Bibliospec for spectral library searching david morgenstern  2020-09-06 11:54
 

Hi,

I'm considering moving to using spectral library searching for glycoprotoemics due to the prohibitive search times (especially for large datasets). apart from the old manuscript - is there any tutorial I can use for it? there are multiple questions I've got regarding the use of the software:

  1. how does FDR performed after the search?
  2. how does it deal with very small database (50 entries) for FDR calculations?
  3. how does the scoring algorithm (as well as the annotator) deal with c/z B/Y spectra from glycopeptides and EThcD/sHCD?
  4. can it look for modifications on top of what comes out of the library?
  5. Can you convert the .blib libraries to .msp?
  6. can it deal with PRM data for library preparation? PRM with separate MS1?

I'd appreciate any resource you can point out to me.

Thanks!
David.
 
 
Brian Pratt responded:  2020-09-08 10:27

Hi David,

These aren't functions of Skyline, I'm not really sure where your questions should be directed.

As to question 5, the .BLIB format is implemented as an SQLite database - schema is documented at https://raw.githubusercontent.com/ProteoWizard/pwiz/master/pwiz_tools/BiblioSpec/tests/reference/tables.check .

It would be fairly simple to write a Python program to generate .MSP from this, if it hasn't been done already (but I don't know if it has).

Best,

Brian Pratt
 
Nick Shulman responded:  2020-09-08 20:10
David,
It sounds like you might be asking about BlibSearch, which is a tool for searching for peptides using a BiblioSpec spectral library.

Here is the web page for BlibSearch:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibSearch

-- Nick