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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 false protein modification assignment. (A) Assignment of an MS/MS spectrum with a doubly charged peptide, NIVD^OxMVGLFIENVQ^PSLMAQCR, identified by Mascot with a score of 35. (B) Assignment of the same MS/MS spectrum with a doubly charged peptide, NIVD^OxMVGLFIENVQSL^2OxMAQ^3OxCR, identified by manual inspection.

False peptide identification caused by false protein modification assignment. (A) Assignment of an MS/MS spectrum with a doubly charged peptide, NIVD^OxMVGLFIENVQ^PSLMAQCR, identified by Mascot with a score of 35. (B) Assignment of the same MS/MS spectrum with a doubly charged peptide, NIVD^OxMVGLFIENVQSL^2OxMAQ^3OxCR, identified by manual inspection.