An updated Bioconductor workflow for correlation profiling subcellular proteomics

Files for users of the workflow "An updated Bioconductor workflow for correlation profiling subcellular proteomics". Files include the Proteome Discoverer (v3.1) processing and consensus workflows used to process the use case raw MS files. For raw data please refer to PRIDE (dataset identifier PXD055123). Also provided are the files required for users to run the workflow on the use-case data. This includes the PSM and protein-level output .txt files corresponding the the Proteome Discoverer identification search, the mrk.csv file containing subcellular markers and the bandleres.rda and tagm_mcmc_params.rda files for users to load the bandleres and mcmc_model objects. The Appendix is provided as a pdf file. The Appendix contains information about 1) the identification search of the use-case data with Proteome Discoverer, 2) alternative data import methods, 3) how to adapt the workflow to MaxQuant output data, and 4) an example DIA correlation profiling workflow using data output from DIA-NN. The input files required to run the example DIA workflow are also provided here (diann_report.tsv and 220813_Universal_Protein_Contaminants_HaoGroup_modified.fasta). Finally, the .Rmd file containing the code used to generate the final F1000 publication is provided, along with a .pdf file of the publication