Library search result "score"

Library search result "score" mmr6q  2022-06-29

How does Skyline calculate the "score" that appears on library match MS2 spectra, and why are many scores 0.000000 when the score of the MS2-sequence match is not zero? Is the Skyline "score" used in any way? Thank you.

Nick Shulman responded:  2022-06-29
That score comes from the peptide search results which were used to create the spectral library.
You can use the Skyline menu item "View > Spectral Libraries" to bring up the Spectral Library Explorer.
In the Spectral Library Explorer, there is a "..." button next to the library name dropdown. If you push that "..." button it will bring up a grid which has a "Score Type" column which will tell you what type of score that number is.
Usually that score is a q-value, where 0 means a very good match. I believe it is very common to see zeroes there. I am not sure whether the peptide search engine really thought the score is exactly zero, or whether it was just a number which is so close to zero it is getting rounded off to zero when Skyline displays the score to you.
-- Nick