Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.
Michael A SkinniderLeonard J FosterPublished in: Nature methods (2021)
Co-fractionation mass spectrometry (CF-MS) has emerged as a powerful technique for interactome mapping. However, there is little consensus on optimal strategies for the design of CF-MS experiments or their computational analysis. Here, we reanalyzed a total of 206 CF-MS experiments to generate a uniformly processed resource containing over 11 million measurements of protein abundance. We used this resource to benchmark experimental designs for CF-MS studies and systematically optimize computational approaches to network inference. We then applied this optimized methodology to reconstruct a draft-quality human interactome by CF-MS and predict over 700,000 protein-protein interactions across 27 eukaryotic species or clades. Our work defines new resources to illuminate proteome organization over evolutionary timescales and establishes best practices for the design and analysis of CF-MS studies.
Keyphrases
- mass spectrometry
- cystic fibrosis
- liquid chromatography
- multiple sclerosis
- ms ms
- high resolution
- gas chromatography
- capillary electrophoresis
- systematic review
- high performance liquid chromatography
- healthcare
- primary care
- endothelial cells
- randomized controlled trial
- quality improvement
- gene expression
- tandem mass spectrometry
- protein protein
- wastewater treatment
- genome wide
- microbial community
- small molecule
- anaerobic digestion