Synonyms
Definition
Protein identification analysis describes the process by which the protein contents of cellular and biological samples are identified through interrogation by mass spectrometry.
Characteristics
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207
Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24:1285–1292
Craig R, Beavis RC (2004) Tandem: matching proteins with tandem mass spectra. Bioinformatics 20:1466–1467
Eng JK, McCormack AL, Yates JR III (1994) An approach to correlate tandem mass spectra data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989
Hather G, Higdon R, Bauman A, von Haller PD, Kolker E (2010) Estimating false discovery rates for peptide and protein identification using randomized databases. Proteomics 10:2369–2373
Higdon R, Kolker E (2007) A predictive model for identifying proteins by a single peptide match. Bioinformatics 23:277–280
Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74:5383–5392
Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75:4646–4658
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–3567
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this entry
Cite this entry
Higdon, R. (2013). Protein Identification Analysis. In: Dubitzky, W., Wolkenhauer, O., Cho, KH., Yokota, H. (eds) Encyclopedia of Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-9863-7_1208
Download citation
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1208
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4419-9862-0
Online ISBN: 978-1-4419-9863-7
eBook Packages: Biomedical and Life SciencesReference Module Biomedical and Life Sciences