fail to recognize spectral library from NIST

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fail to recognize spectral library from NIST 851813663  2020-10-13
 

Dear nick
I have downloaded the Rat's spectral library from NIST, it was in msp format, and when I wanted to use the skyline to build the library, I found that the software could not recognize this format, and I was very eager for your help.
Thank you sincerely

 
 
Nick Shulman responded:  2020-10-14
Are you seeing some sort of error message in Skyline?

The way to tell Skyline to open a NIST library (.msp) that you have downloaded is to go to:
Settings > Peptide Settings > Library
and push the "Edit List" button.

and then push the "Add" button on the "Edit Libraries" dialog.

-- Nick
 
Brendan MacLean responded:  2020-10-14
Given that your request mentions trying to "build the library", I suspect this is just a misunderstanding around how Skyline supports NIST libraries in .msp format.

As Nick suggests, Skyline just understands these libraries without needing to "build" them or convert them to the Skyline native library format BLIB. You can use the instructions Nick has provided above. You can also consult the "Using a Public Spectral Library" section of the Targeted Method Editing tutorial on page 11:

https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/MethodEdit-20_1.pdf#page=11

In this case, the tutorial uses a .hlf file from theGPM, but the steps are the same for a .msp file from NIST, or a .sptxt file from Peptide Atlas.

Hope this helps.

--Brendan
 
851813663 responded:  2020-10-14
Thank you very much nick and Brendan,I have solved my problem according to what you suggested, once again sincerely thank you for your help
 
ref p responded:  2021-04-01
These lines are really helpful! Thanks all because I got prompt as well.
 
ref p responded:  2021-04-01

Herein, I want to post a second question that I think @Brendan and @Nick may help me out.

When I inspected the downloaded NIST *.msp library (Available Link 1), I found that various CE values were indicated in different MS/MS spectra (Appendix 1). However, my QE-HF-X *.RAW runs were acquired at 28 (N)CE. In this case, what I really need is a subset of the library that is appropriate to my experimental CE condition.

How to create such a subset library from NIST *.msp? As the Skyline recommended (Available Link 2) , I need to use a NIST-supplied filtering tool to produce that. But how to do that? Unfortunately, I didn't get success. Please help me on this, though, at your convenience!

Thanks!
--Guihua Jia

Available Link 1:
NIST Consensus Human HCD Libraries Peptide Libraries (May 19, 2020)
https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:lib:humanhcd20160503

Available Link 2:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=building_spectral_libraries&_docid=wiki%3A58131659-9e41-1031-aa4c-da2025825caa

 
Brian Pratt responded:  2021-04-02

NIST provides the MSSEARCH tool as part of its for-pay library offering. It looks like you're using their free offerings, though.

But, good news - there appears to be a download link for that tool on the NIST page you mentioned.

Please let me know how that works out.

Thanks for using the Skyline support board,

Brian Pratt