Today we would like to announce a landmark article on statistical analysis of large-scale DIA analysis published in Nature Methods titled “Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses”. The study was performed by the Ruedi Aebersold’s lab in a collaborative effort with other leading scientists in the proteomics field and also with Biognosys participation.
The article discusses the adaptation of statistical concepts developed for DDA proteomics to large-scale DIA experiments and provide some guidance on their application. The study finds that error rate control on the peptide query-level only is insufficient in experiments employing comprehensive spectral libraries. Furthermore, controlling the protein false discovery rate (FDR) in a global, experiment-wide context was found to be very important for the quality and reproducibility of proteomic results when using comprehensive spectral libraries. In line with these results Biognosys implemented the protein FDR as a feature enabled by default in its latest release of Spectronaut Pulsar software.
The article is available on the Nature Methods homepage here.
In case you would like to hear more about Protein FDR implementation in Spectronaut Pulsar please don’t hesitate to contact us at firstname.lastname@example.org.