TPP-style TITLE headings to your mgf files (pre-Mascot), or convert your raw > data to mzXML, followed by mgf using mzXML2Search. > > For full TPP compatibility, you will also want to rename the Mascot.dat file > (typically named something along the lines of: F0011222.dat) to > <mzXML_BaseName>.dat before running Mascot2XML for conversion to pepXML. > > Hope this helps, > --Luis > > On Tue, Mar 1, 2011 at 1:31 PM, Matthew Chambers > <[email protected]>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. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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