A web-based search tool for visualizing instrument performance using the Triple Knockout (TKO) proteome standard

ABSTRACT: Multiplexing strategies are at the forefront of mass spectrometry-based proteomics, with SPS-MS3 methods becoming increasingly commonplace. A known caveat of isobaric multiplexing is interference resulting from co-isolated and co-fragmented ions that do not originate from the selected precursor of interest. The triple knockout (TKO) standard was designed to benchmark data collection strategies to minimize interference. However, a limitation to its widespread use has been the lack of an automated analysis platform. Here, we present a TKO Visualization Tool (TVT). The TVT viewer allows for automated, web-based, database searching of the TKO standard, returning traditional figures of merit, such as peptide and protein counts, scan-specific ion accumulation times, as well as the TKO-specific metric, the IFI (interference-free index). Moreover, the TVT viewer allows for plotting of multiple TKO standards to assess protocol optimizations, compare instruments, or measure degradation of instrument performance over time. To showcase the TVT viewer, we investigated the selection of 1) stationary phase resin, 2) MS2 isolation window width, and 3) number of SPS ions for SPS-MS3 analysis. Using the TVT viewer will allow the proteomics community to search and compare TKO results to optimize user-specific data collection workflows.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Bos Taurus (bovine) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Joao Paulo  

LAB HEAD: Joao A. Paulo

PROVIDER: PXD011654 | Pride | 2018-12-04

REPOSITORIES: Pride