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Import of search results from Peptideatlas to build the BiblioSpec library

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Import of search results from Peptideatlas to build the BiblioSpec library 2378572477  2024-04-28 00:52
 
Hello.

I am trying to build the BiblioSpec library from Peptideatlas. I downloadsed Honeybee(Database Tables: XML) for building BiblioSpec library. After I added the result. file, an error popped up saying not a valid library input file. Can you please let me know how to fix this? Or what is the other way to build the BiblioSpec library(about Honeybee)?

Thanks,
Zhaoxuanxuan
 
 
Nick Shulman responded:  2024-04-28 10:24
The XML file that you referred to starts with "<SBEAMS_EXPORT>".
Skyline does not understand that format at all.

You can download spectral libraries from Peptide Atlas:
https://peptideatlas.org/speclib/

You can download files from the Peptide Atlas site with the filename extensions ".msp".

Skyline understands the files whose names end in ".msp" and ".sptxt".
The way to use a .msp or .sptxt file in Skyline is to go to:
Settings > Peptide Settings > Library
and then use the "Edit List" button and "Add" to add the library.

The way that you use a .msp or .sptxt file in Skyline is different from the way that you use peptide search results. You usually build a .blib file from the peptide search results. But, with .msp and .sptxt you "Add" them to the list of libraries without creating a .blib.
-- Nick