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Chromosome 19 Annotations with Disease Speciation - A First Report from the Global Research Consortium

Nilsson, Carol L; Berven, Frode; Selheim, Frode; Liu, Huiling; Moskal, Joseph F; Kroes, Roger A; Sulman, Erik P; Conrad, Charles A; Lang, Frederick F and Andrén, Per E, et al. (2013) In Journal of Proteome Research 12(1). p.135-150
Abstract
A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, USA, 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 sub-set 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,... (More)
A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, USA, 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 sub-set 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 in order 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. (Less)
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keywords
Proteins, Genes, Antibodies, mRNA, Mass spectrometry, Bioinformatics, Protein microarray, Human Disease
in
Journal of Proteome Research
volume
12
issue
1
pages
135 - 150
publisher
The American Chemical Society
external identifiers
  • wos:000313156300016
  • scopus:84874033741
ISSN
1535-3893
DOI
10.1021/pr3008607
language
English
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cc6699e9-7eb5-4b09-ad0b-6910bb53e69b (old id 3172684)
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2012-12-13 14:47:22
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@article{cc6699e9-7eb5-4b09-ad0b-6910bb53e69b,
  abstract     = {A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, USA, 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 sub-set 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 in order 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.},
  author       = {Nilsson, Carol L and Berven, Frode and Selheim, Frode and Liu, Huiling and Moskal, Joseph F and Kroes, Roger A and Sulman, Erik P and Conrad, Charles A and Lang, Frederick F and Andrén, Per E and Nilsson, Anna and Carlsohn, Elisabet and Lilja, Hans and Malm, Johan and Fenyö, David and Subramaniyam, Devipriya and Wang, Xiangdong and Gonzales-Gonzales, Maria and Dasilva, Noelia and Diez, Paula and Fuentes, Manuel and Végvári, Ákos and Sjödin, Karin and Welinder, Charlotte and Laurell, Thomas and Fehniger, Thomas and Lindberg, Henrik and Rezeli, Melinda and Edula, Goutham and Hober, Sophia and Marko-Varga, György},
  issn         = {1535-3893},
  keyword      = {Proteins,Genes,Antibodies,mRNA,Mass spectrometry,Bioinformatics,Protein microarray,Human Disease},
  language     = {eng},
  number       = {1},
  pages        = {135--150},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Chromosome 19 Annotations with Disease Speciation - A First Report from the Global Research Consortium},
  url          = {http://dx.doi.org/10.1021/pr3008607},
  volume       = {12},
  year         = {2013},
}