README.md

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

This Github repository conatins the text, code and data for the workflow written by Hutchings et al. entitled "A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data", submitted to F1000Research, 29th June 2023.

Data:

• The raw mass spectrometry data and output data from Proteome Discoverer can be found on the PRIDE database under identifier PXD041794
• The necessary PSM, peptide and protein level data output from Proteome Discoverer can also be found at (1) Zenodo at https://zenodo.org/record/11196770 and (2) in the top level of this directory
• The PSM-level TMT-labelled data is found in cell_pellet_tmt_results_psms.txt and the peptide-level label-free data is found in supernatant_lfq_results_peptides.txt. Please see the workflow for details.

Manuscipt:

• The workflow is available in R Markdown and PDF in the main repo
• The accomanying appendix is also available