Regarding the output of PREGO for a list of peptides from skyline

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Regarding the output of PREGO for a list of peptides from skyline shu upadhyay21  2021-08-23
 

Dear Skyline,
I got some trpysin digested peptides for a protein for which I used PREGO. I got directed to a webpage which has given scores and ranks for each of my peptides. Can you tell me what the scores and the ranks are about? Are they giving any information about the detectability of the peptides in a mass spectrometer? I got the following output from PREGO.

Rank Sequence        Score
1       GGLDLR  0.16867737160352636
2       GDLSLR  -0.06754151848263762
3       GESLFQGR        -0.17631845487837808
4       GEPLQVER        -0.6208215989137332
5       TLIYYLDEIPPK    -0.9140796672874998

I am new to proteomics and it would be really helpful if you guys could help me out :)

Thank you.

 
 
Nick Shulman responded:  2021-08-23
I do not know the answer to your question but I can tell you that this is the paper from 2015 which describes the PREGO algorithm:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4563719/

The higher ranked peptides are expected to be easier to detect in a mass spectrometer, based on the dataset that some machine learning algorithm was trained on.

I imagine that much better algorithms have been developed in the time since then, but I am not sure what those would be.

-- Nick
 
shu upadhyay21 responded:  2021-08-23
Thank you Nick.