Improvements in protein identification by MALDI-TOF-MS peptide mapping

A new strategy for identifying proteins in sequence databases by MALDI-MS p eptide mapping is reported. The strategy corrects for systematic deviations of determined peptide molecular masses using information contained in the opened database and thereby renders unnecessary internal spectrum calibrati on. As a result, data acquisition is simplified and less error prone. Perfo rmance of the new strategy is demonstrated by identification of a set of re combinant, human cDNA expression products as well as native proteins isolat ed from crude mouse brain extracts by 2-D electrophoresis. Using one set of calibration constants for the mass spectrometric analyses, 20 proteins wer e identified without applying any molecular weight restrictions, which was not possible without data correction. A sequence database search program ha s been written that performs all necessary calculations automatically, acce ss to which will be provided to the scientific community in the Internet.