Version 2 for f1000

In response to software updates in the QFeatures R package in Bioconductor (April 2024) we have updated the code in this workflow for compatibility with QFeatures >= v1.14.0, specifically code relating to data import and the downstream plotting of the data.
Following suggestions from the reviewers and to help users make the most out of this workflow, we have provided information on how to adapt the workflow from Proteome Discoverer files to those generated by MaxQuant, a free and accessible search software. This information is provided in a new section in the Appendix located in the associated Github repository (https://github.com/CambridgeCentreForProteomics/f1000_expression_proteomics/blob/main/appendix.pdf). We have added a few sentences in the manuscript to further discuss the expectation of missing values in quantitative proteomics data. We have also simplified the section on normalisation to enhance readability for users. Lastly, for completeness, we have added a short section “Controlling the false discovery rate”.

Conditional acceptance to F1000

Conditionally accepted for publication to F1000 following editors requests.

Submission to F1000Research

v1.0

Update README.md