Shotgun protein identification and quantification by mass spectrometry.
Shotgun proteomics is based on identification and quantification of peptides from digested proteins using tandem mass spectrometry. In this chapter, we discuss computational methods to analyze tandem mass spectra of peptides, including database searching, de novo peptide sequencing, hybrid approaches, library searching, and unrestricted modification search. A special focus is given to database searching programs since they are most widely used. The process of inferring proteins from identified peptides is then discussed. We also provide description of key steps in the quantitative analysis of mass spectrometry proteomics data.
Lu
Bingwen
B
Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Xu
Tao
T
Park
Sung Kyu
SK
Yates
John R
JR
D030562:Databases, Protein; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis; D011506:Proteins / Q000032:analysis*; D020539:Sequence Analysis, Protein / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010446:Peptide Fragments; D011506:Proteins