title: LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris.
abstract: High efficiency capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins extracted from Desulfovibrio vulgaris cells across six treatment conditions. While our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions [W. Zhang, M.A. Gritsenko, R.J. Moore, D.E. Culley, L. Nie, K. Petritis, E.F. Strittmatter, D.G. Camp II, R.D. Smith, F.J. Brockman, A proteomic view of the metabolism in Desulfovibrio vulgaris determined by liquid chromatography coupled with tandem mass spectrometry, Proteomics 6 (2006) 4286-4299], this study describes the global detection and functional inference for hypothetical D. vulgaris proteins. Using criteria that a given peptide of a protein is identified from at least two out of three independent LC-MS/MS measurements and that for any protein at least two different peptides are identified among the three measurements, 129 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins. Functional inference for the conserved hypothetical proteins was performed by a combination of several non-homology based methods: genomic context analysis, phylogenomic profiling, and analysis of a combination of experimental information, including peptide detection in cells grown under specific culture conditions and cellular location of the proteins. Using this approach we were able to assign possible functions to 20 conserved hypothetical proteins. This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification of the expression of hypothetical proteins and improve genome annotation.
authors.affiliation: Microbiology Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352, USA. Weiwen.Zhang@pnl.gov
authors.forename: Weiwen
authors.initials: W
authors.lastname: Zhang
authors.forename: David E
authors.initials: DE
authors.lastname: Culley
authors.forename: Marina A
authors.initials: MA
authors.lastname: Gritsenko
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Lei
authors.initials: L
authors.lastname: Nie
authors.forename: Johannes C M
authors.initials: JC
authors.lastname: Scholten
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Petritis
authors.forename: Eric F
authors.initials: EF
authors.lastname: Strittmatter
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Brockman
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D002853:Chromatography, Liquid / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods; D016969:Desulfovibrio vulgaris / Q000235:genetics / Q000378:metabolism*; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D001426:Bacterial Proteins; D020543:Proteome