Fig. 2. Assessing the background interference, quantitative accuracy, and carrier proteome effect of pasefRiQ.

a A comparison of results from 3 instruments that following analysis of 200 ng of the TMT-TKO yeast digest standard and visualized using the TVT web tool⁶¹. Blue bars, red and green bars represent Δmet6, Δhis4 and Δura2 samples, respectively. (Top) vendor example from an Orbitrap Fusion 2 system using MS3-based quantification. (Middle) vendor example results from a quadrupole Orbitrap system using MS2-based quantification. (Bottom) Results from a pasefRiQ file. b A graph demonstrating the normalized abundance of the E. coli protein TNAa in the two-proteome standard injected at different concentrations on column to illustrate the effects of sample dilution on ratio accuracy. c Quantitative results of a standard protein with a known 5:1 ratio in a two-proteome standard digest with increasing amounts of carrier exceeding 4000x carrier load. d A summary of a second carrier experiment with more precise titrations across between 30x and 300x carrier. Source data are provided as a Source data file.