title: Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification.
abstract: Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross-references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel system can be used to predict its mobility in the other. Thus, as laboratories adopt the immobilized pH gradient-based 2-D gel systems, the only reliable means of translating the data gained with the carrier ampholyte-based gel system is to positively identify the proteins in both 2-D systems.
authors.affiliation: Center for Proteome Analysis in Life Sciences, International Science Park Odense, Denmark.
authors.forename: A
authors.initials: A
authors.lastname: Nawrocki
authors.forename: M R
authors.initials: MR
authors.lastname: Larsen
authors.forename: A V
authors.initials: AV
authors.lastname: Podtelejnikov
authors.forename: O N
authors.initials: ON
authors.lastname: Jensen
authors.forename: M
authors.initials: M
authors.lastname: Mann
authors.forename: P
authors.initials: P
authors.lastname: Roepstorff
authors.forename: A
authors.initials: A
authors.lastname: Görg
authors.forename: S J
authors.initials: SJ
authors.lastname: Fey
authors.forename: P M
authors.initials: PM
authors.lastname: Larsen
mesh_terms: D000665:Ampholyte Mixtures / Q000737:chemistry*; D016208:Databases, Factual; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D005656:Fungal Proteins / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D007525:Isoelectric Focusing / Q000379:methods; D012441:Saccharomyces cerevisiae; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods
chemical_list: D000665:Ampholyte Mixtures; D005656:Fungal Proteins