Identification of individual proteins in complex protein mixtures by high-resolution, high-mass-accuracy MALDI TOF-mass spectrometry analysis of in-solution thermal denaturation/enzymatic digestion.

Identification of individual proteins in complex protein mixtures by high-resolution (HR), high-mass-accuracy matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is demonstrated for synthetic protein mixtures. Instead of chemical denaturation, thermal denaturation followed by in-solution trypsin digestion is used to achieve uniform digestion of the constituents of the protein mixture. Protein identification is carried out using protein database searches with search scoring systems, which seems more effective than conventional peptide mass mapping without using a scoring system. Identification of individual proteins by MALDI HR-TOF-MS peptide mass mapping dramatically reduces data acquisition/analysis time and does not require special equipment for sample preparation/transfer prior to mass spectral analysis.