title: Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome.
abstract: We describe the utility of integrated strategies that employ both translation of ENCODE data and major proteomic technology pillars to improve the identification of the "missing proteins", novel proteoforms, and PTMs. On one hand, databases in combination with bioinformatic tools are efficiently utilized to establish microarray-based transcript analysis and supply rapid protein identifications in clinical samples. On the other hand, sequence libraries are the foundation of targeted protein identification and quantification using mass spectrometric and immunoaffinity techniques. The results from combining proteoENCODEdb searches with experimental mass spectral data indicate that some alternative splicing forms detected at the transcript level are in fact translated to proteins. Our results provide a step toward the directives of the C-HPP initiative and related biomedical research.
authors.affiliation: Department of Pharmacology and Toxicology and ‡Biochemistry and Molecular Biology, UTMB Cancer Center, University of Texas Medical Branch , Galveston, Texas 77555, United States.
authors.forename: Carol L
authors.initials: CL
authors.lastname: Nilsson
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Mostovenko
authors.forename: Cheryl F
authors.initials: CF
authors.lastname: Lichti
authors.forename: Kelly
authors.initials: K
authors.lastname: Ruggles
authors.forename: David
authors.initials: D
authors.lastname: Fenyö
authors.forename: Kate R
authors.initials: KR
authors.lastname: Rosenbloom
authors.forename: William S
authors.initials: WS
authors.lastname: Hancock
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.forename: Joshua
authors.initials: J
authors.lastname: LaBaer
authors.forename: Roger A
authors.initials: RA
authors.lastname: Kroes
authors.forename: Matthias
authors.initials: M
authors.lastname: Uhlén
authors.forename: Sophia
authors.initials: S
authors.lastname: Hober
authors.forename: Ákos
authors.initials: Á
authors.lastname: Végvári
authors.forename: Per E
authors.initials: PE
authors.lastname: Andrén
authors.forename: Erik P
authors.initials: EP
authors.lastname: Sulman
authors.forename: Frederick F
authors.initials: FF
authors.lastname: Lang
authors.forename: Manuel
authors.initials: M
authors.lastname: Fuentes
authors.forename: Elisabet
authors.initials: E
authors.lastname: Carlsohn
authors.forename: Mark R
authors.initials: MR
authors.lastname: Emmett
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Moskal
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Fehniger
authors.forename: György
authors.initials: G
authors.lastname: Marko-Varga
mesh_terms: D006801:Humans; D020033:Protein Isoforms / Q000737:chemistry; D020543:Proteome / Q000737:chemistry*
chemical_list: D020033:Protein Isoforms; D020543:Proteome
keywords: Chromosome-centric Human Protein Project; ENCODE; glioma stem cell; microassays; missing proteins; protein sequence mass spectrometry