Chromosome 19 annotations with disease speciation

A first report from the global research consortium

Carol L. Nilsson, Frode Berven, Frode Selheim, Huiling Liu, Joseph R. Moskal, Roger A. Kroes, Erik P. Sulman, Charles A. Conrad, Frederick F. Lang, Per E. Andrén, Anna Nilsson, Elisabet Carlsohn, Hans Lilja, Johan Malm, David Fenyo, Devipriya Subramaniyam, Xiangdong Wang, Maria Gonzales-Gonzales, Noelia Dasilva, Paula Diez & 11 others Manuel Fuentes, Akos Végväri, Karin Sjodin, Charlotte Welinder, Thomas Laurell, Thomas E. Fehniger, Henrik Lindberg, Melinda Rezeli, Goutham Edula, Sophia Hober, György Marko-Varga

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

A 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.

Original languageEnglish (US)
Pages (from-to)135-150
Number of pages16
JournalJournal of Proteome Research
Volume12
Issue number1
DOIs
StatePublished - Jan 4 2013

Fingerprint

Chromosomes, Human, Pair 19
Chromosomes
Research
Peptides
Assays
Peptide Library
Protein Array Analysis
Kallikreins
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Human Chromosomes
Proteome
Norway
Prostate-Specific Antigen
Early Detection of Cancer
Sweden
Isotopes
Spain
Antibody Formation
India
China

Keywords

  • Antibodies
  • Bioinformatics
  • Genes
  • Human disease
  • Mass spectrometry
  • MRNA
  • Protein microarray
  • Proteins

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Nilsson, C. L., Berven, F., Selheim, F., Liu, H., Moskal, J. R., Kroes, R. A., ... Marko-Varga, G. (2013). Chromosome 19 annotations with disease speciation: A first report from the global research consortium. Journal of Proteome Research, 12(1), 135-150. https://doi.org/10.1021/pr3008607

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 R.; Kroes, Roger A.; Sulman, Erik P.; Conrad, Charles A.; Lang, Frederick F.; Andrén, Per E.; Nilsson, Anna; Carlsohn, Elisabet; Lilja, Hans; Malm, Johan; Fenyo, David; Subramaniyam, Devipriya; Wang, Xiangdong; Gonzales-Gonzales, Maria; Dasilva, Noelia; Diez, Paula; Fuentes, Manuel; Végväri, Akos; Sjodin, Karin; Welinder, Charlotte; Laurell, Thomas; Fehniger, Thomas E.; Lindberg, Henrik; Rezeli, Melinda; Edula, Goutham; Hober, Sophia; Marko-Varga, György.

In: Journal of Proteome Research, Vol. 12, No. 1, 04.01.2013, p. 135-150.

Research output: Contribution to journalArticle

Nilsson, CL, Berven, F, Selheim, F, Liu, H, Moskal, JR, Kroes, RA, Sulman, EP, Conrad, CA, Lang, FF, Andrén, PE, Nilsson, A, Carlsohn, E, Lilja, H, Malm, J, Fenyo, D, Subramaniyam, D, Wang, X, Gonzales-Gonzales, M, Dasilva, N, Diez, P, Fuentes, M, Végväri, A, Sjodin, K, Welinder, C, Laurell, T, Fehniger, TE, Lindberg, H, Rezeli, M, Edula, G, Hober, S & Marko-Varga, G 2013, 'Chromosome 19 annotations with disease speciation: A first report from the global research consortium', Journal of Proteome Research, vol. 12, no. 1, pp. 135-150. https://doi.org/10.1021/pr3008607
Nilsson, Carol L. ; Berven, Frode ; Selheim, Frode ; Liu, Huiling ; Moskal, Joseph R. ; Kroes, Roger A. ; Sulman, Erik P. ; Conrad, Charles A. ; Lang, Frederick F. ; Andrén, Per E. ; Nilsson, Anna ; Carlsohn, Elisabet ; Lilja, Hans ; Malm, Johan ; Fenyo, David ; Subramaniyam, Devipriya ; Wang, Xiangdong ; Gonzales-Gonzales, Maria ; Dasilva, Noelia ; Diez, Paula ; Fuentes, Manuel ; Végväri, Akos ; Sjodin, Karin ; Welinder, Charlotte ; Laurell, Thomas ; Fehniger, Thomas E. ; Lindberg, Henrik ; Rezeli, Melinda ; Edula, Goutham ; Hober, Sophia ; Marko-Varga, György. / Chromosome 19 annotations with disease speciation : A first report from the global research consortium. In: Journal of Proteome Research. 2013 ; Vol. 12, No. 1. pp. 135-150.
@article{454daee7db494272b294fedf60f04e26,
title = "Chromosome 19 annotations with disease speciation: A first report from the global research consortium",
abstract = "A 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.",
keywords = "Antibodies, Bioinformatics, Genes, Human disease, Mass spectrometry, MRNA, Protein microarray, Proteins",
author = "Nilsson, {Carol L.} and Frode Berven and Frode Selheim and Huiling Liu and Moskal, {Joseph R.} and Kroes, {Roger A.} and Sulman, {Erik P.} and Conrad, {Charles A.} and Lang, {Frederick F.} and Andr{\'e}n, {Per E.} and Anna Nilsson and Elisabet Carlsohn and Hans Lilja and Johan Malm and David Fenyo and Devipriya Subramaniyam and Xiangdong Wang and Maria Gonzales-Gonzales and Noelia Dasilva and Paula Diez and Manuel Fuentes and Akos V{\'e}gv{\"a}ri and Karin Sjodin and Charlotte Welinder and Thomas Laurell and Fehniger, {Thomas E.} and Henrik Lindberg and Melinda Rezeli and Goutham Edula and Sophia Hober and Gy{\"o}rgy Marko-Varga",
year = "2013",
month = "1",
day = "4",
doi = "10.1021/pr3008607",
language = "English (US)",
volume = "12",
pages = "135--150",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "1",

}

TY - JOUR

T1 - Chromosome 19 annotations with disease speciation

T2 - A first report from the global research consortium

AU - Nilsson, Carol L.

AU - Berven, Frode

AU - Selheim, Frode

AU - Liu, Huiling

AU - Moskal, Joseph R.

AU - Kroes, Roger A.

AU - Sulman, Erik P.

AU - Conrad, Charles A.

AU - Lang, Frederick F.

AU - Andrén, Per E.

AU - Nilsson, Anna

AU - Carlsohn, Elisabet

AU - Lilja, Hans

AU - Malm, Johan

AU - Fenyo, David

AU - Subramaniyam, Devipriya

AU - Wang, Xiangdong

AU - Gonzales-Gonzales, Maria

AU - Dasilva, Noelia

AU - Diez, Paula

AU - Fuentes, Manuel

AU - Végväri, Akos

AU - Sjodin, Karin

AU - Welinder, Charlotte

AU - Laurell, Thomas

AU - Fehniger, Thomas E.

AU - Lindberg, Henrik

AU - Rezeli, Melinda

AU - Edula, Goutham

AU - Hober, Sophia

AU - Marko-Varga, György

PY - 2013/1/4

Y1 - 2013/1/4

N2 - A 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.

AB - A 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.

KW - Antibodies

KW - Bioinformatics

KW - Genes

KW - Human disease

KW - Mass spectrometry

KW - MRNA

KW - Protein microarray

KW - Proteins

UR - http://www.scopus.com/inward/record.url?scp=84874033741&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874033741&partnerID=8YFLogxK

U2 - 10.1021/pr3008607

DO - 10.1021/pr3008607

M3 - Article

VL - 12

SP - 135

EP - 150

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 1

ER -