Mass spectrometry (MS) has emerged as a sensitive, versatile, and rapid method for protein identification, following the advent of electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The advantages of MALDI-MS over ESI-MS include its relatively high tolerance to contamination from biological matrices, its high sensitivity, the relative ease of interpreting spectra from mixtures, and the formation of singly protonated molecular ions for tandem analysis. Peptide fingerprint mass mapping and partial peptide sequencing using post-source decay and ladder sequencing by MALDI-MS in combination with algorithms for sequence database interrogation have the potential for identification and structural investigation of proteins. This unit describes in-gel digestion for peptide mass mapping of picomole to subpicomole quantities of protein derived from Coomassie- or silver-stained polyacrylamide gels. After digestion, the peptides are extracted from the gel and mass analyzed.