Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry
Abstract
Proteomics 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.
Keywords
Cite
@article{arxiv.2311.07791,
title = {Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry},
author = {Yuming Jiang and Devasahayam Arokia Balaya Rex and Dina Schuster and Benjamin A. Neely and Germán L. Rosano and Norbert Volkmar and Amanda Momenzadeh and Trenton M. Peters-Clarke and Susan B. Egbert and Simion Kreimer and Emma H. Doud and Oliver M. Crook and Amit Kumar Yadav and Muralidharan Vanuopadath and Martín L. Mayta and Anna G. Duboff and Nicholas M. Riley and Robert L. Moritz and Jesse G. Meyer},
journal= {arXiv preprint arXiv:2311.07791},
year = {2023}
}