A universal language for finding mass spectrometry data patterns.
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| Format: | Artículo científico |
| Sprache: | en |
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Nature methods
2025
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| author | Damiani, Tito Jarmusch, Alan K Aron, Allegra T Petras, Daniel Phelan, Vanessa V Zhao, Haoqi Nina Bittremieux, Wout Acharya, Deepa D Ahmed, Mohammed M A Bauermeister, Anelize Bertin, Matthew J Boudreau, Paul D Borges, Ricardo M Bowen, Benjamin P Brown, Christopher J Chagas, Fernanda O Clevenger, Kenneth D Correia, Mario S P Crandall, William J Crüsemann, Max Fahy, Eoin Fiehn, Oliver Garg, Neha Gerwick, William H Gilbert, Jeffrey R Globisch, Daniel Gomes, Paulo Wender P Heuckeroth, Steffen James, C Andrew Jarmusch, Scott A Kakhkhorov, Sarvar A Kang, Kyo Bin Kessler, Nikolas Kersten, Roland D Kim, Hyunwoo Kirk, Riley D Kohlbacher, Oliver Kontou, Eftychia E Liu, Ken Lizama-Chamu, Itzel Luu, Gordon T Luzzatto Knaan, Tal Mannochio-Russo, Helena Marty, Michael T Matsuzawa, Yuki McAvoy, Andrew C McCall, Laura-Isobel Mohamed, Osama G Nahor, Omri Neuweger, Heiko Niedermeyer, Timo H J Nishida, Kozo Northen, Trent R Overdahl, Kirsten E Rainer, Johannes Reher, Raphael Rodriguez, Elys Sachsenberg, Timo T Sanchez, Laura M Schmid, Robin Stevens, Cole Subramaniam, Shankar Tian, Zhenyu Tripathi, Ashootosh Tsugawa, Hiroshi van der Hooft, Justin J J Vicini, Andrea Walter, Axel Weber, Tilmann Xiong, Quanbo Xu, Tao Pluskal, Tomáš Dorrestein, Pieter C Wang, Mingxun |
| author_facet | Damiani, Tito Jarmusch, Alan K Aron, Allegra T Petras, Daniel Phelan, Vanessa V Zhao, Haoqi Nina Bittremieux, Wout Acharya, Deepa D Ahmed, Mohammed M A Bauermeister, Anelize Bertin, Matthew J Boudreau, Paul D Borges, Ricardo M Bowen, Benjamin P Brown, Christopher J Chagas, Fernanda O Clevenger, Kenneth D Correia, Mario S P Crandall, William J Crüsemann, Max Fahy, Eoin Fiehn, Oliver Garg, Neha Gerwick, William H Gilbert, Jeffrey R Globisch, Daniel Gomes, Paulo Wender P Heuckeroth, Steffen James, C Andrew Jarmusch, Scott A Kakhkhorov, Sarvar A Kang, Kyo Bin Kessler, Nikolas Kersten, Roland D Kim, Hyunwoo Kirk, Riley D Kohlbacher, Oliver Kontou, Eftychia E Liu, Ken Lizama-Chamu, Itzel Luu, Gordon T Luzzatto Knaan, Tal Mannochio-Russo, Helena Marty, Michael T Matsuzawa, Yuki McAvoy, Andrew C McCall, Laura-Isobel Mohamed, Osama G Nahor, Omri Neuweger, Heiko Niedermeyer, Timo H J Nishida, Kozo Northen, Trent R Overdahl, Kirsten E Rainer, Johannes Reher, Raphael Rodriguez, Elys Sachsenberg, Timo T Sanchez, Laura M Schmid, Robin Stevens, Cole Subramaniam, Shankar Tian, Zhenyu Tripathi, Ashootosh Tsugawa, Hiroshi van der Hooft, Justin J J Vicini, Andrea Walter, Axel Weber, Tilmann Xiong, Quanbo Xu, Tao Pluskal, Tomáš Dorrestein, Pieter C Wang, Mingxun Damiani, Tito Jarmusch, Alan K Aron, Allegra T Petras, Daniel Phelan, Vanessa V Zhao, Haoqi Nina Bittremieux, Wout Acharya, Deepa D Ahmed, Mohammed M A Bauermeister, Anelize Bertin, Matthew J Boudreau, Paul D Borges, Ricardo M Bowen, Benjamin P Brown, Christopher J Chagas, Fernanda O Clevenger, Kenneth D Correia, Mario S P Crandall, William J Crüsemann, Max Fahy, Eoin Fiehn, Oliver Garg, Neha Gerwick, William H Gilbert, Jeffrey R Globisch, Daniel Gomes, Paulo Wender P Heuckeroth, Steffen James, C Andrew Jarmusch, Scott A Kakhkhorov, Sarvar A Kang, Kyo Bin Kessler, Nikolas Kersten, Roland D Kim, Hyunwoo Kirk, Riley D Kohlbacher, Oliver Kontou, Eftychia E Liu, Ken Lizama-Chamu, Itzel Luu, Gordon T Luzzatto Knaan, Tal Mannochio-Russo, Helena Marty, Michael T Matsuzawa, Yuki McAvoy, Andrew C McCall, Laura-Isobel Mohamed, Osama G Nahor, Omri Neuweger, Heiko Niedermeyer, Timo H J Nishida, Kozo Northen, Trent R Overdahl, Kirsten E Rainer, Johannes Reher, Raphael Rodriguez, Elys Sachsenberg, Timo T Sanchez, Laura M Schmid, Robin Stevens, Cole Subramaniam, Shankar Tian, Zhenyu Tripathi, Ashootosh Tsugawa, Hiroshi van der Hooft, Justin J J Vicini, Andrea Walter, Axel Weber, Tilmann Xiong, Quanbo Xu, Tao Pluskal, Tomáš Dorrestein, Pieter C Wang, Mingxun |
| collection | PubMed - marine biology |
| contents | A universal language for finding mass spectrometry data patterns. Damiani, Tito Jarmusch, Alan K Aron, Allegra T Petras, Daniel Phelan, Vanessa V Zhao, Haoqi Nina Bittremieux, Wout Acharya, Deepa D Ahmed, Mohammed M A Bauermeister, Anelize Bertin, Matthew J Boudreau, Paul D Borges, Ricardo M Bowen, Benjamin P Brown, Christopher J Chagas, Fernanda O Clevenger, Kenneth D Correia, Mario S P Crandall, William J Crüsemann, Max Fahy, Eoin Fiehn, Oliver Garg, Neha Gerwick, William H Gilbert, Jeffrey R Globisch, Daniel Gomes, Paulo Wender P Heuckeroth, Steffen James, C Andrew Jarmusch, Scott A Kakhkhorov, Sarvar A Kang, Kyo Bin Kessler, Nikolas Kersten, Roland D Kim, Hyunwoo Kirk, Riley D Kohlbacher, Oliver Kontou, Eftychia E Liu, Ken Lizama-Chamu, Itzel Luu, Gordon T Luzzatto Knaan, Tal Mannochio-Russo, Helena Marty, Michael T Matsuzawa, Yuki McAvoy, Andrew C McCall, Laura-Isobel Mohamed, Osama G Nahor, Omri Neuweger, Heiko Niedermeyer, Timo H J Nishida, Kozo Northen, Trent R Overdahl, Kirsten E Rainer, Johannes Reher, Raphael Rodriguez, Elys Sachsenberg, Timo T Sanchez, Laura M Schmid, Robin Stevens, Cole Subramaniam, Shankar Tian, Zhenyu Tripathi, Ashootosh Tsugawa, Hiroshi van der Hooft, Justin J J Vicini, Andrea Walter, Axel Weber, Tilmann Xiong, Quanbo Xu, Tao Pluskal, Tomáš Dorrestein, Pieter C Wang, Mingxun Mass Spectrometry Software Metabolomics Data Mining Programming Languages Humans Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community. |
| format | Artículo científico |
| id | pubmed_40355727 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Nature methods |
| record_format | pubmed |
| spellingShingle | A universal language for finding mass spectrometry data patterns. Damiani, Tito Jarmusch, Alan K Aron, Allegra T Petras, Daniel Phelan, Vanessa V Zhao, Haoqi Nina Bittremieux, Wout Acharya, Deepa D Ahmed, Mohammed M A Bauermeister, Anelize Bertin, Matthew J Boudreau, Paul D Borges, Ricardo M Bowen, Benjamin P Brown, Christopher J Chagas, Fernanda O Clevenger, Kenneth D Correia, Mario S P Crandall, William J Crüsemann, Max Fahy, Eoin Fiehn, Oliver Garg, Neha Gerwick, William H Gilbert, Jeffrey R Globisch, Daniel Gomes, Paulo Wender P Heuckeroth, Steffen James, C Andrew Jarmusch, Scott A Kakhkhorov, Sarvar A Kang, Kyo Bin Kessler, Nikolas Kersten, Roland D Kim, Hyunwoo Kirk, Riley D Kohlbacher, Oliver Kontou, Eftychia E Liu, Ken Lizama-Chamu, Itzel Luu, Gordon T Luzzatto Knaan, Tal Mannochio-Russo, Helena Marty, Michael T Matsuzawa, Yuki McAvoy, Andrew C McCall, Laura-Isobel Mohamed, Osama G Nahor, Omri Neuweger, Heiko Niedermeyer, Timo H J Nishida, Kozo Northen, Trent R Overdahl, Kirsten E Rainer, Johannes Reher, Raphael Rodriguez, Elys Sachsenberg, Timo T Sanchez, Laura M Schmid, Robin Stevens, Cole Subramaniam, Shankar Tian, Zhenyu Tripathi, Ashootosh Tsugawa, Hiroshi van der Hooft, Justin J J Vicini, Andrea Walter, Axel Weber, Tilmann Xiong, Quanbo Xu, Tao Pluskal, Tomáš Dorrestein, Pieter C Wang, Mingxun Mass Spectrometry Software Metabolomics Data Mining Programming Languages Humans A universal language for finding mass spectrometry data patterns. Damiani, Tito Jarmusch, Alan K Aron, Allegra T Petras, Daniel Phelan, Vanessa V Zhao, Haoqi Nina Bittremieux, Wout Acharya, Deepa D Ahmed, Mohammed M A Bauermeister, Anelize Bertin, Matthew J Boudreau, Paul D Borges, Ricardo M Bowen, Benjamin P Brown, Christopher J Chagas, Fernanda O Clevenger, Kenneth D Correia, Mario S P Crandall, William J Crüsemann, Max Fahy, Eoin Fiehn, Oliver Garg, Neha Gerwick, William H Gilbert, Jeffrey R Globisch, Daniel Gomes, Paulo Wender P Heuckeroth, Steffen James, C Andrew Jarmusch, Scott A Kakhkhorov, Sarvar A Kang, Kyo Bin Kessler, Nikolas Kersten, Roland D Kim, Hyunwoo Kirk, Riley D Kohlbacher, Oliver Kontou, Eftychia E Liu, Ken Lizama-Chamu, Itzel Luu, Gordon T Luzzatto Knaan, Tal Mannochio-Russo, Helena Marty, Michael T Matsuzawa, Yuki McAvoy, Andrew C McCall, Laura-Isobel Mohamed, Osama G Nahor, Omri Neuweger, Heiko Niedermeyer, Timo H J Nishida, Kozo Northen, Trent R Overdahl, Kirsten E Rainer, Johannes Reher, Raphael Rodriguez, Elys Sachsenberg, Timo T Sanchez, Laura M Schmid, Robin Stevens, Cole Subramaniam, Shankar Tian, Zhenyu Tripathi, Ashootosh Tsugawa, Hiroshi van der Hooft, Justin J J Vicini, Andrea Walter, Axel Weber, Tilmann Xiong, Quanbo Xu, Tao Pluskal, Tomáš Dorrestein, Pieter C Wang, Mingxun Mass Spectrometry Software Metabolomics Data Mining Programming Languages Humans Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community. |
| title | A universal language for finding mass spectrometry data patterns. |
| topic | Mass Spectrometry Software Metabolomics Data Mining Programming Languages Humans |
| url | https://pubmed.ncbi.nlm.nih.gov/40355727/ |