title: Proteomics based on peptide fractionation by SDS-free PAGE.
abstract: Here we demonstrate the usefulness of peptide fractionation by SDS-free polyacrylamide gel electrophoresis and its applicability to proteomics studies. In the absence of SDS, the driving force for the electrophoretic migration toward the anode is supplied by negatively charged acidic amino acid residues and other residues as phosphate, sulfate and sialic acid, while the resulting mobility depends on both the charge and the molecular mass of the peptides. A straightforward method was achieved for SDS-PAGE of proteins, enzyme digestion, peptide transfer and fractionation by SDS-free PAGE, which was named dual-fractionation polyacrylamide gel electrophoresis (DF-PAGE). This method increases the number of identified proteins 2.5-fold with respect to the proteins identified after direct analysis, and more than 80% of assigned peptides were found in unique SDS-free gel slices. A vast majority of identified peptides (93%) have p I values below 7.0, and 7% have p I values between 7.0 and 7.35. Peptide digests that were derived from complex protein mixtures were in consequence simplified as peptides that are positively charged are not recovered in the present conditions. The analysis of a membrane protein extract from Neisseria meningitidis by this approach allowed the identification of 97 proteins, including low-abundance components.
authors.affiliation: Center for Genetic Engineering and Biotechnology, La Habana, Cuba.
authors.forename: Yassel
authors.initials: Y
authors.lastname: Ramos
authors.forename: Elain
authors.initials: E
authors.lastname: Gutierrez
authors.forename: Yoan
authors.initials: Y
authors.lastname: Machado
authors.forename: Aniel
authors.initials: A
authors.lastname: Sánchez
authors.forename: Lila
authors.initials: L
authors.lastname: Castellanos-Serra
authors.forename: Luis J
authors.initials: LJ
authors.lastname: González
authors.forename: Jorge
authors.initials: J
authors.lastname: Fernández-de-Cossio
authors.forename: Yasset
authors.initials: Y
authors.lastname: Pérez-Riverol
authors.forename: Lázaro
authors.initials: L
authors.lastname: Betancourt
authors.forename: Jeovanis
authors.initials: J
authors.lastname: Gil
authors.forename: Gabriel
authors.initials: G
authors.lastname: Padrón
authors.forename: Vladimir
authors.initials: V
authors.lastname: Besada
mesh_terms: D002364:Caseins / Q000032:analysis / Q000737:chemistry; D002851:Chromatography, High Pressure Liquid; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D029968:Escherichia coli Proteins / Q000032:analysis / Q000737:chemistry; D008565:Membrane Proteins / Q000032:analysis / Q000737:chemistry; D009345:Neisseria meningitidis / Q000737:chemistry; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry / Q000302:isolation & purification; D010748:Phosphopeptides / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization; D013300:Streptokinase / Q000032:analysis / Q000737:chemistry; D053719:Tandem Mass Spectrometry; D014357:Trypsin / Q000737:chemistry
chemical_list: D002364:Caseins; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D010446:Peptide Fragments; D010748:Phosphopeptides; D013300:Streptokinase; D014357:Trypsin