Jiang, YumingRex, Devasahayam Arokia BalayaSchuster, DinaNeely, Benjamin A.Rosano, Germán L.Volkmar, NorbertMomenzadeh, AmandaPeters-Clarke, Trenton M.Egbert, Susan B.Kreimer, SimionDoud, Emma H.Crook, Oliver M.Yadav, Amit KumarVanuopadath, MuralidharanMayta, Martín L.Duboff, Anna G.Riley, Nicholas M.Moritz, Robert L.Meyer, Jesse G.2024-04-172024-04-172023-11-13Jiang Y, Rex DAB, Schuster D, et al. Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry. Preprint. ArXiv. 2023;arXiv:2311.07791v1. Published 2023 Nov 13.https://hdl.handle.net/1805/40084Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.en-USAttribution-NonCommercial-NoDerivatives 4.0 InternationalProteomicsProtein structureProtein functionMass spectrometryArticle