Collins, B.C. et al. Nat. Commun. 8, 291 (2017).

SWATH is a data-independent acquisition-based mass spectrometry (MS) technique for detecting and quantifying peptides of interest in a targeted fashion. This and other data-independent acquisition techniques are growing in popularity in proteomics, as they are not subject to the same stochastic sampling issues as traditional data-dependent acquisition-based MS. Collins et al. recently performed a large-scale study to assess the reproducibility of SWATH-MS in 11 labs around the world. Each lab evaluated an identical sample consisting of stable-isotope-labeled standard peptides spiked into an HEK293 cell digest. Each lab also acquired MS data in equivalent ways: i.e., they used the same instrument and same data acquisition parameters. The authors found that the data produced in the different labs were both qualitatively and quantitatively similar, and all labs consistently detected and quantified more than 4,000 proteins with good sensitivity and dynamic range.