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dc.contributor.authorGonzález González, María-
dc.contributor.authorDasilva, Noelia-
dc.contributor.authorDíez, Paula-
dc.contributor.authorFuentes, Manuel-
dc.contributor.authorMarko-Varga, György-
dc.identifierdoi: 10.1021/pr3008607-
dc.identifierissn: 1535-3893-
dc.identifiere-issn: 1535-3907-
dc.identifier.citationJournal of Proteome Research 12(1): 135-150 (2013)-
dc.descriptionPMCID: PMC3539432; NIHMSID: NIHMS430346.-- et al.-
dc.description.abstractA first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, United States, China and India, a part of the Chromosome-centric Human Proteome Project (C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159 peptides, a pilot study was conducted using a subset with 125 isotope-labeled peptides. We applied an annotation strategy with triple quadrupole, ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality of data within and in between these instrumental set-ups. LC-MS conditions were outlined by multiplex assay developments, followed by MRM assay developments. SRM was applied to biobank samples, quantifying kallikrein 3 (prostate specific antigen) in plasma from prostate cancer patients. The antibody production has been initiated for more than 1200 genes from the entire chromosome 19, and the progress developments are presented. We developed a dedicated transcript microarray to serve as the mRNA identifier by screening cancer cell lines. NAPPA protein arrays were built to align with the transcript data with the Chromosome 19 NAPPA chip, dedicated to 90 proteins, as the first development delivery. We have introduced an IT-infrastructure utilizing a LIMS system that serves as the key interface for the research teams to share and explore data generated within the project. The cross-site data repository will form the basis for sample processing, including biological samples as well as patient samples from national Biobanks. © 2012 American Chemical Society.-
dc.description.sponsorshipThis work was supported by grants from the Swedish Academy of Pharmaceutical Sciences who is the core founder our consortium, Swedish Research Council, the Swedish Foundation for Strategic Research, Vinnova, Ingabritt & Arne Lundbergs forskningsstiftelse, the Crafoord Foundation and by Thermo Fisher Scientific for mass spectrometry instrument support. T.E.F. is supported by the Mobilitas Program sponsored by the European Union Social Fund and administered by the Estonian Science Foundation. We gratefully acknowledge financial support to M.F. from Health Institute Carlos III of Spain (ISCIII, FIS PI02114) and M.G.-G. is supported by a PhD scholarship of ISCIII FI08/00721. C.L.N. is supported by the Cancer Prevention and Research Institute of Texas and the University of Texas Medical Branch. [11-0624]; National Cancer Institute [R33 CA 127768-03, R01CA160816, and P50-CA92629]; Sidney Kimmel Center for Prostate and Urologic Cancers; and David H. Koch through the Prostate Cancer Foundation.-
dc.publisherAmerican Chemical Society-
dc.titleChromosome 19 annotations with disease speciation: A first report from the global research consortium-
dc.description.versionPeer Reviewed-
dc.contributor.funderVINNOVA (Sweden)-
dc.contributor.funderThermo Fisher Scientific-
dc.contributor.funderEuropean Commission-
dc.contributor.funderInstituto de Salud Carlos III-
dc.contributor.funderUniversity of Texas-
dc.contributor.funderSwedish Cancer Society-
dc.contributor.funderNational Cancer Institute (US)-
dc.contributor.funderProstate Cancer Foundation of Australia-
dc.contributor.funderMemorial Sloan Kettering Cancer Center-
dc.contributor.funderCrafoord Foundation-
dc.contributor.funderSwedish Research Council-
dc.contributor.funderSwedish Foundation for Strategic Research-
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