Proteomics is the study of proteomes, which are the collections of proteins expressed in cells. Whereas genomes are essentially invariant in different cells in an organism, proteomes vary from cell to cell, with time and as a function of environmental stimuli and stress.Proteome analysis of Arabidopsis peroxisomes has been established as the major unbiased approach for identifying new peroxisomal proteins on a large scale.Proteomics relies on three basic technological cornerstones that include a method to fractionate complex protein or peptide mixtures, MS to acquire the data necessary to identify individual proteins, and bioinformatics to analyze and assemble the MS data.