ABRF PRG STUDY TO EVALUATE DATA-INDEPENDENT ACQUISITION FOR PROTEIN QUANTIFICATION IN CORE FACILITY SETTINGS

The field of proteomics is on the cusp of realizing the promise of Data-Independent Acquisition (DIA), but there is still a need to develop best practices and improve opportunity for adoption. The Proteomics Research Group (PRG) within the Association of Biomolecular Resource Facilities (ABRF) conducted a study to promote adoption of DIA. We developed a study sample set consisting of a HeLa digest spiked with four non-human proteins at different concentrations. These samples were sent to 63 labs from 20 countries around the globe. We provided participants recommended LC gradients and DIA methods for specific instrument platforms, as well as guidelines for method generation on other platforms. Samples were injection-ready, and data was analyzed by PRG members. Of the 63 labs, 40 labs uploaded data as of January 2019, 53 labs filled out survey, and 35 data sets were used for preliminary analysis. Based on survey information, most participants were experienced LCMS users, but few had previously used DIA. Data from most participants reflects expected fold-change of spike-in proteins. Interestingly, accuracy of quantitation was not correlated to previous DIA experience. Overall, by providing a standard sample set and recommended methods for different instrument platforms, and extended trial software licenses for users, the PRG provided an opportunity for labs to evaluate their readiness to carry out DIA analysis. Ongoing work will analyze the complete data set as more labs completed the study after this pilot analysis, providing additional opportunities to evaluate LC and instrument parameters.