Phosphoproteins or phosphopeptides
Alkaline treatment (NaOH, Na2CO2, etc.)
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FIGURE 21.2. Outline of complementary strategies for the specific recovery of PM proteins. The left part of the figure indicates strategies aiming at the recovery of the largest proteome. They allow isolating proteomes differing at least partly by the physicochemical properties of the identified proteins. The compilation of these proteomes led to the more extensive overview of the PM proteome so far. On the right part of the figure, different strategies devoted to the retrieve specific protein categories are listed. See insert for color representation of this figure.
with NaOH  and especially carbonate buffers (Na2CO3 or (NH4)2CO3) was frequently used for the proteome analysis of plant PMs [10, 12-15, 19, 20]. A precise analysis of this set of PM proteomes highlights the high efficiency of carbonate buffers for isolating a large variety of proteins in terms of physicochemical and functional properties.
Treatments of membrane vesicles by organic solvents, like C/M, are expected to extract the most hydrophobic proteins of the analyzed membrane system. It was originally demonstrated that most of the proteins that are extracted in organic solvents contain a high ratio of residues number present in TMDs [21, 22]. This method was applied to A. thaliana PM fractions  in order to retrieve the most hydrophobic proteins of these fractions. Although the yield of proteins extracted from a purified membrane fraction is low (5%) , C/M extraction allows highly hydrophobic proteins to be enriched and, thus, further identified via a proteomics approach.
Salt and alkaline treatments, as well as organic solvent extraction and detergent use, are expected to solubilize proteins from the most hydrophilic to the more hydrophobic ones. Other specific treatments, as shown in the following section, can be applied to PM fraction to extract proteins showing specific features.
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