How to build an Arabidopsis library?

support
How to build an Arabidopsis library? xndmgp  2023-05-26 23:40
 

I want to build an Arabidopsis library, which file(s) should I download and import into Skyline from PeptideAtlas? Thank you!

 
 
Nick Shulman responded:  2023-05-27 05:08
I do not know where to download an Arabidopsis spectral library.

I can tell you that Skyline can understand spectral library files with any of the following filename extensions:
.msp : NIST
.sptxt : SpectraST
.hlf : XHunter

Skyline can also read .blib (BiblioSpec) spectral libraries.
When you import peptide search results into Skyline, Skyline always creates a BiblioSpec spectral library from the peptide search results.

If you have a spectral library with the filename extension ".msp", ".sptxt", or ".hlf" you can use that directly in Skyline without building a BiblioSpec spectral library.
You can add a ".msp", ".sptxt", or ".hlf" spectral library to your Skyline document by going to:
Settings > Peptide Settings > Library
and pushing the "Edit List" to create an entry for your spectral library file.

-- Nick
 
xndmgp responded:  2023-05-27 05:37
Thanks for the responding. Could you kindly help me look into this link? https://peptideatlas.org/builds/arabidopsis/ Here, some arabidopsis library related files are ready for downloading, however, I can't find one fitted for Skyline. What I want is to identify and predict one target protein's peptide used for SRM. Is the info provided by this site covered all the possible peptides I should monitor?
 
Nick Shulman responded:  2023-06-01 15:47
I do not see anything that looks like a spectral library for Arabidopsis on that peptideatlas page. It certainly seems like there would be a spectral library on that web site, but all I see for that species is stuff related to DNA. I am not very familiar with any of these websites so I would not know how to find it.

I did find a library for that species on this PRIDE page:
https://www.ebi.ac.uk/pride/spectrumlibrary
The file you would download would be a .msp.gz file, so you would first need to extract it using a program such as 7-Zip and then add the .msp file to Skyline's list of libraries.
-- Nick