title: Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins.
abstract: Recently, multidimensional shotgun proteomics has proven to be an alternative technology able to identify hundreds of proteins from single samples. Two major limitations of the technology are the presence of high abundance proteins (e.g. RUBISCO in plant leaf tissue) and the enormous number of co-eluting peptides that overstrain the loading and resolving capacity of conventional particle-packed columns as well as the capacity of electrospray ionisation due to ion suppression. Here, the coupling of fast performance liquid chromatography (FPLC) pre-fractionation of an Arabidopsis leaf protein extract and subsequent two-dimensional liquid chromatography/mass spectrometry with improved resolution using a monolithic silica C18 capillary column allowed the identification of 1032 unique proteins in a single 4 mg total protein plant leaf tissue sample. The reassignment of peptide IDs to distinct FPLC protein fractions enhances the identification procedure, especially in the case of present protein isoforms. The proposed strategy is useful to detect proteins otherwise not seen in conventional multidimensional chromatography/mass spectrometry approaches.
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wienkoop
authors.forename: Mirko
authors.initials: M
authors.lastname: Glinski
authors.forename: Nobuo
authors.initials: N
authors.lastname: Tanaka
authors.forename: Vladimir
authors.initials: V
authors.lastname: Tolstikov
authors.forename: Oliver
authors.initials: O
authors.lastname: Fiehn
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D002852:Chromatography, Ion Exchange / Q000379:methods*; D045424:Complex Mixtures; D008969:Molecular Sequence Data; D018515:Plant Leaves / Q000737:chemistry; D028321:Plant Preparations / Q000737:chemistry; D010940:Plant Proteins / Q000032:analysis*; D020543:Proteome / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D045424:Complex Mixtures; D028321:Plant Preparations; D010940:Plant Proteins; D020543:Proteome