Multiple derivatization by chemical reactions of analytes for mass spectrometry is disclosed. The derivatizations enhance the use of MS techniques for analyzing protein samples, particularly when the sequence of a polypeptide is determined by tandem MS/MS. Accurate mass analysis techniques are described for use in sequencing polypeptides, together with the use of sequencing data in protein analysis. An apparatus and method for calibrating a mass spectrometer by internally introducing calibration masses at a post-source stage of the mass spectrometer is also provided. Lock mass ions mix with the derivatized polypeptide analyte ions prior to mass analysis.
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