Who wants to manually quality check peptides?!
Took 8.5 hours on a Sunday night, but I calculated an error rate for Skyline! I randomly selected 100 proteins in Skyline, and for each protein I checked one peptide. Ideally, these peptides had data availabe for every replicate. I evaluated whether or not Skyline chose the right peak, and if the peak boundaries were correctly deliniated.
For each peak, I assigned a “0” if Skyline picked the wrong peak and a “1” if it picked the peak correctly. For some peptides, there was no data available for a replicate. This would be a blank screen, so I gave it the value “N/A.” I then calculated error rates per replicate and peptide. You can find my spreadsheet here.
Here are some examples of Skyline spectra.
1: Skyline picked the right peak
0: I assigned this value when Skyline picked the wrong peak. I also assigned this value when Skyline picked a peak where there was just noise.
Changing peak boundaries: