- For example, assuming I searched a Uniprot human database with the mgf file in (from the Compomics tutorial) - https://drive.google.com/file/d/0B4sW8rLWPbRydlFNWEthX1hLUEk/view - using MS-GF+, and I transformed the mzid file into a pepXML using:
idconvert qExactive01819.msgf.mzid --pepXML -v -o . obtained a qExactive01819.pepXML file what would be the command line I need to analyse the file as stated in http://tools.proteomecenter.org/wiki/index.php?title=Tutorial:StPeter1? Prior to using PeptideProphet, I placed the decoy label as a prefix, instead of a suffix as SearchGUI does, using this sed command sed 's/|\(\w*\)_REVERSED|/|REVERSED_\1|/' qExactive01819.pepXML > qExactive01819_prefix.pepXML - - then, if I try to run PeptideProphetParser on this file with the flags I infered from the tutorial: - PeptideProphetParser qExactive01819_prefix.pepXML ZERO ACCMASS YES EXPECTSCORE YES DECOY=REVERSED_ NONPARAM YES DECOYPROBS - - I get this output using Accurate Mass Bins Using Decoy Label "REVERSED_". Decoy Probabilities will be reported. Using non-parametric distributions (MS-GF+) (minprob 0) WARNING: Support of MSGF+ may not be full. There exist known issues with the way MSGF+ encodes certain modifications in pep.xml that may not be correct. Also, high-scoring DECOY have been observed in MSGF+ analysis. The user is encouraged to be vigilant in comparing model estimated error-rates to the DECOY-estimated error-rates to make sure the two agree and set CLEVEL parameter accordingly: see http: //tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3F adding ACCMASS mixture distribution init with MS-GF+ Trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.1.0 Syzygy, Build 201804301819-exported (Linux- x86_64)) AKeller@ISB read in 5 1+, 5355 2+, 2108 3+, 1057 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 769 Decoys, and 7756 Non-Decoys PeptideProphetParser: /nfs/home/aoj/opt/tpp/tpp/src/Validation/Distribution/ DiscreteDistribution.cpp:91: virtual double DiscreteDistribution::getProb( int): Assertion `val >= 0 && val < num_bins_' failed. Iterations: Aborted (core dumped) - I will soon try with Comet. Best Antonio - søndag den 20. maj 2018 kl. 02.03.35 UTC+2 skrev Antonio Ortega: > > Hi all! I was wondering what are the command lines required to process > with PeptideProphet, iProphet and ProteinProphet the output produced by > search engines like comet when run through SearchGUI. > > The raw files are in the mgf format and I used a decoy database with the > label in the suffix, not the prefix as peptideprophet expects. Everytime I > have tried runing this programs I would end up with a 1Kb file containing > almost no information. My goal is to link the output of SearchGUI to > StPeter, to perform Protein Quantification. I haven't been able to find an > in depth guide on how to use these programs, other than the tutorials, > which are addressed to people using Petunia, and the help messages of the > commands. But no big guide so far on the CLI. > Any help would be very much appreciated! > > Thank you very much for your help! > > Best regards > > Antonio > -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
