Precursor intensity

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Precursor intensity smanda  2019-02-18
 

Hi Team,

I am trying to export spectral library as a report with the OpenSwath template. I have the fragment intensity figured out but I would like to get the precursor intensity as well as one of my columns, where can I find that?

Any pointers appreciated. The spectral is built from a mzid input.

Regards,
Srikanth

 
 
Brendan MacLean responded:  2019-02-19

That should be PrecursorResults.TotalArea, assuming you want the total intensity of all the transitions. Here also is another thread on exporting spectral library reports from Skyline for other tools.

https://skyline.ms/announcements/home/support/thread.view?rowId=38631

 
smanda responded:  2019-02-19

Thanks Brendan,

I had a look at the Total area and Total area MS1 and it gives me #N/A for my data for these columns. What do you think is missing?
I am using a mzid file from peptideshaker to build the library.

Regards,
Srikanth

 
Brendan MacLean responded:  2019-02-19

Can you use File > Share - Complete to save your file to a .sky.zip and post that to https://skyline.ms/files.url ?

Probably the quickest route to an answer for you is to have a look at your file. You would at least need to post some screenshots of your data for me to have a hope of guessing the answer to your question.

--Brendan

 
smanda responded:  2019-02-19

I have uploaded a file threeorganism.sky.zip. Please have a look and let me know the issue.

Regards,
Srikanth

 
Nick Shulman responded:  2019-02-20
Hi, Srikanth,

You have a Skyline document with a spectral library. The "PrecursorResults.TotalArea" thing would have been the right answer if you had used Skyline to extract chromatograms from raw files.

It sounds like you want the MS1 intensities of the peaks that were selected for fragmentation in the results that were used to build the spectral library.

MS1 intensities do not get stored in the .blib file, so there is no way for Skyline to give you that information. Currently, Skyline does not make it easy to get any information out of the spectral library. In the future, I could imagine that we might have something similar to the Document Grid, but for spectral libraries, that would let you output lots of information from spectral libraries.

Currently, the only way to get information out of a .blib file would be to use database tools on it. The .blib file is a SQLite database. The fragment intensities are stored in a compressed binary blob which you would have to write code to interpret. But, nowhere in the .blib is the precursor intensity stored.

It sounds like your best bet is to go back to the OpenSwath results which you built the spectral library from.

I hope this answers your question.
-- Nick