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Nicole Sikora
Researcher at University of Montana
Publications - 13
Citations - 578
Nicole Sikora is an academic researcher from University of Montana. The author has contributed to research in topics: Metabolome & Mass spectrometry. The author has an hindex of 6, co-authored 12 publications receiving 268 citations. Previous affiliations of Nicole Sikora include University of California, San Diego.
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Journal ArticleDOI
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
Allegra T. Aron,Emily C. Gentry,Kerry L. McPhail,Louis-Félix Nothias,Mélissa Nothias-Esposito,Amina Bouslimani,Daniel Petras,Daniel Petras,Julia M. Gauglitz,Nicole Sikora,Fernando Vargas,Fernando Vargas,Justin J. J. van der Hooft,Madeleine Ernst,Kyo Bin Kang,Christine M. Aceves,Andrés Mauricio Caraballo-Rodríguez,Irina Koester,Irina Koester,Kelly C. Weldon,Kelly C. Weldon,Samuel Bertrand,Catherine Roullier,Kunyang Sun,Richard M. Tehan,Cristopher A. Boya P.,Martin H. Christian,Marcelino Gutiérrez,Aldo Moreno Ulloa,Javier Andres Tejeda Mora,Randy Mojica-Flores,Johant Lakey-Beitia,Victor Vásquez-Chaves,Yilue Zhang,Angela I. Calderón,Nicole Tayler,Robert A. Keyzers,Fidele Tugizimana,Nombuso Ndlovu,Alexander A. Aksenov,Alan K. Jarmusch,Robin Schmid,Andrew W. Truman,Nuno Bandeira,Mingxun Wang,Pieter C. Dorrestein +45 more
TL;DR: This protocol describes how to use GNPS to explore uploaded metabolomics data, and provides step-by-step instructions for creating reproducible, high-quality molecular networks.
Journal ArticleDOI
Mass spectrometry searches using MASST
Mingxun Wang,Alan K. Jarmusch,Fernando Vargas,Fernando Vargas,Alexander A. Aksenov,Julia M. Gauglitz,Kelly C. Weldon,Kelly C. Weldon,Daniel Petras,Ricardo Silva,Robert A. Quinn,Robert A. Quinn,Alexey V. Melnik,Justin J. J. van der Hooft,Justin J. J. van der Hooft,Andrés Mauricio Caraballo-Rodríguez,Louis-Félix Nothias,Christine M. Aceves,Morgan Panitchpakdi,Elizabeth Brown,Francesca Di Ottavio,Nicole Sikora,Emmanuel O. Elijah,Lara Labarta-Bajo,Emily C. Gentry,Shabnam Shalapour,Kathleen E. Kyle,Sara P. Puckett,Jeramie D. Watrous,Carolina S. Carpenter,Amina Bouslimani,Madeleine Ernst,Austin D. Swafford,Elina I. Zuniga,Marcy J. Balunas,Jonathan L. Klassen,Rohit Loomba,Rob Knight,Nuno Bandeira,Nuno Bandeira,Pieter C. Dorrestein +40 more
TL;DR: A webenabled mass spectrometry (MS) search engine, named Mass Spectrometry Search Tool (MASST), is introduced by enabling searches of all small-molecule tandem MS (MS/MS) data in public metabolomics repositories, it is proposed that MASST will unlock these resources for clinical, environmental and natural product applications.
Journal ArticleDOI
ReDU: a framework to find and reanalyze public mass spectrometry data
Alan K. Jarmusch,Alan K. Jarmusch,Mingxun Wang,Mingxun Wang,Christine M. Aceves,Christine M. Aceves,Rohit S. Advani,Rohit S. Advani,Shaden Aguirre,Shaden Aguirre,Alexander A. Aksenov,Alexander A. Aksenov,Gajender Aleti,Allegra T. Aron,Allegra T. Aron,Anelize Bauermeister,Anelize Bauermeister,Sanjana Bolleddu,Sanjana Bolleddu,Amina Bouslimani,Amina Bouslimani,Andrés M. C. Rodríguez,Andrés M. C. Rodríguez,Rama Chaar,Rama Chaar,Roxana Coras,Emmanuel O. Elijah,Emmanuel O. Elijah,Madeleine Ernst,Madeleine Ernst,Madeleine Ernst,Julia M. Gauglitz,Julia M. Gauglitz,Emily C. Gentry,Emily C. Gentry,Makhai Husband,Makhai Husband,Scott A. Jarmusch,Kenneth L. Jones,Kenneth L. Jones,Zdenek Kamenik,Audrey Le Gouellec,Aileen Lu,Aileen Lu,Laura-Isobel McCall,Kerry L. McPhail,Michael J. Meehan,Michael J. Meehan,Alexey V. Melnik,Alexey V. Melnik,Riya Christina Menezes,Yessica Alejandra Montoya Giraldo,Ngoc Hung Nguyen,Ngoc Hung Nguyen,Louis-Félix Nothias,Louis-Félix Nothias,Mélissa Nothias-Esposito,Mélissa Nothias-Esposito,Morgan Panitchpakdi,Morgan Panitchpakdi,Daniel Petras,Daniel Petras,Robert A. Quinn,Nicole Sikora,Nicole Sikora,Justin J. J. van der Hooft,Justin J. J. van der Hooft,Fernando Vargas,Fernando Vargas,Alison Vrbanac,Kelly C. Weldon,Kelly C. Weldon,Rob Knight,Nuno Bandeira,Nuno Bandeira,Pieter C. Dorrestein +75 more
TL;DR: Repository-scale reanalysis of public mass spectrometry-based metabolomics data is facilitated by the Reanalysis of Data User (ReDU) interface, a system that uses consistent formatting and controlled vocabularies for metadata capture.
Journal ArticleDOI
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.
Julia M. Gauglitz,Julia M. Gauglitz,Christine M. Aceves,Alexander A. Aksenov,Gajender Aleti,Jehad Almaliti,Amina Bouslimani,Elizabeth Brown,Anaamika Campeau,Andrés Mauricio Caraballo-Rodríguez,Rama Chaar,Ricardo Silva,Alyssa M. Demko,Francesca Di Ottavio,Emmanuel O. Elijah,Madeleine Ernst,L. Paige Ferguson,Xavier Holmes,Alan K. Jarmusch,Lingjing Jiang,Kyo Bin Kang,Irina Koester,Brian Kwan,Jie Li,Yueying Li,Alexey V. Melnik,Carlos Molina-Santiago,Bohan Ni,Aaron L. Oom,Morgan Panitchpakdi,Daniel Petras,Robert A. Quinn,Nicole Sikora,Katharina Spengler,Bahar Teke,Anupriya Tripathi,Sabah Ul-Hasan,Justin J. J. van der Hooft,Fernando Vargas,Alison Vrbanac,Anthony Q. Vu,Steven C Wang,Kelly C. Weldon,Kayla Wilson,Jacob M. Wozniak,Michael Yoon,Nuno Bandeira,Pieter C. Dorrestein,Pieter C. Dorrestein +48 more
TL;DR: The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products.
Journal ArticleDOI
Enhancing untargeted metabolomics using metadata-based source annotation.
Julia M. Gauglitz,Kiana West,Wout Bittremieux,Candace L. Williams,Kelly C. Weldon,Morgan Panitchpakdi,Francesca Di Ottavio,Christine M. Aceves,Elizabeth Brown,Nicole Sikora,Alan K. Jarmusch,Cameron Martino,Anupriya Tripathi,Michael J. Meehan,Kathleen Dorrestein,Justin P. Shaffer,Roxana Coras,Fernando Vargas,Lindsay DeRight Goldasich,Tara Schwartz,MacKenzie Bryant,Gregory Humphrey,Abigail J. Johnson,Katharina Spengler,Pedro Belda-Ferre,Edgar Diaz,Daniel McDonald,Qiyun Zhu,Emmanuel O. Elijah,Mingxun Wang,Clarisse Marotz,Kate E. Sprecher,Daniela Vargas-Robles,Dana Withrow,Gail Ackermann,Lourdes Herrera,Barry J. Bradford,Lucas M. M. Marques,Juliano Geraldo Amaral,Rodrigo Moreira da Silva,Flávio P. Veras,Thiago Mattar Cunha,Renê Donizeti Ribeiro de Oliveira,Paulo Louzada-Junior,Robert H. Mills,Paulina K. Piotrowski,Stephanie L. Servetas,Sandra M. Da Silva,Christina M. Jones,Nancy J. Lin,Katrice A. Lippa,Scott Jackson,Rima Kaddurah Daouk,Douglas Galasko,Parambir S. Dulai,Tatyana I. Kalashnikova,Curt Wittenberg,Robert Terkeltaub,Megan M. Doty,Jae H. Kim,Kyung E. Rhee,Julia Beauchamp-Walters,Kenneth P. Wright,Maria Gloria Dominguez-Bello,Mark J. Manary,Michelli F. Oliveira,Brigid S. Boland,Norberto Peporine Lopes,Monica Guma,Austin D. Swafford,Rachel J. Dutton,Rob Knight,Pieter C. Dorrestein +72 more
TL;DR: Reference-data-driven analysis was used to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS reference library as discussed by the authors .