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The current revolution in proteomics has been generated by the combination of very sensitive mass spectrometers coupled to microcapillary liquid chromatography, specific proteolysis of protein mixtures and software that is capable of searching vast numbers of mass measurements against predicted peptides from sequenced genomes. The challenges of post-genomic plant biology include characterization of protein function, post-translational modifications and composition of protein complexes as well as deciphering protein complements in intracellular compartments - proteomes of cell organelles. In this review we summarize the current mass spectrometry methods currently being used in plant proteomics and discuss the various tagging strategies that are being used for purification and proteomic analysis of plant protein complexes. Abbreviations: BCCD, biotin carboxyl carrier protein domain; CBP, calmodulin-binding protein; CID, collision-induced dissociation; ESI, electrospray ionization; EST, expressed sequence tag; FT-ICR, Fourier transform ion cyclotron resonance; GFP, green fluorescent protein; GST, glutathione S-transferase; HA, haemagglutinin; HILEP, hydroponic isotope labelling of entire plants; His, histidine; HPB, HA-PreScission-Biotin; HPLC, high-performance liquid chromatography; ICAT, isotope-coded affinity tags; ICPL, isotope-coded protein label; iTRAQ, isobaric tag for relative and absolute quantification; LC, liquid chromatography; MALDI, matrix-assisted laser desorption ionization; MBP, maltose-binding protein; MS, mass spectrometry; SDS-PAGE, sodium dodecyl sulphate-polyacrylamide gel electrophoresis; SILAC, stable isotope labelling with amino acids in cell culture; SILIP, stable isotope labelling in planta; Strep, streptavidin; TAP, tandem affinity purification; TBP, TATA-box-binding protein; TOF, time-of-flight; UPLC, ultraperformance liquid chromatography [ABSTRACT FROM AUTHOR]