Fig. 3.

Skyline MS1 filtering graphical user interface. A, Skyline peptide tree for peptide YAPVAKacDLASR (Kac is acetyllysine, and R is ¹³C₆¹⁵N₄-Arg) showing three extracted molecular ion isotope peaks M, M + 1, and M + 2. B, chromatograms and peak intensity traces for four acquisitions from two samples run in duplicates with heavy peptides spiked at 1 and 3 fmol (S1R1, S1R2, S2R1, and S2R2, respectively). The vertical lines with annotated retention times and identification (ID) mark underlying MS/MS sampling that initially directed MS1 peak picking. C, Skyline displays a library of MS/MS spectra for the selected peptide that provides underlying peptide identification information for a specific acquisition replicate. In this case, the underlying MS/MS spectra for two of the four replicates, S1R1 and S2R2 are shown, although all spectra can be displayed. D and E, established Skyline visual displays previously developed for targeted LC-MRM data processing, include peak area replicate views (D) and retention time replicates (E) (further details on Skyline graphical displays, settings, and parameters see supplemental Figs. S1–S3).