Hi Guatam, If you are doing this through the command line and the suffix is troublesome, as long as you know the wiff files only contain a single "sample", you could index the final files and then delete the suffix. I think it would work, especially as it will be the same suffix.
Cheers, Gavin. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Matthew Chambers Sent: 19 January 2012 17:38 To: [email protected] Subject: Re: [spctools-discuss] msconvert for ABI wiff files suffixes the output file with "-Sample" -- why? Hi Gautam, This is because a single WIFF can contain multiple "samples", each of which translate to a separate mzML document. Each document can't be named the same, so we append the "sample name", or if that's not unique, we add a duplicate count like "(2)". An override was recently added to msconvert for setting the output filename, but I expect that would explode for a multi-sample WIFF file (which are not at all uncommon). -Matt On 1/19/2012 8:41 AM, Gautam Saxena wrote: > Hi, > > When using msconvert on ABI wiff files, it seems to suffix the > converted output file with the word "-Sample". Is this intended? This > suffixing does not occurr with Thermo .raw files, so why should it > occur with wiff files? Here's an example output: > > =========================== > R:\programs\windows_programs\msconvert\msconvert.exe --filter "msLevel > 2-" --mzXML --64 --mz64 --inten32 F:/JHU_NHLBI_MS_FILES/ > Melanies_iTRAQ_data/wiff_files/Fraction1/Fr1_1.wiff > > format: mzXML (Precision_64 [ 1000514:Precision_64 > 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) > indexed="true" > outputPath: . > extension: .mzXML > contactFilename: > > filters: > msLevel 2- > > filenames: > F:/JHU_NHLBI_MS_FILES/Melanies_iTRAQ_data/wiff_files/Fraction1/ > Fr1_1.wiff > > processing file: F:/JHU_NHLBI_MS_FILES/Melanies_iTRAQ_data/wiff_files/ > Fraction1/Fr1_1.wiff > writing output file: ./Fr1_1-Sample.mzXML > ========================= > > The version of msconvert being used is shown below: > > ========================================== > W:\lab1\jsmith_university_edu\Workflow_Outputs\DJ8C>R:\programs > \windows_programs\msconvert\msconvert.exe --version > unknown option version > Please report this error to [email protected]. > Attach the command output and this version information in your report: > > ProteoWizard release: 2.2.2997 (2011-9-19) > ProteoWizard MSData: 2.2.2997 (2011-9-19) > ProteoWizard Analysis: 2.2.2976 (2011-9-14) > Build date: Sep 19 2011 17:00:29 > =========================================== > -- 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. -- 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.
