  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.
