A large-scale targeted proteomics assay resource based on an in vitro human proteome

Masaki Matsumoto, Fumiko Matsuzaki, Kiyotaka Oshikawa, Naoki Goshima, Masatoshi Mori, Yoshifumi Kawamura, Koji Ogawa, Eriko Fukuda, Hirokazu Nakatsumi, Tohru Natsume, Kazuhiko Fukui, Katsuhisa Horimoto, Takeshi Nagashima, Ryo Funayama, Keiko Nakayama, Keiichi Nakayama

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Targeted proteomics approaches are of value for deep and accurate quantification of protein abundance. Extending such methods to quantify large numbers of proteins requires the construction of predefined targeted assays. We developed a targeted proteomics platform-in vitro proteome-assisted multiple reaction monitoring (MRM) for protein absolute quantification (iMPAQT)-by using >18,000 human recombinant proteins, thus enabling protein absolute quantification on a genome-wide scale. Our platform comprises experimentally confirmed MRM assays of mass tag (mTRAQ)-labeled peptides to allow for rapid and straightforward measurement of the absolute abundance of predefined sets of proteins by mass spectrometry. We applied iMPAQT to delineate the quantitative metabolic landscape of normal and transformed human fibroblasts. Oncogenic transformation gave rise to relatively small but global changes in metabolic pathways resulting in aerobic glycolysis (Warburg effect) and increased rates of macromolecule synthesis. iMPAQT should facilitate quantitative biology studies based on protein abundance measurements.

Original languageEnglish
Pages (from-to)251-258
Number of pages8
JournalNature Methods
Volume14
Issue number3
DOIs
Publication statusPublished - Feb 28 2017

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Proteome
Proteomics
Assays
Proteins
Monitoring
Glycolysis
Fibroblasts
Metabolic Networks and Pathways
Macromolecules
Recombinant Proteins
Mass spectrometry
In Vitro Techniques
Mass Spectrometry
Genes
Genome
Peptides

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

A large-scale targeted proteomics assay resource based on an in vitro human proteome. / Matsumoto, Masaki; Matsuzaki, Fumiko; Oshikawa, Kiyotaka; Goshima, Naoki; Mori, Masatoshi; Kawamura, Yoshifumi; Ogawa, Koji; Fukuda, Eriko; Nakatsumi, Hirokazu; Natsume, Tohru; Fukui, Kazuhiko; Horimoto, Katsuhisa; Nagashima, Takeshi; Funayama, Ryo; Nakayama, Keiko; Nakayama, Keiichi.

In: Nature Methods, Vol. 14, No. 3, 28.02.2017, p. 251-258.

Research output: Contribution to journalArticle

Matsumoto, M, Matsuzaki, F, Oshikawa, K, Goshima, N, Mori, M, Kawamura, Y, Ogawa, K, Fukuda, E, Nakatsumi, H, Natsume, T, Fukui, K, Horimoto, K, Nagashima, T, Funayama, R, Nakayama, K & Nakayama, K 2017, 'A large-scale targeted proteomics assay resource based on an in vitro human proteome', Nature Methods, vol. 14, no. 3, pp. 251-258. https://doi.org/10.1038/nmeth.4116
Matsumoto, Masaki ; Matsuzaki, Fumiko ; Oshikawa, Kiyotaka ; Goshima, Naoki ; Mori, Masatoshi ; Kawamura, Yoshifumi ; Ogawa, Koji ; Fukuda, Eriko ; Nakatsumi, Hirokazu ; Natsume, Tohru ; Fukui, Kazuhiko ; Horimoto, Katsuhisa ; Nagashima, Takeshi ; Funayama, Ryo ; Nakayama, Keiko ; Nakayama, Keiichi. / A large-scale targeted proteomics assay resource based on an in vitro human proteome. In: Nature Methods. 2017 ; Vol. 14, No. 3. pp. 251-258.
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