spectral library creation problem

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spectral library creation problem egulyas  2018-08-28 07:14
 

Dear Brendan,

I would like to use Skyline(64-bit, 4.1.0.18169) for quantitative
proteomic analysis. I have managed to create a spectral library
already several times, but now I am unable. I use ProteinProspector
for DDA database search and generated pep.xml files, but the Skyline
said: "ERROR: 180802_03.pep.xml(line452): The .pep.xml file is not
from one of the recognized sources".
Could you suggest what should I change?

I attach the pep.xml file.

Thanks for your help in advance,

Best,
Eva Hunyadi-Gulyas

 
 
Brian Pratt responded:  2018-08-28 11:21
It looks like something changed in Protein Prospector. BiblioSpec was expecting the line

<search_summary base_name="/var/lib/prospector/web/temp/Aug_28_2018/fileZKIOgd1/180802_03" search_engine="PROTEINPROSPECTOR" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">

to look more like this:

<search_summary base_name="/var/lib/prospector/web/temp/Aug_28_2018/fileZKIOgd1/180802_03" search_engine="protein prospector search compare" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">

If you make this substitution, does everything else work for you? If so, we can update BiblioSpec to understand them to be the same thing.

Best Regards,

Brian Pratt
 
Matt Chambers responded:  2018-08-28 12:16
I've made the update. Also updated a few other strings so they'd work with or without spaces ("X! Tandem" or "X!Tandem" for example). Brian can tell you whether to expect it to be in the next Skyline-daily. His suggestion of replacing the search_engine string should help you in the meantime.
 
Brian Pratt responded:  2018-08-28 14:09
Those changes should be available now, at https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=Download%20and%20build - there's a link at the bottom of the page int the "Pre-compiled binaries" section for downloading our most recently built test version.

Brian
 
egulyas responded:  2018-08-29 02:20
Dear Brian,

Thanks for your help!
 Substituting "Proteinprospector" to "protein prospector search compare" in the pep.xml files solved my problem.

Best Regards,

Eva