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 <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
>
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