Protocol

General Method for MALDI-MS Analysis of Proteins and Peptides

This protocol was adapted from "The Use of Mass Spectrometry in Proteomics," in Proteins and Proteomics (ed. Simpson). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2003.

INTRODUCTION

For MALDI-TOF-MS analysis of proteins and peptides, samples are cocrystallized with an excess of organic matrix that absorbs at a specific wavelength (usually, UV_337nm). Typically, sinapinic acid (SA) is the matrix of choice for large proteins, whereas -cyano-4-hydroxy-cinnamic acid (HCCA) is the preferred matrix for peptide mapping. Following a short laser pulse, analytes are protonated and desorbed into the gas phase, and their m/z values are determined in a TOF mass analyzer. Mass accuracy determinations vary from ±0.01% to 0.1% depending on the sample preparation technique and the method used for mass calibration.