Enhancing untargeted metabolomics using metadata-based source annotation

Autor: Julia M. Gauglitz, Kiana A. West, Wout Bittremieux, Candace L. Williams, Kelly C. Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M. Aceves, Elizabeth Brown, Nicole C. 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 Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro 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 A. 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 Manary, Michelli F. Oliveira, Brigid S. Boland, Norberto Peporine Lopes, Monica Guma, Austin D. Swafford, Rachel J. Dutton, Rob Knight, Pieter C. Dorrestein

Publikováno v: Nature biotechnology, vol 40, iss 12
Nat Biotechnol

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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fadcc5a8ebaed4c919d942163887bc61
https://doi.org/10.1038/s41587-022-01368-1

Pyruvate:ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria

Autor: Jens Appel, Marko Boehm, Martin Hagemann, Yingying Wang, Natalia Battchikova, Karoline Terberger, Kirstin Gutekunst, Xi Chen, Katharina Spengler, Thomas Barske, Stefan Timm

Publikováno v: eLife. 11

The decarboxylation of pyruvate is a central reaction in the carbon metabolism of all organisms. Both the pyruvate:ferredoxin oxidoreductase (PFOR) and the pyruvate dehydrogenase (PDH) complex catalyze this reaction. Whereas PFOR reduces ferredoxin,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::324585569626cce55be27005447d8199
https://doi.org/10.7554/elife.71339

Reference data-set driven metabolomics

Autor: Rodrigo Moreira da Silva, Tara Schwartz, Juliano Geraldo Amaral, Thiago M. Cunha, Scott Jackson, MacKenzie Bryant, Francesca Diottavio, Robert H. Mills, Norberto Peporine Lopes, Robert Terkeltaub, Katrice Lippa, Brigid S. Boland, Christina Jones, Pieter C. Dorrestein, Morgan Panitchpakdi, Mingxun Wang, Megan M. Doty, Christine M. Aceves, Candace L. Williams, Fernando Vargas, Monica Guma, Michael J. Meehan, Lucas Miranda Marques, Renê Donizeti Ribeiro de Oliveira, Rachel J. Dutton, Stephanie Servetas, Nancy Lin, Qiyun Zhu, Paulo Louzada-Junior, Jae H. Kim, Edgar Diaz, Douglas Galasko, Austin D. Swafford, Maria Gloria Dominguez-Bello, Nicole Sikora, Paulina Piotrowski, Wout Bittremieux, Abigail J. Johnson, Cameron Martino, Clarisse Marotz, Rob Knight, Lourdes Herrera, Michelli F. Oliveira, Kate E. Sprecher, Rima Kaddurah Daouk, Elijah Emmanuel, Dana Withrow, Tatyana Kalashnikova, Curt Wittenberg, Kiana West, Pedro Belda-Ferre, Alan K. Jarmusch, Daniela Vargas Robles, Mark Manery, Barry J. Bradford, Kathleen Dorrestein, Flávio Protaso Veras, Kenneth P. Wright, Gail Ackermann, Greg Humphrey, Daniel McDonald, Lindsay DeRight Goldasich, Anupriya Tripathi, Sandra DaSilva, Julia Gauglitz, David Gonzalez, Roxana Coras, Elizabeth Brown, Kyung E. Rhee, Katharina Spengler, Parambir S. Dulai, Julia Beauchamp-Walters, Kelly C. Weldon, Justin P. Shaffer

Human untargeted metabolomics studies succeed in annotating only ~10% of molecular features. We, therefore, introduce reference data-driven analysis that uses the source data as a pseudo-MS/MS reference library to match against human metabolomics MS/

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::e9f8b9788cae579d9220939f069d2709
https://doi.org/10.21203/rs.3.rs-654519/v1

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages

Autor: Alexey V. Melnik, Francesca Di Ottavio, Carlos Molina-Santiago, Jacob M. Wozniak, Anaamika Campeau, Daniel Petras, Kyo Bin Kang, Jehad Almaliti, Morgan Panitchpakdi, Steven C Wang, Robert A. Quinn, Irina Koester, Nuno Bandeira, Katharina Spengler, Brian Kwan, Gajender Aleti, Alexander A. Aksenov, Fernando Vargas, Yueying Li, Kelly C. Weldon, Jie Li, Xavier Holmes, Bohan Ni, Aaron L. Oom, Elizabeth Brown, Rama Chaar, Lingjing Jiang, Ricardo Silva, Alison Vrbanac, Emmanuel O. Elijah, Bahar Teke, Pieter C. Dorrestein, Kayla Wilson, Madeleine Ernst, Anupriya Tripathi, Amina Bouslimani, Michael Yoon, Justin J. J. van der Hooft, Christine M. Aceves, Alyssa M. Demko, Nicole Sikora, Anthony Q. Vu, Julia M. Gauglitz, Andrés Mauricio Caraballo-Rodríguez, Sabah Ul-Hasan, Alan K. Jarmusch, L. Paige Ferguson

Publikováno v: Food Chemistry, 302
Food Chemistry 302 (2020)

In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrom

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e00b2d8f8476b30588157d87616ba2c9
https://research.wur.nl/en/publications/untargeted-mass-spectrometry-based-metabolomics-approach-unveils-

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

Autor: Anthony Q. Vu, Kyo Bin Kang, Francesca Di Ottavio, Justin J. J. van der Hooft, Christine M. Aceves, Alyssa M. Demko, Pieter C. Dorrestein, Bohan Ni, Robert A. Quinn, Fernando Vargas, Katharina Spengler, Daniel Petras, Ricardo Silva, Julia M. Gauglitz, Emmanuel O. Elijah, Amina Bouslimani, Jehad Almaliti, Lingjing Jiang, Nicole Sikora, Anaamika Campeau, L. Paige Ferguson, Yueying Li, Sabah Ul-Hasan, Bahar Teke, Kelly C. Weldon, Xavier Holmes, Morgan Panitchpakdi, Jacob M. Wozniak, Michael Yoon, Steven C Wang, Madeleine Ernst, Alexander A. Aksenov, Irina Koester, Elizabeth Brown, Alison Vrbanac, Nuno Bandeira, Jie Li, Gajender Aleti, Rama Chaar, Brian Kwan, Aaron L. Oom, Alan K. Jarmusch, Andrés Mauricio Caraballo-Rodríguez, Anupriya Tripathi, Kayla Wilson, Alexey V. Melnik, Carlos Molina-Santiago

A major aspect of our daily lives is the need to acquire, store and prepare our food. Storage and preparation can have drastic effects on the compositional chemistry of our foods, but we have a limited understanding of the temporal nature of processe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7c550241a4e2fa8c7f1ad6cef63edc8d