Skyline MS1 filtering graphical user interface. 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). Birgit Schilling et al. Mol Cell Proteomics 2012;11:202-214 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.