Table I. List of isotopically labeled peptides used to monitor total Ub and various polyUb linkages.
Signature peptides representing isopeptide-linked polyUb linkages are denoted by a superscript “GG” adjacent to the modified lysine. Isotopically labeled amino acids are underlined and italicized. The oxidation state of Met-containing peptides (MQIF, GGMQ, and K6) is denoted by “(ox)” for sulfoxide or “(ox)2” for sulfone. For each peptide, the optimal precursor ion, fragment ion, and collision energy (CE) used in the SRM transition are shown. Dwell times correspond to those used in a segmented SRM analyses where the four colored regions of the table represent the distribution of peptides into four segments based on chromatographic retention time. For Orbitrap data, accurate precursor ion m/z values shown in the Light and Heavy Q1 columns are used to generate narrow window extracted ion chromatograms.
