Simplified Sample Preparation Method for Protein Identification by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: In-Gel Digestion on the Probe Surface

Identification and detailed characterization of complex mixtures of proteins separated by polyacrylamide gel electrophoresis (PAGE) require optimized and robust methods for interfacing electrophoretic techniques to mass spectrometry. Peptide mapping by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS) is used as the first protein screening method in many laboratories because of its inherent simplicity, mass accuracy, sensitivity and relatively high sample throughput. We present a simplified sample preparation method for MALDI MS that enables in-gel digestion of protein samples directly on the MALDI MS metal probe. Removal of detergent and reagents as well as protein reduction and S-alkylation were performed prior to cutting of protein samples from the polyacrylamide gel slab. The general utility of this approach was demonstrated by on-probe digestion and MALDI MS peptide mapping of femtomole amounts of standard proteins isolated by sodium dodecyl sulfate (SDS) PAGE. A representative set of 47 human proteins obtained from a silver stained two-dimensional electrophoretic gel was analyzed by the new method and resulted in a success rate for protein identification similar to that obtained by the traditional protocols for in-gel digestion and MALDI peptide mass mapping of human proteins, i.e. approximately 60%. The overall performance of the novel on-probe digestion method is comparable with that of the standard in-gel sample preparation protocol while being less labor-intensive and more cost-effective due to minimal consumption of reagents, enzymes and consumables. Preliminary data obtained on a MALDI quadrupole-TOF tandem mass spectrometer demonstrated the utility of the on-probe digestion protocol for peptide mass mapping and peptide sequencing on this instrument. Automation of the on-probe protein digestion procedure and its combination with automated MALDI tandem mass spectrometry should be advantageous in proteomics research aimed at the systematic identification and analysis of large sets of proteins from electrophoretic gels.