Is there for me to create spectra library manually?

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Is there for me to create spectra library manually? davidz  2019-07-08
 

Hi there,

We've compiled spectra library data ourselves, is there a way to build a spectra library for Skyline from tab delimited data?
Thanks,

David

 
 
Brendan MacLean responded:  2019-07-08
 
davidz responded:  2019-07-09

Thanks, Brendan, it's useful, but I don't see where I can feed the ms2 data as I know the which fragments to use, and the relative intensities for each.

David

 
Brian Pratt responded:  2019-07-09

You can communicate those by creating an ms2 data file and referencing it by the "file" and "scan" columns in the SSL file.

 
Brian Pratt responded:  2019-07-09

Or you can populate a SQLite database directly, which is a bit more advanced but probably tidier if you have the capability. Details on that can be found on the same page Brendan's reply linked to, at the bottom.

 
Brendan MacLean responded:  2019-07-09

This method expects you still to be pointing at empirically collected spectra. Though, you could also use the .ms2 format, which I just added an explanation for to the page linked above. Here also is the paper that explains MS2:

https://www.ncbi.nlm.nih.gov/pubmed/15317041

What you describe, however, sounds a bit like what the Aebersold lab coined as an "Assay Library", minus relative retention times, unless you also have those, in which you are essentially talking about one of these "Assay Libraries" which we also support through File > Import > Assay Library. If you don't have the retention time information, we will still recognize a Transition List with relative ion abundance values in a column named one of (case-insensitive):

libraryintensity
relativeintensity
relative_intensity
relativefragmentintensity
library_intensity

I guess these are all the names we have seen this column given in the wild.

When you add this column to a normal transition list, Skyline will notice it when you use File > Import > Transition List and ask if you want to create a spectral library for your document based on the values.

Hope this helps. By the way, are you trying to create a peptide spectral library or a small molecule spectral library?

--Brendan

 
davidz responded:  2019-07-10

Thanks, Brendan, I was trying to create a peptide spectral library, and actually we do have elution time information so maybe assay library is the way to go. I will read about the assay library then, thanks a lot for the help!

David

 
Brendan MacLean responded:  2019-07-10

You can still go the SSL and MS2 route since MS2 files allow for specifying retention times. If you have real measured spectra or you just want to be able to specify more spectrum peaks than you necessarily want to create transitions for in your Skyline document, then you may still want to consider these files, but if you mostly want to deal in relative ion intensities for the transitions you want chromatograms for and normalized retention times, then Assay Libraries are frequently used in this case.

--Brendan

 
davidz responded:  2019-07-11

I'm following the "assay library" tutorial, and ran into this error at the last step:
"Spectrum must have a source file"

BTW, the library intensity has to be absolute intensity values, can it be relative intensity in percentage?
Thanks,

David

 
Brendan MacLean responded:  2019-07-11

What version of Skyline are you using? That is really odd.

 
davidz responded:  2019-07-11

Skyline (64-bit) 4.2.0.19072

 
Brendan MacLean responded:  2019-07-11

Can you provide a small snippet of your library, with itensities changed to whatever you like that causes this error for us to debug why it occurs?

You should be able to attach it as you have the screenshots.

 
davidz responded:  2019-07-11
 
Brendan MacLean responded:  2019-07-11

Wow! Great find. I guess Google finds it. Though, this is otherwise an orphaned tutorial (written for Skyline 2.6), which is not mentioned on the Skyline Tutorials page:

https://skyline.ms/tutorials.url

There are actually 2 of these:

https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/ImportingIntegrationBoundaries-2_6.pdf

And, unfortunately, no one ever wrote automated tests for them to make sure they stay working, as we have for the more official tutorials that are mentioned on the tutorials page.

Maybe we should try to fix that. I will have a closer look at what got broken since version 2.6. Thanks for the pointer.

--Brendan

 
davidz responded:  2019-07-11

Thanks, Brendan, I will try to create an assay library of my own and give it a try and see what happens.

David