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. Author manuscript; available in PMC: 2010 Jun 1.

Published in final edited form as: J Proteome Res. 2009 Jun;8(6):3141–3147. doi: 10.1021/pr900172v

False peptide identification caused by enzymatic digestion at an abnormal site. (A) Assignment of an MS/MS spectrum with a triply charged peptide, VL^OxML^PTLQNDPPSLETGVQDK, which was identified by Mascot with Mascot score of 36. (B) Assignment of the same MS/MS spectrum with a doubly charged peptide, QNDPPSLETGVQDK, identified by manual inspection. The labels b and y designate the N- and C-terminal fragment ions, respectively, of the peptide produced by breakage at the peptide bond in the mass spectrometer. The label a designates N-terminal fragments produced by breakage at the backbone C-C bond adjacent to the peptide bond. The subscripted number in each label represents the number of N- or C-terminal residues present in the peptide fragment. The label Δ designates b, y or a ions with loss of water, ammonia or both. All unassigned peaks with relative intensity more than 5% of the base peak are labeled with a question mark. The same nomenclature system is used for all the other figures.

False peptide identification caused by enzymatic digestion at an abnormal site. (A) Assignment of an MS/MS spectrum with a triply charged peptide, VL^OxML^PTLQNDPPSLETGVQDK, which was identified by Mascot with Mascot score of 36. (B) Assignment of the same MS/MS spectrum with a doubly charged peptide, QNDPPSLETGVQDK, identified by manual inspection. The labels b and y designate the N- and C-terminal fragment ions, respectively, of the peptide produced by breakage at the peptide bond in the mass spectrometer. The label a designates N-terminal fragments produced by breakage at the backbone C-C bond adjacent to the peptide bond. The subscripted number in each label represents the number of N- or C-terminal residues present in the peptide fragment. The label Δ designates b, y or a ions with loss of water, ammonia or both. All unassigned peaks with relative intensity more than 5% of the base peak are labeled with a question mark. The same nomenclature system is used for all the other figures.