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Large-Scale Identification of Caenorhabditis elegans Proteins by Multidimensional Liquid Chromatography−Tandem Mass Spectrometry

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Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan, Integrated Proteomics System Project, Pioneer Research on Genome the Frontier, MEXT, Japan, and Department of Applied Bioscience, United Graduate School of Agriculture Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
Cite this: Journal of Proteome Research 2003, 2, 1, 23–35
Publication Date (Web):October 16, 2002
Copyright © 2003 American Chemical Society

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    A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-resolution hybrid mass spectrometer with an automated data analysis system. Soluble and insoluble protein fractions were prepared from a mixed growth phase culture of the worm C. elegans, digested with trypsin, and fractionated separately on the 2DLC system. The separated peptides were directly analyzed by on-line ESI−MS/MS in a data-dependent mode, and the resultant spectral data were automatically processed to search a genome sequence database, wormpep 66, for protein identification. The total number of proteins of the composite proteome identified in this method was 1616, including 110 secreted/targeted proteins and 242 transmembrane proteins. The codon adaptation indices of the identified proteins suggested that the system could identify proteins of relatively low abundance, which are difficult to identify by conventional 2D-gel electrophoresis (GE) followed by an offline mass spectrometric analysis such as peptide mass fingerprinting. Among the ∼5400 peptides assigned in this study, many peptides with post-translational modifications, such as N-terminal acetylation and phosphorylation, were detected. This expression profile of C. elegans, containing 571 hypothetical gene products, will serve as the basic data of a major proteome set expressed in the worm.

    Keywords: liquid chromatography • tandem mass spectrometry • peptide signature • C. elegans

     Tokyo Metropolitan University.

     These authors contributed equally to this work.


     To whom correspondence should be addressed. Fax:  81-426-77-2525. E-mail:  [email protected].



     Tokyo University of Agriculture and Technology.

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