MS-based proteomics: A short introduction to the core concepts of proteomics and mass spectrometry

A short introduction to the core concepts of MS-based proteomics, which is the use of mass spectrometry to simultaneously measure the abundances, post-translational modifications (PTMs), or interactions of many proteins. I will start by introducing the diverse types of proteomics experiments, how mass spectrometry works, how it is usually combined to do liquid chromatography tandem mass spectrometry (LC-MS-MS), and how it can be used to do either non-targeted or targeted proteomics. I will then move on to the computational aspects of how one can identify what the spectra are and estimate false discovery rate. I explain the differences between label-free and label-based quantification methods and, finally, how statistical analysis is performed to identify statistically significant regulation of proteins, modifications, or interactions.

0:00 Introduction: definition of proteomics, the many flavors, and the steep learning curve
0:41 Experiment types: top-down vs. bottom-up proteomics, quantitative proteomics, phosphoproteomics, PTMs, and affinity purification-mass spectrometry
2:27 Mass spectrometry: a fancy scale, ionization, deflection, detection, mass-to-charge ratio, and peak intensity
3:44 LC-MS-MS: liquid chromatography, tandem mass spectrometry, non-targeted proteomics, and targeted proteomics
5:54 Identification of spectra: de novo peptide sequencing, database search, computed fragment spectra, spectral libraries, peptide spectral matches (PSMs), decoy spectra, false discovery rate, and protein groups
7:54 Quantification: label-free quantification (LFQ), stable isotope labeling, and advantages of comparison within runs vs. between runs
9:33 Statistical analysis: MS-specific analysis software, normalization, and statistical tests