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. Author manuscript; available in PMC: 2020 Jul 3.
Published in final edited form as: J Am Soc Mass Spectrom. 2020 Mar 27;31(7):1344–1349. doi: 10.1021/jasms.0c00029

Figure 3.

Figure 3.

Example analysis using the TKOpro9 standard. (A) The TKOpro9 standard is composed of three replicates of deletion strains (Δmet6, Δhis4, and Δura2) each labeled with the specified TMTpro reagent and separated by unit resolution. (B) Schematic of two acquisition methods investigated: the classic Orbitrap-based SPS-MS3 (OT-MS3) and the alternative ion trap-based SPS-MS3 (IT-MS3). We highlight the mass analyzer for each stage of m/z measurement. (C) Bar plot of interference-free index (IFI) for duplicates of the acquisition methods outlined in (B). (D) Combination plot indicating the number of proteins (circle) and peptides (bars) for the acquisition methods outlined in (B). OT, Orbitrap; IT, ion trap.