Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Protein Identification Analysis

  • Roger Higdon
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1208



Protein identification analysis describes the process by which the protein contents of cellular and biological samples are identified through interrogation by mass spectrometry.


The most common method for identifying proteins in biological samples is known as “shotgun” or “bottom-up” proteomics (Aebersold and Mann 2003). The approach is detailed in Fig.  1. The approach typically begins by enzymatically digesting (most commonly with trypsin) protein sequences into peptides and separating them using liquid chromatography (LC), and then analyzing them via tandem mass spectrometry (MS/MS). Tandem mass spectrometry generates data by first analyzing the masses of the peptides eluting from an LC column and then fragmenting those peptides and performing a second round of MS analysis to generate MS/MS spectra.
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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Seattle Children’s Research InstituteSeattleUSA