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=85.891281:91.3,174.844437:57.05,311.813507:81.99,375.793213:101,450.780975:69.69,632.835754:89.87,926.932861:136.2,128.844223:76.01,240.782654:50.81,243.792587:48.49,356.814117:69.49,454.723877:69.17,591.914917:62.51,929.205750:134.9,119.835655:50.81,146.810730:44.12,313.753174:46.04,432.699707:66.65,490.830780:59.32,931.451904:119.3,69.872475:50.47,178.782593:43.7,272.742065:43.81,408.824493:45.39,942.880249:115,117.840309:49.52,198.775986:42.92,324.805359:42.99,344.773254:39.04,109.852356:47.57,187.770813:39.76,133.594757:43.39,160.772324:39.08,56.943443:39.36,226.134232:38.81,67.875641:38.61,171.799027:38.8,111.822693:35.59,176.832809:38.53,42.978138:23.79,50.916721:27.19,52.566887:26.87,54.913723:22.46,72.841072:34.07,76.249527:23.81,82.256073:22.03,93.497459:24.16,94.913765:31.94,96.887436:34.87,115.820259:35.2,157.781494:33.38,162.763641:32.95,180.753448:29.66,189.855454:30.07,194.830963:27.97,196.772705:34.92,201.053894:36.89,216.776947:38.16,220.865006:34.84
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
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