Dear Delphine, Thank you for using M2Lite.
Although M2Lite was developed to primarily convert MSF to mzidentML files, pepXMLs and tabs-delimited-text outputs were added as extra features. M2Lite's pepXMLs were tested and successfully integrated into downstream analysis in IDPicker version 3. We are yet to test and troubleshoot M2Lite-derived pepXMLs in TPP - particularly with Peptide-Prophet. We hope to do this as well in other downstream analytical tools implementing mzIdentMLs and/or pepXMLs. Yes, it will be possible to have the DeltaCn [and many other possible identification metrics] with subsequent iterations of M2Lite's development. Kind regards, Paul. On Tuesday, June 10, 2014 9:38:47 AM UTC-4, Delphine wrote: > > 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], [email protected] >> >> ... >> '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.
