I will also add that the file I generated by converting from raw here, with options from my earlier message, didn't exclude any scans but did apply peak picking and 32 bit encoding. My file is 327 megabytes but your files are about 1.3 gigabytes. So if you are concerned about space I would recommend converting with the my options.
On Mon, Feb 5, 2018 at 5:32 PM, David Shteynberg < david.shteynb...@systemsbiology.org> wrote: > Thibault, > > I checked both files and it appears they both reference the scans > correctly. I am not sure why the two files would be of different > size/content if you ran the gui and commandline with the same set of > options. This would be a question for the proteowizard/msconvert > developers. From the TPP standpoint both should work ok. > > -David > > On Mon, Feb 5, 2018 at 1:00 PM, Thibault Robin <vyns...@gmail.com> wrote: > >> Maybe I confused the files, sorry if that is the case. >> >> However there is indeed a difference between the conversion through >> command lines or the GUI: >> Results of a file comparison: >> ***** gui.mzML >> ccession="MS:1000040" unitName="m/z"/> >> <cvParam cvRef="MS" accession="MS:1000796" name="spectrum >> title" value="a.1.1. File:"a.raw", NativeID:" >> ;controllerType=0 controllerNumber=1 scan=1""/> >> <scanList count="1"> >> ***** cmd.mzML >> ccession="MS:1000040" unitName="m/z"/> >> <scanList count="1"> >> ***** >> [...] >> >> Here is the mzML converted using the GUI: >> https://www.dropbox.com/s/7lne9itvgexhcm8/gui.mzML?dl=0 >> >> And the one with command lines: >> https://www.dropbox.com/s/l2bbyz3rzo22pmi/cmd.mzML?dl=0 >> >> Both converted just now from the raw file. >> >> I will have to try tomorrow to see how this impact the tandem results >> >> Thibault >> >> >> 2018-02-05 21:05 GMT+01:00 David Shteynberg < >> david.shteynb...@systemsbiology.org>: >> >>> You can try sending me your mzML file again, but the one I have states >>> that the input was an mgf file: >>> >>> <fileDescription> >>> <fileContent> >>> <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" >>> value=""/> >>> <cvParam cvRef="MS" accession="MS:1000127" name="centroid >>> spectrum" value=""/> >>> </fileContent> >>> <sourceFileList count="1"> >>> <sourceFile id="_x0032_0131226_HeLa_bRP01_120min.mgf" >>> name="20131226_HeLa_bRP01_120min.mgf" location="file:////media/vynsk >>> ir/Seagate/HeLa/MGF/PXD00 >>> 1441"> >>> <cvParam cvRef="MS" accession="MS:1000774" name="multiple peak >>> list nativeID format" value=""/> >>> <cvParam cvRef="MS" accession="MS:1001062" name="Mascot MGF >>> format" value=""/> >>> </sourceFile> >>> </sourceFileList> >>> </fileDescription> >>> >>> >>> On Mon, Feb 5, 2018 at 10:07 AM, Thibault Robin <vyns...@gmail.com> >>> wrote: >>> >>>> Hi David, >>>> >>>> I really think the mzML was converted from a raw file. But I think I >>>> understand the problem. I am using msconvert through the GUI since I am not >>>> a fan of Dos, and I just realized that one of the default parameters is >>>> >>>> >>>> *"titleMaker <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState> >>>> File:"<SourcePath>", NativeID:"<Id>"* >>>> Could it be the root of the problem ? However when I remove it it >>>> automatically reappears in the parameter file... >>>> Am I forced to use command lines ? >>>> >>>> Cheers, >>>> >>>> Thibault >>>> >>>> -- >>>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>>> To post to this group, send email to spctools-discuss@googlegroups.com. >>>> 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 a topic in the >>> Google Groups "spctools-discuss" group. >>> To unsubscribe from this topic, visit https://groups.google.com/d/to >>> pic/spctools-discuss/6srdMeRzmd8/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> spctools-discuss+unsubscr...@googlegroups.com. >>> To post to this group, send email to spctools-discuss@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
