A Typical Experimental Workflow of Protein Identification and Characterisation Using MS/MS Data

Protein identification and characterisation play very crucial roles in some biological experiments. In this post, we are going to introduce the main workflow of protein identification and characterisation by using MS/MS data.

This experiment is beginning with protein samples, which can be a single protein or a complex mixture of proteins. And then an enzyme, such as trypsin can be used to digest the proteins to peptides. In most cases, one even more stages of chromatography can be used to regulate the flow of peptides into the mass spectrometer. By using the first stage of mass analysis, peptides are selected one at a time. And then these isolated peptides are induced to fragment possibly by collision. The second stage of mass analysis is used to capture MS/MS spectrum.

Following are the detailed workflow of this experiment:


These are the typical experimental workflow details. Hope this can be useful for new researchers.

Reference: http://www.sciencedirect.com/science/article/pii/S1874391911002053