An Introduction to Mass Spectrometry-Based Proteomics

Mass spectrometry is unmatched in its versatility forstudyingpractically any aspect of the proteome. Because the foundations ofmass spectrometry-based proteomics are complex and span multiple scientificfields, proteomics can be perceived as having a high barrier to entry.This tutorial is intended to be an accessible illustrated guide tothe technical details of a relatively simple quantitative proteomicexperiment. An attempt is made to explain the relevant concepts tothose with limited knowledge of mass spectrometry and a basic understandingof proteins. An experimental overview is provided, from the beginningof sample preparation to the analysis of protein group quantities,with explanations of how the data are acquired, processed, and analyzed.A selection of advanced topics is briefly surveyed and works for furtherreading are cited. To conclude, a brief discussion of the future ofproteomics is given, considering next-generation protein sequencingtechnologies that may complement mass spectrometry to create a fruitfulfuture for proteomics.