In the last decade proteomics studies have gained increasing importance in plant research. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins have been particularly instrumental to characterize proteomes and their modulation during plant development, biotic and abiotic stresses. Despite important advances, plant proteome analysis, including those of model plant species, remain constrained by limitations inherent to proteomics techniques and data interpretation. Here we review the approaches and achievements of proteomics with model plant and crop species (i.e. Arabidopsis and rice) and discuss the current limitations of crop proteomics. We anticipate future directions that could advance the contribution of plant proteomics to crop improvement.