Re: [proteowizard-support] BlibBuild question

[Chambers, M. <mat...@gm...>]

Hi Mike,

MGF is currently not supported when importing pepXML results. MzML would be best because its nativeIDs allow spectrum matching to be 
unambiguous. But pepXML doesn't have a standard attribute to refer to nativeID, so BiblioSpec recognizes the non-standard "spectrumNativeID" 
attribute on the <spectrum_query> element. Without that, it will use the "start_scan" scan number value to lookup spectra (i.e. it look for 
that number in a spectrum id in a mzML or mzXML file).

There's no such (reliable) way to look up scan numbers in MGF files because the scan number attributes are optional and/or mixed in with the 
title string.

Hope this helps,
-Matt


On 3/29/2019 5:14 PM, Mike Trnka wrote:
> I'm not sure where best to direct Bibliospec questions, but will try here.  I am setting up a workflow that involves building blibs from protein prospector generated pep.xml results files.  Is it possible to use mgf as the peaklist format, or do I need to generate mzml?  Best,
>
> Mike Trnka
> UCSF