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 <
[email protected]>:
> 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/
> vynskir/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
>>
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