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

[keerthana]

You summarised my entire semester of listening to droning lectures. I don't know why we don't have more effective teaching in schools. THIS WAS SO MUCH BETTER.

[sarah_knig]

"A mass spectrometre is nothing but a fancy scale" is definitely a quote I will remember :D

[gastonvaghi]

Terrific! Great summary of proteomic process. Very clear and easy to understand, even if you do not know much about MS-based proteomics.

[laurencebindschedler-spanu]

Lovely 10 min course, a great introduction for students!

[biruk]

This is a very great introduction for beginners in HRMS. Thank you.

[JS]

This was such a great overview, thank you so much!! 😊

[IgnatiusPang]

An excellent introduction and as you said it is a difficult one to fit in 10 mins and you did it.

[BrandonNewell]

This was really well done. Thank you, it actually helped me a great deal

[iot]

Thank you for the excellent presentation Professor. I have a question if you could answer or link to another video of you would be greatful.

What are the different types of proteomics quantification methods?

1. Does it always LC-MSMS data analysis use peak area of XIC for quantification? Is isn’t possible to use peak intensity values?
2. In Label Free Quantification (LFQ / MaxQuant) what does it use ? What is the mechanism behind this?

[MohsenDana-sulq]

That was great! Thank you. But I dont know which Maxquant output should I use for DEP analysis. Which files?

[mongolitosking]

Does the multiplex approach that you mentioned refers to the SWATH method ?

[kajalpanchal]

hey! this is a great overeview, cn you share proper refeerences

[toddrinaldi]

What do you think of Quantum SI's approach? Will they become the leader in single molecule, protein sequencing?

[apostolismoschopoulos]

can someone explain what does the peak intensity mean? it is the number of ions we measure that have the same m/z ratio? How do we use this information? Also, does it relate with the term 'base peaks'?

[padmas]

Why are you reading. Can you just explain informally at a slow pace.