Proteomics

As I’m alway curious what is Mass Spectrometry for proteomics study. So today finally I spend sometime to learn it . The paper I mainily read is “Introduction to Compuational Proteomics” from Jacques Colinge and Keiryn L. Bennett and website of Thermo Fisher Scientific.

Now I’m still not know the details of MS but a genenral impression. From my understanding. In a typical proteomics study:

  1. It first involves preotein sepration, enzymatic digestion of separated proteins and further separation of produced peptide.
  2. Then a ion source will be used to ionized peptides. Previous to this step, peptide is ususaly vaporized.
  3. Then the ions/peptides will pass mass analyzer in which either electic or magnetic fields are applied. So the time of ions passing the analyzer and maybe be other metrics are mainly decided by the mass-to-charge ratio(m/z) of these peptides and detected by ion detector at the end of whole pipeline
  4. In the end, after ions and their m/z ratios were collected, these ions/peptides will be serached against some popular protein database for further protein identification,chracterization, quantification and so on. Usually not protein sequences in proteins database are used directy but first be digested into a set of peptides in silico .

Schemetic of basic components of Mass Spectrometer from Thermo Fisher webiste

Scementic of basic components of Mass Spectrometer from Thermo Fisher webiste