This repository provides a landing page to explore the data generated in our study, “A comprehensive meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments,” and the source code used to generate and analyze this data.
Some of the key resources generated by our study are:
- A resource of uniformly processed co-fractionation mass spectrometry (CF-MS) data from 206 different experiments, containing >11 million measurements of protein abundance across almost 13,000 fractions
- An R package, 'CFTK', that implements a variety of analytical approaches to CF-MS data, with the best-performing settings in our analysis of 206 datasets as the defaults
- Predicted CF-MS interactomes for 27 species or clades, including a core CF-MS human interactome at comparable quality to the largest-scale Y2H or AP-MS screens
The easiest way to begin exploring the uniformly processed resource of CF-MS data is through the CF-MS browser. This interactive web application allows you to specify up to ten proteins of interest, using a number of different identifiers (e.g., gene names, UniProt accessions, Entrez gene IDs, or eggNOG orthogroups). The web application will visualize the elution profiles of these proteins in the experiments where they were quantified, or allow you to download the underlying CF-MS data for these proteins only.
For users with more specific needs, all of the data generated in this study is available, at various levels of analysis, from the following locations:
- CF-MS-browser (https://cf-ms-browser.msl.ubc.ca): download processed CF-MS chromatograms for up to ten proteins through an interactive web application
- Download all of the processed CF-MS chromatograms from Zenodo (doi: 10.5281/zenodo.4106578, 152.8 MB)
- Download all of the raw MaxQuant output files from PRIDE (accession: PXD022048, 92 GB)
- Download predicted interactomes for 27 species and clades, including the consensus human CF-MS interactome, from Zenodo (doi: 10.5281/zenodo.4245282, 2.5 GB)
Source code is available from the following repositories:
- The CFTK R package is available from https://github.com/skinnider/fosterlab/CFTK. To install it, simply run
devtools::install_github(fosterlab/CFTK), or see the package README for more detailed instructions. - The code used to download published CF-MS data from ProteomeXchange repositories and re-analyze it using MaxQuant is available from https://github.com/skinnider/CF-MS-searches
- The code used to carry out the analyses presented in the paper is available from https://github.com/skinnider/CF-MS-analysis
- The code for the CF-MS browser is available from https://github.com/skinnider/CF-MS-browser
For any questions, please contact Leonard Foster (foster at msl dot ubc dot ca).