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 <[email protected]> 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.Shteynberg@ > 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 <[email protected]> >> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 >> [email protected]. >> To post to this group, send email to [email protected]. >> 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
