Hello, I tried your tool and succeed in getting pepxml files from msf files. However, I tried to run peptideprophet on the resulting pepxml files and didn't succeed. I corrected as many parts as I could in the pepxml file but I still got an error when running peptideprophet:
running: "C:/Inetpub/tpp-bin/PeptideProphetParser "312_15_03_002_140409_01.sequest.interact.pep.xml" MINPROB=0" (SEQUEST) (minprob 0) init with SEQUEST trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap Elite, Ionization: nanoelectrospray, Analyzer: radial ejection linear ion trap, Detector: electron multiplier PeptideProphet (TPP v4.7 POLAR VORTEX rev 0, Build 201402281256 (MinGW)) AKeller@ISB read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. read in no data command "C:/Inetpub/tpp-bin/PeptideProphetParser "312_15_03_002_140409_01.sequest.interact.pep.xml" MINPROB=0" failed: Operation not permitted Do you have any idea on how to correct this problem? I detected another thing in the pepxml files: only the xcorr value appears, wouldn't it be possible to have the deltacn value as well? Thanks for your help Delphine Le mercredi 4 juin 2014 16:45:22 UTC+2, apauls a écrit : > > Dear All, > > May we announce to the group the release of our new tool - M2Lite. M2Lite > converts Proteome Discoverer's MSF file(s) to the mzIdentML standard data > format. The tool's associated paper "*M2Lite: an Open-Source, > Light-Weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML > Tool" *may be found here > http://www.bowenpublishing.com/jbi/paperInfo.aspx?PaperID=15750 > > M2Lite may also optionally convert MSF(s) to pepXML(s) or a tab-delimited > text output(s). M2Lite’s source code is available as open-source at > https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and > documentation can be freely downloaded at > https://bitbucket.org/paiyetan/m2lite/downloads. It is made available > under the BSD 3-Clause open source license. > > We welcome feedback and recommendations for future adaptations and > developments as we seek to serve the community. > > Kind regards, > > Paul. > > -- > _______________________________________ > Paul Aiyetan, MD, MS > Postdoctoral Fellow | Department of Pathology > The Johns Hopkins University School of Medicine. > 1550 Orleans Street, CRB II, Room 3M 01-07 > Baltimore, MD. 21231 > Office Phone: (443) 287 4306 > Office Fax: (443) 287 6388 > Email: [email protected], <javascript:> [email protected] <javascript:> > > ... > 'Tis not too late to seek a newer world. > ... > Not to exist like brutes, but made were ye > To follow virtue and intelligence > - Alfred, Lord Tennyson, Ulysses > -- 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
