How to create library (BiblioSpec spectral library), background Proteome (Background Proteome file:- human, yeast, BSA, and others). shelkarmicrobio23591  2021-02-25 20:56
 

I need all primary files to prepare the library (BiblioSpec spectral library), background Proteome (Background Proteome file:- human, yeast, BSA, and others).

So in your first tutorial that you have mentioned the interact-prob.pep.xml file which is not getting.

Please help to design the SRM experiment.

Regards
Yogesh
 
 
Nick Shulman responded:  2021-02-25 21:42
I do not know a good place to download BiblioSpec (.blib) spectral libraries from.

You can download other types of library files from here:
http://www.peptideatlas.org/speclib/
Skyline understands libraries on that site which have the extension ".sptxt" and ".msp".

After you have downloaded and unzipped a library file, you can add it to your Skyline document by using:
Settings > Peptide Settings > Library > Edit List > Add

You should build your own background proteome (.protdb) file. The way to build a .protdb file in Skyline is:
Settings > Peptide Settings > Digestion
and choose "Add" in the Background Proteome dropdown

You need a FASTA file in order to build a background proteome.
You can download a human protein fasta file from here:
https://www.uniprot.org/proteomes/UP000005640

I hope this helps,
-- Nick
 
shelkarmicrobio23591 responded:  2021-02-25 22:27
Thank you, Nick, for your response.
There are some problems downloading the Sepc. lib from NIST, download option not opened, and ISB spec. lib file not supporting in Skyline.
Please find the attachment.
 
Nick Shulman responded:  2021-02-25 23:18
There is a checkbox on the web page which says "I Acknowledge" that you have to check in order for the Download buttons to become enabled.
 
shelkarmicrobio23591 responded:  2021-02-26 01:05
Still not enable
 
Brendan MacLean responded:  2021-02-26 11:13
Those buttons enable when I check that checkbox. Maybe pursue support from the PeptideAtlas team, or try to find someone else or some other computer. Time to start looking for other help and other ideas.
 
shelkarmicrobio23591 responded:  2021-02-27 03:14
Thank you sir for your reply.

I have downloaded but the ".sptxt" and ".msp", Skyline can not understanding. Also, the .msp file showing the windows installer patch formate.

Anyone, have a human spectral library that is readable to Skyline, please forward it to my email "shelkarmicrobio@gmail.com".

Regards
Yogesh
 
Nick Shulman responded:  2021-02-27 19:52
Skyline does understand NIST (.msp) and SpectraST (.sptxt) libraries.

The way to use the library in Skyline is to go to:
Settings > Peptide Settings > Library
and push the "Edit List" button and then "Add".

You might find the Spectral Library Explorer tutorial useful:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_library_explorer

On page 2 of the tutorial it shows you how to add a library to your document using the "Edit Library" dialog. In the tutorial, it has you add a .blib file, but it would also work with .msp or .sptxt.

-- Nick
 
shelkarmicrobio23591 responded:  2021-02-28 22:14
Dear Skyline experts, please help to sort out this problem.
Please find the attachment of the issue in creating the spectral library.

Sincerely
Yogesh
 
Nick Shulman responded:  2021-02-28 22:37
It looks like you pushed the "Build Library" button on the peptide settings dialog.

You need to push the "Edit List" button instead.
After that, you should push the "Add" button.
And then on the Edit Library dialog, you can give the library any name that you want, and press the "Browse" button to find your .msp file.
-- Nick