Bioinformatics tools to identify and quantify proteins using mass spectrometry data

So Young Ryu

doi:10.1016/B978-0-12-800168-4.00001-9

Bioinformatics tools to identify and quantify proteins using mass spectrometry data

Adv Protein Chem Struct Biol. 2014:94:1-17. doi: 10.1016/B978-0-12-800168-4.00001-9.

Author

So Young Ryu¹

Affiliation

¹ Stanford Genome Technology Center, Biochemistry Department, Stanford University, Stanford, California, USA. Electronic address: clairesr@stanford.edu.

PMID: 24629183
DOI: 10.1016/B978-0-12-800168-4.00001-9

Abstract

Proteomics tries to understand biological function of an organism by studying its protein expressions. Mass spectrometry is used in the field of shotgun proteomics, and it generates mass spectra that are used to identify and quantify proteins in biological samples. In this chapter, we discuss the bioinformatics algorithms to analyze mass spectrometry data. After briefly describing how mass spectrometry generates data, we illustrate the bioinformatics algorithms and software for protein identification such as de novo approach and database-searching approach. We also discuss the bioinformatics algorithms and software to quantify proteins and detect the differential proteins using isotope-coded affinity tags and label-free mass spectrometry data.

Keywords: Bioinformatics; Mass spectrometry; Protein identification; Protein quantification; Proteomics; Software.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Amino Acids / chemistry
Computational Biology*
Databases, Protein
Mass Spectrometry / methods*
Proteins / analysis
Proteins / chemistry*

Substances

Amino Acids
Proteins

Grants and funding

T32-GM007035/GM/NIGMS NIH HHS/United States