Targeted proteomics profiling in plasma samples of the Bruneck Study (year 2000 evaluation) was performed using multiple reaction monitoring (PlasmaDive kits; Biognosys AG), which allowed quantification of 92 proteins (for details, see Supplementary Data ). During continuous operation over 2 weeks, the interday relative SD was <20% and <5% without and with adjustment for the peak area of the authentic standard peptides, respectively.
Proteomics analysis of livers from antagomiR-treated mice was performed after an in-solution digest by liquid chromatography tandem mass spectrometry. Differential protein expression was assessed by two methods (for details, seeSupplementary Data ): by spectral counting using a high-mass accuracy instrument (Q-Exactive HF; Thermo Fisher Scientific) and by labeling with Tandem Mass Tags (TMT) (Thermo Fisher Scientific) using the triple-stage mass spectrometry (MS3) capability on an Orbitrap Fusion Tribrid MS (Thermo Fisher Scientific). MS3 can overcome the inherent interference of more commonly used two-stage (MS2) workflows when isobaric labeling strategies are used with complex samples (20 (link)).
Proteomics analysis of livers from antagomiR-treated mice was performed after an in-solution digest by liquid chromatography tandem mass spectrometry. Differential protein expression was assessed by two methods (for details, see