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1. Quantitative assay of targeted proteome in tomato trichome glandular cells using a large-scale selected reaction monitoring strategy

Author:
Takemori, Nobuaki,   et al.   ; Takemori, Ayako; Nakashima, Taiken; Ômura, Hisashi; Tanaka, Yuki; Nakata, Keisuke; Nonami, Hiroshi;     Show all 7 Authors
Source:
Plant methods 2019 v.15 no.1 pp. 40
ISSN:
1746-4811
Subject:
calyx; chromatography; fruits; leaves; liquids; mass spectrometry; models; monitoring; proteins; proteome; proteomics; secondary metabolites; spectrometers; tomatoes; trichomes; vascular plants
Abstract:
... BACKGROUND: Glandular trichomes found in vascular plants are called natural cell factories because they synthesize and store secondary metabolites in glandular cells. To systematically understand the metabolic processes in glandular cells, it is indispensable to analyze cellular proteome dynamics. The conventional proteomics methods based on mass spectrometry have enabled large-scale protein analy ...
DOI:
10.1186/s13007-019-0427-7

2. Top-down/Bottom-up Mass Spectrometry Workflow Using Dissolvable Polyacrylamide Gels

Author:
Takemori, Nobuaki,   et al.   ; Takemori, Ayako; Wongkongkathep, Piriya; Nshanian, Michael; Loo, Rachel R. Ogorzalek; Lermyte, Frederik; Loo, Joseph A.;     Show all 7 Authors
Source:
Analytical chemistry 2017 v.89 no.16 pp. 8244-8250
ISSN:
1520-6882
Subject:
biologists; crosslinking; gels; mass spectrometry; molecular weight; polyacrylamide; polyacrylamide gel electrophoresis; proteins
Abstract:
... Biologists’ preeminent toolbox for separating, analyzing, and visualizing proteins is SDS-PAGE, yet recovering the proteins embedded in these polyacrylamide media as intact species is a long-standing challenge for mass spectrometry. In conventional workflows, protein mixtures from crude biological samples are electrophoretically separated at high-resolution within N,N′-methylene-bis-acrylamide cro ...
DOI:
10.1021/acs.analchem.7b00357
PubMed:
28723075
PubMed Central:
PMC5590889

3. H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

Author:
Takemori, Nobuaki,   et al.   ; Valgepea, Kaspar; de Souza Pinto Lemgruber, Renato; Abdalla, Tanus; Binos, Steve; Takemori, Ayako; Tanaka, Yuki; Tappel, Ryan; Köpke, Michael; Simpson, Séan Dennis; Nielsen, Lars Keld; Marcellin, Esteban;     Show all 12 Authors
Source:
Biotechnology for biofuels 2018 v.11 no.1 pp. 55
ISSN:
1754-6834
Subject:
Clostridium autoethanogenum; acetates; biomass; carbon; carbon dioxide; carbon monoxide; energy; energy conservation; ethanol; fermentation; formates; hydrogen; metabolomics; models; oxidation; proteome; proteomics; synthesis gas
Abstract:
... BACKGROUND: The global demand for affordable carbon has never been stronger, and there is an imperative in many industrial processes to use waste streams to make products. Gas-fermenting acetogens offer a potential solution and several commercial gas fermentation plants are currently under construction. As energy limits acetogen metabolism, supply of H₂ should diminish substrate loss to CO₂ and fa ...
DOI:
10.1186/s13068-018-1052-9
PubMed:
29507607
PubMed Central:
PMC5831606

4. Enzymatic protein digestion using a dissolvable polyacrylamide gel and its application to mass spectrometry-based proteomics

Author:
Takemori, Nobuaki,   et al.   ; Takemori, Ayako; Ishizaki, Jun; Hasegawa, Hitoshi;     Show all 4 Authors
Source:
Journal of Chromatography B 2014 v.967 pp. 36-40
ISSN:
1570-0232
Subject:
ambient temperature; chromatography; gels; ionization; mass spectrometry; peptides; phosphine; polyacrylamide; proteomics
Abstract:
... Enzymatic protein digestion in polyacrylamide gel has been used for sample pretreatment in mass spectrometry-based proteomics due to its effectiveness in removing contaminants that interfere with sample ionization. However, the difficulty of recovering the digested peptides from the solid gel matrix has been a drawback of this method. Here we have developed a novel in-gel digestion method to enhan ...
DOI:
10.1016/j.jchromb.2014.07.006