  The ultimate goal of proteomic analysis of a cell compartment should be the
exhaustive identification of resident proteins; excluding proteins from other
cell compartments. Plant cell walls possess specific difficulties. Several
reported procedures to isolate cell walls for proteomic analyses led to the
isolation of a high proportion (more than 50%) of predicted intracellular
proteins. The rationales of several published procedures to isolate cell walls
for proteomics were analyzed, with regard to the bioinformatic-predicted
subcellular localization of the identified proteins. A new procedure was
developed to prepare cell walls from etiolated hypocotyls of Arabidopsis
thaliana. After salt extraction, a high proportion of proteins predicted to be
secreted was released (73%), belonging to the same functional classes as
proteins identified using previously described protocols. The new cell wall
preparation described in this paper gives the lowest proportion of proteins
predicted to be intracellular when compared to available protocols. The
application of its principles should lead to a more realistic view of the cell
wall proteome, at least for the weakly bound CWP extractable by salts. In
addition, it offers a clean cell wall preparation for subsequent extraction of
strongly bound CWP.
