title: A molecular scanner to automate proteomic research and to display proteome images.
abstract: Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today's commonly used high-throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, a number of limitations still adversely affect the rate of protein identification and annotation in 2-DE databases: the sequential excision process of pieces of gel containing protein; the enzymatic digestion step; the interpretation of mass spectra (reliability of identifications); and the manual updating of 2-DE databases. We present a highly automated method that generates a fully annoated 2-DE map. Using a parallel process, all proteins of a 2-DE are first simultaneously digested proteolytically and electro-transferred 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 proteome that contains interpreted PMF data in addition to protein identification results. This "MS-imaging" method represents a major step toward the development of a clinical molecular scanner.
authors.affiliation: Swiss Institute of Bioinformatics, University Medical Center, Geneva, Switzerland. Pierre-Alain.Binz@dim.hcuge.ch
authors.forename: P A
authors.initials: PA
authors.lastname: Binz
authors.forename: M
authors.initials: M
authors.lastname: Müller
authors.forename: D
authors.initials: D
authors.lastname: Walther
authors.forename: W V
authors.initials: WV
authors.lastname: Bienvenut
authors.forename: R
authors.initials: R
authors.lastname: Gras
authors.forename: C
authors.initials: C
authors.lastname: Hoogland
authors.forename: G
authors.initials: G
authors.lastname: Bouchet
authors.forename: E
authors.initials: E
authors.lastname: Gasteiger
authors.forename: R
authors.initials: R
authors.lastname: Fabbretti
authors.forename: S
authors.initials: S
authors.lastname: Gay
authors.forename: P
authors.initials: P
authors.lastname: Palagi
authors.forename: M R
authors.initials: MR
authors.lastname: Wilkins
authors.forename: V
authors.initials: V
authors.lastname: Rouge
authors.forename: L
authors.initials: L
authors.lastname: Tonella
authors.forename: S
authors.initials: S
authors.lastname: Paesano
authors.forename: G
authors.initials: G
authors.lastname: Rossellat
authors.forename: A
authors.initials: A
authors.lastname: Karmime
authors.forename: A
authors.initials: A
authors.lastname: Bairoch
authors.forename: J C
authors.initials: JC
authors.lastname: Sanchez
authors.forename: R D
authors.initials: RD
authors.lastname: Appel
authors.forename: D F
authors.initials: DF
authors.lastname: Hochstrasser
mesh_terms: D001331:Automation; D001798:Blood Proteins / Q000032:analysis / Q000737:chemistry; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods; D014360:Trypsin Inhibitor, Kunitz Soybean / Q000032:analysis / Q000737:chemistry
chemical_list: D001798:Blood Proteins; D014360:Trypsin Inhibitor, Kunitz Soybean