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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 misinterpretation of charge state and modifications. (A) Assignment of an MS/MS spectrum with a triply charged peptide, ^PY^PTLVLTDPDAPSR, by the Mascot algorithm with a Mascot score of 32. (B) Assignment of the same MS/MS spectrum with a doubly charged unmodified VLTDPDAPSR with a Mascot score of 51.

False peptide identification caused by misinterpretation of charge state and modifications. (A) Assignment of an MS/MS spectrum with a triply charged peptide, ^PY^PTLVLTDPDAPSR, by the Mascot algorithm with a Mascot score of 32. (B) Assignment of the same MS/MS spectrum with a doubly charged unmodified VLTDPDAPSR with a Mascot score of 51.