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Peptide sequence tag
Introduction
A peptide sequence tag is a piece of information about a peptide obtained by tandem mass spectrometry that can be used to identify this peptide in a protein database.[1][2][3]
Mass spectrometry
Mass spectrometry
In general, peptides can be identified by fragmenting them in a mass spectrometer. For example, during collision-induced dissociation peptides collide with a gas within the mass spectrometer and break into pieces at their peptide bonds. The resulting fragment ions (called b-ions and y-ions) have mass differences corresponding to the residue masses of the respective amino acids. Thus, a tandem mass spectrum contains partial information about the amino acid sequence of the peptide. The peptide sequence tag approach, developed by Matthias Wilm and Matthias Mann at the EMBL,[4] uses this information to identify the peptide in a database. Briefly, a couple of masses is extracted from the spectrum in order to obtain the peptide sequence tag. This peptide sequence tag is a unique identifier of a specific peptide and can be used to find it in a database containing all possible peptide sequences.
Peptide fragment notation
Peptide fragment notation
A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum.[5] Peptide fragment ions are indicated by a, b, or c if the charge is retained on the N-terminus and by x, y or z if the charge is maintained on the C-terminus. The subscript indicates the number of amino acid residues in the fragment.
References
References
- ↑ Hardouin J (2007). “Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry”. Mass spectrometry reviews. 26 (5): 672–82. doi:10.1002/mas.20142. PMID 17492750.
- ↑ Shadforth I, Crowther D, Bessant C (2005). “Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines”. Proteomics. 5 (16): 4082–95. doi:10.1002/pmic.200402091. PMID 16196103.
- ↑ Mørtz E, O’Connor PB, Roepstorff P, Kelleher NL, Wood TD, McLafferty FW, Mann M (1996). “Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases”. Proc. Natl. Acad. Sci. U.S.A. 93 (16): 8264–7. PMID 8710858.
- ↑ Mann M, Wilm M (1994). “Error-tolerant identification of peptides in sequence databases by peptide sequence tags”. Anal. Chem. 66 (24): 4390–9. PMID 7847635.
- ↑ 5.0 5.1 Roepstorff P, Fohlman J (1984). “Proposal for a common nomenclature for sequence ions in mass spectra of peptides”. Biomed. Mass Spectrom. 11 (11): 601. doi:10.1002/bms.1200111109. PMID 6525415.