A molecular scanner to automate proteomic research and to display proteomeimages

Identification and characterization of all proteins expressed by a genome i n biological samples represent major challenges in proteomics. Today's comm only used high-throughput approaches combine two-dimensional electrophoresi s (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automati on is often possible, a number of limitations still adversely affect the ra te of protein identification and annotation in 2-DE databases: the sequenti al excision process of pieces of gel containing protein; the enzymatic dige stion step; the interpretation of mass spectra (reliability of identificati ons); and the manual updating of 2-DE databases. We present a highly automa ted method that generates a fully annotated 2-DE map. Using a parallel proc ess, all proteins of a 2-DE are first simultaneously digested proteolytical ly and electrotransferred onto a poly(vinylidene difluoride) membrane. The membrane is then directly scanned by MALDI-TOF MS. After automated protein identification from the obtained peptide mass fingerprints using PeptIdent software (http://www.expasy.ch/tools/peptident.html), a fully annotated 2-D map is created on-line. It is a multidimensional representation of a prote ome that contains interpreted PMF data in addition to protein identificatio n results. This "MS-imaging" method represents a major step toward the deve lopment of a clinical molecular scanner.