Literature DB >> 35798960

Enhancing untargeted metabolomics using metadata-based source annotation.

Julia M Gauglitz1,2, Kiana A West1,2, Wout Bittremieux1,2, Candace L Williams3, Kelly C Weldon1,2,4, Morgan Panitchpakdi1,2, Francesca Di Ottavio1, Christine M Aceves1,2, Elizabeth Brown2,5, Nicole C Sikora1,2, Alan K Jarmusch1,2, Cameron Martino4,6,7, Anupriya Tripathi2,5,6, Michael J Meehan1,2, Kathleen Dorrestein1,2, Justin P Shaffer6, Roxana Coras8, Fernando Vargas1,2,5, Lindsay DeRight Goldasich6, Tara Schwartz6, MacKenzie Bryant6, Gregory Humphrey6, Abigail J Johnson9, Katharina Spengler1, Pedro Belda-Ferre4,6, Edgar Diaz6, Daniel McDonald6, Qiyun Zhu6, Emmanuel O Elijah1,2, Mingxun Wang1,2, Clarisse Marotz6, Kate E Sprecher10,11, Daniela Vargas-Robles12, Dana Withrow10, Gail Ackermann6, Lourdes Herrera13, Barry J Bradford14, Lucas Maciel Mauriz Marques15, Juliano Geraldo Amaral16, Rodrigo Moreira Silva17, Flavio Protasio Veras15, Thiago Mattar Cunha15, Rene Donizeti Ribeiro Oliveira18, Paulo Louzada-Junior18, Robert H Mills1,2,6,19, Paulina K Piotrowski20, Stephanie L Servetas20, Sandra M Da Silva20, Christina M Jones20, Nancy J Lin20, Katrice A Lippa20, Scott A Jackson20, Rima Kaddurah Daouk21,22,23, Douglas Galasko24, Parambir S Dulai25, Tatyana I Kalashnikova26, Curt Wittenberg26, Robert Terkeltaub8,27, Megan M Doty6,28, Jae H Kim29, Kyung E Rhee6, Julia Beauchamp-Walters30, Kenneth P Wright10, Maria Gloria Dominguez-Bello31, Mark Manary32, Michelli F Oliveira33, Brigid S Boland25, Norberto Peporine Lopes17, Monica Guma8, Austin D Swafford4, Rachel J Dutton5, Rob Knight34,35,36,37,38, Pieter C Dorrestein39,40,41,42,43.   

Abstract

Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

Entities:  

Year:  2022        PMID: 35798960     DOI: 10.1038/s41587-022-01368-1

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


  30 in total

1.  The human microbiome project.

Authors:  Peter J Turnbaugh; Ruth E Ley; Micah Hamady; Claire M Fraser-Liggett; Rob Knight; Jeffrey I Gordon
Journal:  Nature       Date:  2007-10-18       Impact factor: 49.962

2.  Mass spectral molecular networking of living microbial colonies.

Authors:  Jeramie Watrous; Patrick Roach; Theodore Alexandrov; Brandi S Heath; Jane Y Yang; Roland D Kersten; Menno van der Voort; Kit Pogliano; Harald Gross; Jos M Raaijmakers; Bradley S Moore; Julia Laskin; Nuno Bandeira; Pieter C Dorrestein
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-14       Impact factor: 11.205

Review 3.  Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy.

Authors:  Robert A Quinn; Louis-Felix Nothias; Oliver Vining; Michael Meehan; Eduardo Esquenazi; Pieter C Dorrestein
Journal:  Trends Pharmacol Sci       Date:  2016-11-11       Impact factor: 14.819

4.  Lifestyle chemistries from phones for individual profiling.

Authors:  Amina Bouslimani; Alexey V Melnik; Zhenjiang Xu; Amnon Amir; Ricardo R da Silva; Mingxun Wang; Nuno Bandeira; Theodore Alexandrov; Rob Knight; Pieter C Dorrestein
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-14       Impact factor: 11.205

5.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Authors:  Mingxun Wang; Jeremy J Carver; Vanessa V Phelan; Laura M Sanchez; Neha Garg; Yao Peng; Don Duy Nguyen; Jeramie Watrous; Clifford A Kapono; Tal Luzzatto-Knaan; Carla Porto; Amina Bouslimani; Alexey V Melnik; Michael J Meehan; Wei-Ting Liu; Max Crüsemann; Paul D Boudreau; Eduardo Esquenazi; Mario Sandoval-Calderón; Roland D Kersten; Laura A Pace; Robert A Quinn; Katherine R Duncan; Cheng-Chih Hsu; Dimitrios J Floros; Ronnie G Gavilan; Karin Kleigrewe; Trent Northen; Rachel J Dutton; Delphine Parrot; Erin E Carlson; Bertrand Aigle; Charlotte F Michelsen; Lars Jelsbak; Christian Sohlenkamp; Pavel Pevzner; Anna Edlund; Jeffrey McLean; Jörn Piel; Brian T Murphy; Lena Gerwick; Chih-Chuang Liaw; Yu-Liang Yang; Hans-Ulrich Humpf; Maria Maansson; Robert A Keyzers; Amy C Sims; Andrew R Johnson; Ashley M Sidebottom; Brian E Sedio; Andreas Klitgaard; Charles B Larson; Cristopher A Boya P; Daniel Torres-Mendoza; David J Gonzalez; Denise B Silva; Lucas M Marques; Daniel P Demarque; Egle Pociute; Ellis C O'Neill; Enora Briand; Eric J N Helfrich; Eve A Granatosky; Evgenia Glukhov; Florian Ryffel; Hailey Houson; Hosein Mohimani; Jenan J Kharbush; Yi Zeng; Julia A Vorholt; Kenji L Kurita; Pep Charusanti; Kerry L McPhail; Kristian Fog Nielsen; Lisa Vuong; Maryam Elfeki; Matthew F Traxler; Niclas Engene; Nobuhiro Koyama; Oliver B Vining; Ralph Baric; Ricardo R Silva; Samantha J Mascuch; Sophie Tomasi; Stefan Jenkins; Venkat Macherla; Thomas Hoffman; Vinayak Agarwal; Philip G Williams; Jingqui Dai; Ram Neupane; Joshua Gurr; Andrés M C Rodríguez; Anne Lamsa; Chen Zhang; Kathleen Dorrestein; Brendan M Duggan; Jehad Almaliti; Pierre-Marie Allard; Prasad Phapale; Louis-Felix Nothias; Theodore Alexandrov; Marc Litaudon; Jean-Luc Wolfender; Jennifer E Kyle; Thomas O Metz; Tyler Peryea; Dac-Trung Nguyen; Danielle VanLeer; Paul Shinn; Ajit Jadhav; Rolf Müller; Katrina M Waters; Wenyuan Shi; Xueting Liu; Lixin Zhang; Rob Knight; Paul R Jensen; Bernhard O Palsson; Kit Pogliano; Roger G Linington; Marcelino Gutiérrez; Norberto P Lopes; William H Gerwick; Bradley S Moore; Pieter C Dorrestein; Nuno Bandeira
Journal:  Nat Biotechnol       Date:  2016-08-09       Impact factor: 54.908

6.  Perspective: Dietary Biomarkers of Intake and Exposure-Exploration with Omics Approaches.

Authors:  Padma Maruvada; Johanna W Lampe; David S Wishart; Dinesh Barupal; Deirdra N Chester; Dylan Dodd; Yannick Djoumbou-Feunang; Pieter C Dorrestein; Lars O Dragsted; John Draper; Linda C Duffy; Johanna T Dwyer; Nancy J Emenaker; Oliver Fiehn; Robert E Gerszten; Frank B Hu; Robert W Karp; David M Klurfeld; Maren R Laughlin; A Roger Little; Christopher J Lynch; Steven C Moore; Holly L Nicastro; Diane M O'Brien; José M Ordovás; Stavroula K Osganian; Mary Playdon; Ross Prentice; Daniel Raftery; Nichole Reisdorph; Helen M Roche; Sharon A Ross; Shengmin Sang; Augustin Scalbert; Pothur R Srinivas; Steven H Zeisel
Journal:  Adv Nutr       Date:  2020-03-01       Impact factor: 11.567

7.  Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Authors:  Zijuan Lai; Hiroshi Tsugawa; Gert Wohlgemuth; Sajjan Mehta; Matthew Mueller; Yuxuan Zheng; Atsushi Ogiwara; John Meissen; Megan Showalter; Kohei Takeuchi; Tobias Kind; Peter Beal; Masanori Arita; Oliver Fiehn
Journal:  Nat Methods       Date:  2017-11-27       Impact factor: 28.547

8.  MetaboLights: a resource evolving in response to the needs of its scientific community.

Authors:  Kenneth Haug; Keeva Cochrane; Venkata Chandrasekhar Nainala; Mark Williams; Jiakang Chang; Kalai Vanii Jayaseelan; Claire O'Donovan
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

9.  RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes.

Authors:  Hiromasa Ono; Osamu Ogasawara; Kosaku Okubo; Hidemasa Bono
Journal:  Sci Data       Date:  2017-08-29       Impact factor: 6.444

10.  All of gene expression (AOE): An integrated index for public gene expression databases.

Authors:  Hidemasa Bono
Journal:  PLoS One       Date:  2020-01-24       Impact factor: 3.240

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  3 in total

Review 1.  Derivatization with fatty acids in peptide and protein drug discovery.

Authors:  Peter Kurtzhals; Søren Østergaard; Erica Nishimura; Thomas Kjeldsen
Journal:  Nat Rev Drug Discov       Date:  2022-08-24       Impact factor: 112.288

2.  Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter.

Authors:  Carsten Simon; Kai Dührkop; Daniel Petras; Vanessa-Nina Roth; Sebastian Böcker; Pieter C Dorrestein; Gerd Gleixner
Journal:  Environ Sci Technol       Date:  2022-07-14       Impact factor: 11.357

3.  Mass spectrometry data on specialized metabolome of medicinal plants used in East Asian traditional medicine.

Authors:  Kyo Bin Kang; Eunah Jeong; Seungju Son; Eunjin Lee; Seungjin Lee; Seong Yeon Choi; Hyun Woo Kim; Heejung Yang; Sang Hee Shim
Journal:  Sci Data       Date:  2022-08-27       Impact factor: 8.501

  3 in total

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