Sorry I hit send before my email was finished....continuing.....
3. PeptideProphetParser interact.pep.xml ZERO ACCMASS PPM DECOY=REVERSED NONPARAM This should help you get your msgfplus results processed. Let me know what further problem you encounter. Cheers, -David On Sun, May 20, 2018 at 3:39 PM, David Shteynberg < [email protected]> wrote: > 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 <[email protected]> > 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_i >> s_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 [email protected]. >> To post to this group, send email to [email protected]. >> 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
