Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

ABSTRACT: The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstra

SUBMITTER: Walzer M 

PROVIDER: S-EPMC9197839 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature