Multidimensional protein identification technology helps in identifying a large number of proteins with EST by sequencing several peptides with MS/MS methods. When ionization and separation of different hydrophobic and hydrophilic peptides in a single process are difficult, a combination of LC-coupled linear ion trap MS and MALDI TOF/TOF can be used for identification of proteins as shown in the present study. We have used this combinational approach to identify membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, which are separated by SDS gel electrophoresis. Although the genome of P. syringae Lz4W has not been sequenced, the known genome sequences of mesophilic Pseudomonas species have been used for the identification of the proteins. Broadly, many membrane proteins, proteins with a wide range of molecular weight and pI including some integral membrane proteins could be identified using this procedure. Some of the identified proteins are involved in low temperature adaptation.