Yaamini’s Notebook: Skyline Error Checking Round 2

This time it only took 4 hours!

Due to a combination of not working late at night, using the same proteins and transitions as last time, and knowing what good and bad peaks look like, I was able to spot check 100 peptides in the revised Skyline document. Because I was in a rush to finish and head to the airport, I didn’t take any side-by-side comparison pictures. I do however, have revised error rates.

Ovearll, I think the new .blib improved Skyline peak selection. I haven’t compared error rates so I don’t have anything quantitative to base my assertion on, but I have a few observations:

  • More instances of a peak being chosen correctly for all replicates
  • Way less missing peaks
  • Fewer noisy peak selections

The previous error checking document is here, revised error checking document can be found here.

After error checking, I re-exported my Skyline reports.


Proteins and peak areas only


MSstats document, replicate not pivoted

from the responsible grad student http://ift.tt/2sPPH59