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

0:00 Introduction: definition of proteomics, its 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 nice scale, ionization, deflection, detection, mass-to-charge ratio and peak intensity
3:44 LC-MS-MS: liquid chromatography, tandem mass spectrometry, untargeted proteomics and targeted proteomics
5:54 Identification of spectra: de novo peptide sequencing, database searching, calculated fragment spectra, spectral libraries, peptide spectral matches (PSMs), decoy spectra, false discovery rates and protein groups
7:54 Quantification: label-free quantification (LFQ), stable isotope labeling and benefits of within-run vs. between-run comparison
9:33 Statistical analysis: MS specific analysis software, normalization and statistical tests

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