Hello Antonio, The TPP tools are pretty specific in term of accepted formats and required elements. For example, msgfplus has some issues with its mzid format so we run the following replacement script before converting the mzid output it creates to pepXML.
perl -pi -e 's/"\?"/"-"/' $root.mzid Second if you are not using the xinteract tool to process your pepXML then I suggest you do the steps xinteract performs for analysis in the following order. 1. InteractParser interact.pep.xml qExactive01819.pepXML This tool will fix many of the issues observed in pepXML 2. RefreshParser interact.pep.xml <FASTA_DATABASE> Change your database to have REVERSED be in the prefix of the fasta file protein names and run the tool RefreshParser to remap the peptides in your pepXML to the proteins in the database 3. PeptideProphetParser PeptideProphetParser qExactive01819_prefix.pepXML ZERO ACCMASS YES EXPECTSCORE YES DECOY=REVERSED_ NONPARAM On Sun, May 20, 2018 at 9:44 AM, Antonio Ortega <ntoni...@gmail.com> wrote: > > - 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.or > g/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. > -- 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. 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