A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data.

ABSTRACT: Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quant

SUBMITTER: Hutchings C 

PROVIDER: S-EPMC10683783 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature