Abstract Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of four exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analysed by focusing on two datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings and skill levels. Competing Interest Statement B.C.S. is a founder and shareholder in Proteome Software, which operates in the field of proteomics. B.S. is the CEO at Bioinformatics Solutions Inc., which creates software for the field of proteomics. The other authors declare no competing interests. Footnotes * https://doi.org/doi:10.25345/C5819R...

2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study

10.1101/2020.11.20.391300