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 are 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 fragmentation notation using the scheme of Roepstorff and Fohlman (1984).[5]
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.
Prime symbols indicate the number of protons or hydrogens added to the fragment to form the observed ion. For example, y'' denotes the singly charged ion analogous to a protonated peptide, (y''')2+ is a doubly charged ion analogous to a doubly protonated peptide.[6]
^Hardouin J (2007). "Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry". Mass Spectrometry Reviews. 26 (5): 672–82.
Bibcode:
2007MSRv...26..672H.
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10.1002/mas.20142.
PMID17492750.
^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.
PMID16196103.
S2CID38068737.
^Mann M, Wilm M (1994). "Error-tolerant identification of peptides in sequence databases by peptide sequence tags". Anal. Chem. 66 (24): 4390–9.
doi:
10.1021/ac00096a002.
PMID7847635.
^
abRoepstorff 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.
PMID6525415.
^Tang XJ, Thibault P, Boyd RK (October 1993). "Fragmentation reactions of multiply protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation". Anal. Chem.65 (20): 2824–34.
doi:
10.1021/ac00068a020.
PMID7504416.