Profiling of Caenorhabditis elegans proteins using two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry

The nematode Caenorhabditis elegans (C. elegans) is the first animal whose whole 97 Mb genome sequence, encoding ca. 19 000 open reading frames (ORF's ), has been essentially determined. We tried to establish a 2-DE map of the nematode proteome by means of two-dimensional polyacrylamide gel electroph oresis (2-D PAGE). A soluble protein fraction of mixed stages of the worm, wild-type strain N2, was applied to 2-D PAGE. After Coomassie Brilliant Blu e (CBB) staining, 1200 spots were detected and 140 major spots were excised from the gel and subjected to in-gel digestion with Achromobacter protease I (lysyl endopeptidase). Resulting peptides were analyzed by matrix assist ed laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF- MS) followed by peptide mass fingerprinting for protein identification. Wit h this approach we have obtained a two-dimensional electrophoresis (2-DE) p rotein map in which 69 spots were localized as landmarks for comparison of expression profiles to elucidate the basis of various biological events.