title: Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.
abstract: The Spanish team of the Human Proteome Project (SpHPP) marked the annotation of Chr16 and data analysis as one of its priorities. Precise annotation of Chromosome 16 proteins according to C-HPP criteria is presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of DNA Elements (ENCODE) data sets were used to obtain further information relative to cell/tissue specific chromosome 16 coding gene expression patterns and to infer the presence of missing proteins. Twenty-four shotgun 2D-LC-MS/MS and gel/LC-MS/MS MIAPE compliant experiments, representing 41% coverage of chromosome 16 proteins, were performed. Furthermore, mapping of large-scale multicenter mass spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines into RNA-Seq data allowed further insights relative to correlation of chromosome 16 transcripts and proteins. Detection and quantification of chromosome 16 proteins in biological matrices by SRM procedures are also primary goals of the SpHPP. Two strategies were undertaken: one focused on known proteins, taking advantage of MS data already available, and the second, aimed at the detection of the missing proteins, is based on the expression of recombinant proteins to gather MS information and optimize SRM methods that will be used in real biological samples. SRM methods for 49 known proteins and for recombinant forms of 24 missing proteins are reported in this study.
authors.affiliation: ProteoRed-ISCIII, Center for Applied Medical Research (CIMA), University of Navarra , Pío XII, 55; Ed. CIMA, 31008 Pamplona, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: Segura
authors.forename: Juan Alberto
authors.initials: JA
authors.lastname: Medina-Aunon
authors.forename: Maria I
authors.initials: MI
authors.lastname: Mora
authors.forename: Salvador
authors.initials: S
authors.lastname: Martínez-Bartolomé
authors.forename: Joaquín
authors.initials: J
authors.lastname: Abian
authors.forename: Kerman
authors.initials: K
authors.lastname: Aloria
authors.forename: Oreto
authors.initials: O
authors.lastname: Antúnez
authors.forename: Jesús M
authors.initials: JM
authors.lastname: Arizmendi
authors.forename: Mikel
authors.initials: M
authors.lastname: Azkargorta
authors.forename: Silvia
authors.initials: S
authors.lastname: Barceló-Batllori
authors.forename: Jabier
authors.initials: J
authors.lastname: Beaskoetxea
authors.forename: Joan J
authors.initials: JJ
authors.lastname: Bech-Serra
authors.forename: Francisco
authors.initials: F
authors.lastname: Blanco
authors.forename: Mariana B
authors.initials: MB
authors.lastname: Monteiro
authors.forename: David
authors.initials: D
authors.lastname: Cáceres
authors.forename: Francesc
authors.initials: F
authors.lastname: Canals
authors.forename: Monserrat
authors.initials: M
authors.lastname: Carrascal
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Casal
authors.forename: Felipe
authors.initials: F
authors.lastname: Clemente
authors.forename: Nuria
authors.initials: N
authors.lastname: Colomé
authors.forename: Noelia
authors.initials: N
authors.lastname: Dasilva
authors.forename: Paula
authors.initials: P
authors.lastname: Díaz
authors.forename: Félix
authors.initials: F
authors.lastname: Elortza
authors.forename: Patricia
authors.initials: P
authors.lastname: Fernández-Puente
authors.forename: Manuel
authors.initials: M
authors.lastname: Fuentes
authors.forename: Oscar
authors.initials: O
authors.lastname: Gallardo
authors.forename: Severine I
authors.initials: SI
authors.lastname: Gharbi
authors.forename: Concha
authors.initials: C
authors.lastname: Gil
authors.forename: Carmen
authors.initials: C
authors.lastname: González-Tejedo
authors.forename: María Luisa
authors.initials: ML
authors.lastname: Hernáez
authors.forename: Manuel
authors.initials: M
authors.lastname: Lombardía
authors.forename: Maria
authors.initials: M
authors.lastname: Lopez-Lucendo
authors.forename: Miguel
authors.initials: M
authors.lastname: Marcilla
authors.forename: José M
authors.initials: JM
authors.lastname: Mato
authors.forename: Marta
authors.initials: M
authors.lastname: Mendes
authors.forename: Eliandre
authors.initials: E
authors.lastname: Oliveira
authors.forename: Irene
authors.initials: I
authors.lastname: Orera
authors.forename: Alberto
authors.initials: A
authors.lastname: Pascual-Montano
authors.forename: Gorka
authors.initials: G
authors.lastname: Prieto
authors.forename: Cristina
authors.initials: C
authors.lastname: Ruiz-Romero
authors.forename: Manuel M
authors.initials: MM
authors.lastname: Sánchez del Pino
authors.forename: Daniel
authors.initials: D
authors.lastname: Tabas-Madrid
authors.forename: Maria L
authors.initials: ML
authors.lastname: Valero
authors.forename: Vital
authors.initials: V
authors.lastname: Vialas
authors.forename: Joan
authors.initials: J
authors.lastname: Villanueva
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Albar
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: Corrales
mesh_terms: D002853:Chromatography, Liquid; D002885:Chromosomes, Human, Pair 16; D006801:Humans; D013058:Mass Spectrometry; D020543:Proteome; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D020543:Proteome