Literature DB >> 30923379

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms.

Hiroshi Tsugawa1,2, Ryo Nakabayashi3, Tetsuya Mori3, Yutaka Yamada3, Mikiko Takahashi3, Amit Rai4, Ryosuke Sugiyama3, Hiroyuki Yamamoto5, Taiki Nakaya4, Mami Yamazaki4, Rik Kooke6, Johanna A Bac-Molenaar6, Nihal Oztolan-Erol6, Joost J B Keurentjes6, Masanori Arita3,7, Kazuki Saito8,9.   

Abstract

We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully 13C-labeled and non-labeled plants and LC-MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.

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Year:  2019        PMID： 30923379     DOI： 10.1038/s41592-019-0358-2

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  53 in total

1.  Cognitive analysis of metabolomics data for systems biology.

Authors:  Erica L-W Majumder; Elizabeth M Billings; H Paul Benton; Richard L Martin; Amelia Palermo; Carlos Guijas; Markus M Rinschen; Xavier Domingo-Almenara; J Rafael Montenegro-Burke; Bradley A Tagtow; Robert S Plumb; Gary Siuzdak
Journal:  Nat Protoc       Date:  2021-01-22       Impact factor: 13.491

2.  Botanical metabolite ions extraction from full electrospray ionization mass spectrometry using high-dimensional penalized regression.

Authors:  Bety Rostandy; Xiaoli Gao
Journal:  Metabolomics       Date:  2019-10-04       Impact factor: 4.290

3.  Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity.

Authors:  Wenyun Lu; Xi Xing; Lin Wang; Li Chen; Sisi Zhang; Melanie R McReynolds; Joshua D Rabinowitz
Journal:  Anal Chem       Date:  2020-08-12       Impact factor: 6.986

4.  Mosquito metabolomics reveal that dengue virus replication requires phospholipid reconfiguration via the remodeling cycle.

Authors:  Thomas Vial; Wei-Lian Tan; Eric Deharo; Dorothée Missé; Guillaume Marti; Julien Pompon
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-21       Impact factor: 11.205

5.  A lipidome atlas in MS-DIAL 4.

Authors:  Hiroshi Tsugawa; Kazutaka Ikeda; Mikiko Takahashi; Aya Satoh; Yoshifumi Mori; Haruki Uchino; Nobuyuki Okahashi; Yutaka Yamada; Ipputa Tada; Paolo Bonini; Yasuhiro Higashi; Yozo Okazaki; Zhiwei Zhou; Zheng-Jiang Zhu; Jeremy Koelmel; Tomas Cajka; Oliver Fiehn; Kazuki Saito; Masanori Arita; Makoto Arita
Journal:  Nat Biotechnol       Date:  2020-06-15       Impact factor: 54.908

6.  Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.

Authors:  Kai Dührkop; Louis-Félix Nothias; Markus Fleischauer; Raphael Reher; Marcus Ludwig; Martin A Hoffmann; Daniel Petras; William H Gerwick; Juho Rousu; Pieter C Dorrestein; Sebastian Böcker
Journal:  Nat Biotechnol       Date:  2020-11-23       Impact factor: 54.908

7.  Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.

Authors:  Paolo Bonini; Tobias Kind; Hiroshi Tsugawa; Dinesh Kumar Barupal; Oliver Fiehn
Journal:  Anal Chem       Date:  2020-05-21       Impact factor: 6.986

8.  Metabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plants.

Authors:  Jeffrey P Simpson; Cole Wunderlich; Xu Li; Elizabeth Svedin; Brian Dilkes; Clint Chapple
Journal:  Plant Cell       Date:  2021-05-05       Impact factor: 11.277

9.  Metabolomic profiling of wheat genotypes resistant and susceptible to root-lesion nematode Pratylenchus thornei.

Authors:  Md Motiur Rahaman; Rebecca S Zwart; Thusitha W T Rupasinghe; Helen L Hayden; John P Thompson
Journal:  Plant Mol Biol       Date:  2021-05-10       Impact factor: 4.076

10.  Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana.

Authors:  Ryosuke Sugiyama; Rui Li; Ayuko Kuwahara; Ryo Nakabayashi; Naoyuki Sotta; Tetsuya Mori; Takehiro Ito; Naoko Ohkama-Ohtsu; Toru Fujiwara; Kazuki Saito; Ryohei Thomas Nakano; Paweł Bednarek; Masami Yokota Hirai
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-01       Impact factor: 11.205
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