Literature DB >> 32541957

A lipidome atlas in MS-DIAL 4.

Hiroshi Tsugawa1,2, Kazutaka Ikeda3,4, Mikiko Takahashi5, Aya Satoh5, Yoshifumi Mori6, Haruki Uchino3,7, Nobuyuki Okahashi3,8, Yutaka Yamada5, Ipputa Tada9, Paolo Bonini10, Yasuhiro Higashi5, Yozo Okazaki5,11, Zhiwei Zhou12,13, Zheng-Jiang Zhu12, Jeremy Koelmel14,15, Tomas Cajka16, Oliver Fiehn17, Kazuki Saito5,18, Masanori Arita5,19, Makoto Arita20,21,22.   

Abstract

We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.

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Year:  2020        PMID： 32541957     DOI： 10.1038/s41587-020-0531-2

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  36 in total

Review 1.  The importance of bioinformatics for connecting data-driven lipidomics and biological insights.

Authors:  Hiroshi Tsugawa; Kazutaka Ikeda; Makoto Arita
Journal:  Biochim Biophys Acta Mol Cell Biol Lipids       Date:  2017-05-14       Impact factor: 4.698

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

Authors:  Hiroshi Tsugawa; Ryo Nakabayashi; Tetsuya Mori; Yutaka Yamada; Mikiko Takahashi; Amit Rai; Ryosuke Sugiyama; Hiroyuki Yamamoto; Taiki Nakaya; Mami Yamazaki; Rik Kooke; Johanna A Bac-Molenaar; Nihal Oztolan-Erol; Joost J B Keurentjes; Masanori Arita; Kazuki Saito
Journal:  Nat Methods       Date:  2019-03-28       Impact factor: 28.547

Review 3.  Identification of small molecules using accurate mass MS/MS search.

Authors:  Tobias Kind; Hiroshi Tsugawa; Tomas Cajka; Yan Ma; Zijuan Lai; Sajjan S Mehta; Gert Wohlgemuth; Dinesh Kumar Barupal; Megan R Showalter; Masanori Arita; Oliver Fiehn
Journal:  Mass Spectrom Rev       Date:  2017-04-24       Impact factor: 10.946

Review 4.  Update of the LIPID MAPS comprehensive classification system for lipids.

Authors:  Eoin Fahy; Shankar Subramaniam; Robert C Murphy; Masahiro Nishijima; Christian R H Raetz; Takao Shimizu; Friedrich Spener; Gerrit van Meer; Michael J O Wakelam; Edward A Dennis
Journal:  J Lipid Res       Date:  2008-12-19       Impact factor: 5.922

Review 5.  Understanding the diversity of membrane lipid composition.

Authors:  Takeshi Harayama; Howard Riezman
Journal:  Nat Rev Mol Cell Biol       Date:  2018-02-07       Impact factor: 94.444

6.  Shorthand notation for lipid structures derived from mass spectrometry.

Authors:  Gerhard Liebisch; Juan Antonio Vizcaíno; Harald Köfeler; Martin Trötzmüller; William J Griffiths; Gerd Schmitz; Friedrich Spener; Michael J O Wakelam
Journal:  J Lipid Res       Date:  2013-04-02       Impact factor: 5.922

7.  Proposal for a common nomenclature for fragment ions in mass spectra of lipids.

Authors:  Josch K Pauling; Martin Hermansson; Jürgen Hartler; Klaus Christiansen; Sandra F Gallego; Bing Peng; Robert Ahrends; Christer S Ejsing
Journal:  PLoS One       Date:  2017-11-21       Impact factor: 3.240

8.  Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma.

Authors:  John A Bowden; Alan Heckert; Candice Z Ulmer; Christina M Jones; Jeremy P Koelmel; Laila Abdullah; Linda Ahonen; Yazen Alnouti; Aaron M Armando; John M Asara; Takeshi Bamba; John R Barr; Jonas Bergquist; Christoph H Borchers; Joost Brandsma; Susanne B Breitkopf; Tomas Cajka; Amaury Cazenave-Gassiot; Antonio Checa; Michelle A Cinel; Romain A Colas; Serge Cremers; Edward A Dennis; James E Evans; Alexander Fauland; Oliver Fiehn; Michael S Gardner; Timothy J Garrett; Katherine H Gotlinger; Jun Han; Yingying Huang; Aveline Huipeng Neo; Tuulia Hyötyläinen; Yoshihiro Izumi; Hongfeng Jiang; Houli Jiang; Jiang Jiang; Maureen Kachman; Reiko Kiyonami; Kristaps Klavins; Christian Klose; Harald C Köfeler; Johan Kolmert; Therese Koal; Grielof Koster; Zsuzsanna Kuklenyik; Irwin J Kurland; Michael Leadley; Karen Lin; Krishna Rao Maddipati; Danielle McDougall; Peter J Meikle; Natalie A Mellett; Cian Monnin; M Arthur Moseley; Renu Nandakumar; Matej Oresic; Rainey Patterson; David Peake; Jason S Pierce; Martin Post; Anthony D Postle; Rebecca Pugh; Yunping Qiu; Oswald Quehenberger; Parsram Ramrup; Jon Rees; Barbara Rembiesa; Denis Reynaud; Mary R Roth; Susanne Sales; Kai Schuhmann; Michal Laniado Schwartzman; Charles N Serhan; Andrej Shevchenko; Stephen E Somerville; Lisa St John-Williams; Michal A Surma; Hiroaki Takeda; Rhishikesh Thakare; J Will Thompson; Federico Torta; Alexander Triebl; Martin Trötzmüller; S J Kumari Ubhayasekera; Dajana Vuckovic; Jacquelyn M Weir; Ruth Welti; Markus R Wenk; Craig E Wheelock; Libin Yao; Min Yuan; Xueqing Heather Zhao; Senlin Zhou
Journal:  J Lipid Res       Date:  2017-10-06       Impact factor: 5.922

9.  LipidBlast in silico tandem mass spectrometry database for lipid identification.

Authors:  Tobias Kind; Kwang-Hyeon Liu; Do Yup Lee; Brian DeFelice; John K Meissen; Oliver Fiehn
Journal:  Nat Methods       Date:  2013-06-30       Impact factor: 28.547

10.  mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Authors:  Nils Hoffmann; Joel Rein; Timo Sachsenberg; Jürgen Hartler; Kenneth Haug; Gerhard Mayer; Oliver Alka; Saravanan Dayalan; Jake T M Pearce; Philippe Rocca-Serra; Da Qi; Martin Eisenacher; Yasset Perez-Riverol; Juan Antonio Vizcaíno; Reza M Salek; Steffen Neumann; Andrew R Jones
Journal:  Anal Chem       Date:  2019-02-13       Impact factor: 6.986
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  74 in total

Review 1.  Advancements in capturing and mining mass spectrometry data are transforming natural products research.

Authors:  Scott A Jarmusch; Justin J J van der Hooft; Pieter C Dorrestein; Alan K Jarmusch
Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

2.  Sample Preparation, Data Acquisition, and Data Analysis for 15N-Labeled and Nonlabeled Monoterpene Indole Alkaloids in Catharanthus roseus.

Authors:  Ryo Nakabayashi
Journal:  Methods Mol Biol       Date:  2022

3.  A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows.

Authors:  Aivett Bilbao; Bryson C Gibbons; Sarah M Stow; Jennifer E Kyle; Kent J Bloodsworth; Samuel H Payne; Richard D Smith; Yehia M Ibrahim; Erin S Baker; John C Fjeldsted
Journal:  J Proteome Res       Date:  2021-08-12       Impact factor: 4.466

4.  ADIPOR1 deficiency-induced suppression of retinal ELOVL2 and docosahexaenoic acid levels during photoreceptor degeneration and visual loss.

Authors:  Hideto Osada; Eriko Toda; Kohei Homma; Naymel A Guzman; Norihiro Nagai; Mamoru Ogawa; Kazuno Negishi; Makoto Arita; Kazuo Tsubota; Yoko Ozawa
Journal:  Cell Death Dis       Date:  2021-05-07       Impact factor: 8.469

Review 5.  New software tools, databases, and resources in metabolomics: updates from 2020.

Authors:  Biswapriya B Misra
Journal:  Metabolomics       Date:  2021-05-11       Impact factor: 4.290

Review 6.  Interpreting the lipidome: bioinformatic approaches to embrace the complexity.

Authors:  Jennifer E Kyle; Lucila Aimo; Alan J Bridge; Geremy Clair; Maria Fedorova; J Bernd Helms; Martijn R Molenaar; Zhixu Ni; Matej Orešič; Denise Slenter; Egon Willighagen; Bobbie-Jo M Webb-Robertson
Journal:  Metabolomics       Date:  2021-06-06       Impact factor: 4.290

7.  High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra.

Authors:  Erandika Karunaratne; Dennis W Hill; Philipp Pracht; José A Gascón; Stefan Grimme; David F Grant
Journal:  Anal Chem       Date:  2021-07-21       Impact factor: 8.008

8.  Ion mobility-based sterolomics reveals spatially and temporally distinctive sterol lipids in the mouse brain.

Authors:  Tongzhou Li; Yandong Yin; Zhiwei Zhou; Jiaqian Qiu; Wenbin Liu; Xueting Zhang; Kaiwen He; Yuping Cai; Zheng-Jiang Zhu
Journal:  Nat Commun       Date:  2021-07-15       Impact factor: 14.919

9.  Bio-Guided Fractionation and Molecular Networking Reveal Fatty Acids to Be Principal Anti-Parasitic Compounds in Nordic Seaweeds.

Authors:  Charlotte Smith Bonde; Louis Bornancin; Yi Lu; Henrik Toft Simonsen; María Martínez-Valladares; Miguel Peña-Espinoza; Helena Mejer; Andrew R Williams; Stig Milan Thamsborg
Journal:  Front Pharmacol       Date:  2021-06-02       Impact factor: 5.810

10.  Untargeted metabolomics approach to discriminate mistletoe commercial products.

Authors:  Cécile Vanhaverbeke; David Touboul; Nicolas Elie; Martine Prévost; Cécile Meunier; Sylvie Michelland; Valérie Cunin; Ling Ma; David Vermijlen; Cédric Delporte; Stéphanie Pochet; Audrey Le Gouellec; Michel Sève; Pierre Van Antwerpen; Florence Souard
Journal:  Sci Rep       Date:  2021-07-09       Impact factor: 4.379
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