Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Analysis of Peptides

Abstract Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) is a simple, effective, and widely used technique for determining the mass of biomolecules, with exceptional capabilities for mass analysis of peptides. Relative to other ionization techniques, MALDI‐MS offers a high tolerance of salts and other common buffer components. MALDI‐MS ionization of peptides results in predominantly singly charged, protonated ion species (M+H + ), rendering analysis relatively straightforward. MALDI‐TOF/TOF‐MS instruments enable true tandem MS/MS fragmentation of peptide ions, facilitating peptide sequencing and identity. Routine detection limits for peptides are in the low parts per million range. This unit will focus on the application of MALDI‐MS to the analysis of peptides on time‐of‐flight (TOF) mass spectrometers. Instrument configuration and calibration, matrix options, and sample preparation are discussed. Finally, this unit describes methods for obtaining sequence information on peptides by tandem mass spectrometry. Curr. Protoc. Protein Sci . 77:16.2.1‐16.2.11. © 2014 by John Wiley & Sons, Inc.