We have 2.0.7 file formats and the cmd line for msconvert works for mzXML and mzML. It fails on .mgf conversion. We also run MzCv which is a GUI for msconvert and it only works for mzML. The GUI still points to same cmd line msconvert so not sure why it fails but it is the same unable to open file error as below.
C:\Inetpub\tpp-bin\pwiz-bin-windows-x86-vc90-1_6_1386.tar\pwiz-bin- windows-x86-v c90-1_6_1386>msconvert 16Jun201107.RAW --mzXML format: mzXML (Precision_64 [ 1000514:Precision_64 1000515:Precision_32 ], ByteO rder_LittleEndian, Compression_None) indexed="true" outputPath: . extension: .mzXML contactFilename: filters: filenames: 16Jun201107.RAW processing file: 16Jun201107.RAW writing output file: ./16Jun201107.mzXML C:\Inetpub\tpp-bin\pwiz-bin-windows-x86-vc90-1_6_1386.tar\pwiz-bin- windows-x86-v c90-1_6_1386>msconvert 16Jun201107.RAW --mgf format: MGF outputPath: . extension: .mgf contactFilename: filters: filenames: 16Jun201107.RAW processing file: 16Jun201107.RAW [ThermoRawFile] [RawFile::ctor] Unable to open file 16Jun201107.RAW Error processing file 16Jun201107.RAW On Jul 27, 3:52 pm, JAM <[email protected]> wrote: > I read the msconvert threads and the warnings about ReAdW. But our > mass spec facility is using an old version of XCalibur (2.0.7), and I > could not get msconvert to work, either on its own or through the TPP > interface. I assumed it was an issue with the older Xcalibur format. > ReAdW worked fine. Should I give msconvert another try, or does it > indeed have problems with older Xcalibur files? > > On Jul 27, 10:19 am, Joseph Slagel <[email protected]> > wrote: > > > > > > > > > The TPP team also strongly recommends msconvert. > > > On Tue, Jul 26, 2011 at 1:59 PM, Parag Mallick <[email protected]> wrote: > > > Hiya, > > > > Umm....*when* were you using ReAdW? The ProteoWizard team mostly suggests > > > msConvert these days. Moving this to spctools list for feedback. > > > > For pwiz we typically suggest referencing: > > > > ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. > > > Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. > > > Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323. > > > > Best, > > > ~ Parag M ~ > > > > On Jul 26, 2011, at 11:55 AM, Jacob Mayfield wrote: > > > > > To whom it may concern, > > > > > I am finishing a manuscript in which I used ReAdW (but not other TPP > > > > tools) to centroid mass spec data. I would like to cite it. How > > > > should I do so? > > > > > Thanks, > > > > Jake > > > > > Jacob Mayfield > > > > [email protected] > > > > --------------------------------------------------------------------------- > > > --- > > > > Magic Quadrant for Content-Aware Data Loss Prevention > > > > Research study explores the data loss prevention market. Includes > > > in-depth > > > > analysis on the changes within the DLP market, and the criteria used to > > > > evaluate the strengths and weaknesses of these DLP solutions. > > > >http://www.accelacomm.com/jaw/sfnl/114/51385063/ > > > > _______________________________________________ > > > > proteowizard-support mailing list > > > > [email protected] > > > >https://lists.sourceforge.net/lists/listinfo/proteowizard-support > > > > --------------------------------------------------------------------------- > > > --- > > > Got Input? Slashdot Needs You. > > > Take our quick survey online. Come on, we don't ask for help often. > > > Plus, you'll get a chance to win $100 to spend on ThinkGeek. > > >http://p.sf.net/sfu/slashdot-survey > > > _______________________________________________ > > > proteowizard-support mailing list > > > [email protected] > > >https://lists.sourceforge.net/lists/listinfo/proteowizard-support -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
