Peptide mass fingerprinting: identification of proteins by MALDI-TOF

MALDI-TOF peptide mass fingerprinting (PMF) is the fastest and cheapest method of protein identification; the studied genome is sequenced and annotated, and the protein is amenable to separation and detection in 2D gel electrophoresis. In plant proteomics there are two main difficulties: few plant genomes are sequenced, and major contaminants are non-plant specific. This chapter describes the classical "bottom-up" method (i.e., from peptide to protein identification) of gel cutting, in-gel digestion, peptide recovery and purification, MALDI-TOF mass spectrometry, and critical survey of protein database queries.