New Results
A Universal Language for Finding Mass Spectrometry Data Patterns
Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, View ORCID ProfileVanessa V. Phelan, View ORCID ProfileWout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Tito Damiani, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, View ORCID ProfileKyo Bin Kang, Roland D Kersten, Hyunwoo Kim, Riley D. Kirk, View ORCID ProfileOliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, View ORCID ProfileMichael T. Marty, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Timo H.J. Niedermeyer, Trent R. Northen, Kirsten E. Overdahl, Tomáš Pluskal, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Kozo Nishida, Yuki Matsuzawa, View ORCID ProfileJustin J.J. van der Hooft, Andrea Vicini, Axel Walter, View ORCID ProfileTilmann Weber, Quanbo Xiong, Tao Xu, Haoqi Nina Zhao, Pieter C. Dorrestein, View ORCID ProfileMingxun Wang
doi: https://doi.org/10.1101/2022.08.06.503000
Alan K. Jarmusch
1Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States
Allegra T. Aron
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Daniel Petras
3Functional Metabolomics Lab, CMFI Cluster of Excellence, University of Tuebingen, University of Tuebingen, Tuebingen, Germany
Vanessa V. Phelan
4Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, United States
Wout Bittremieux
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Deepa D. Acharya
5Biologicals and Natural Products Discovery, Crop Protection R & D, Corteva Agriscences, 9330 Zionsville Rd, Indianapolis, IN, 46268, United States
Mohammed M. A. Ahmed
6BioMolecular Sciences, School of Pharmacy, University of Mississippi, 408 Faser Hall, University, Mississippi, 38677-1848, United States
7Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, 1 El Mokhayam El Daem St., Nasr City, Cairo, 11371, Egypt
Anelize Bauermeister
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Matthew J. Bertin
8Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, 02881, United States
Paul D. Boudreau
9BioMolecular Sciences, School of Pharmacy, University of Mississippi, 405 Faser Hall, University, Mississippi, 38677-1848, United States
Ricardo M. Borges
10Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
Benjamin P. Bowen
11Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, California, United States
12The Joint Genome Institute, Lawrence Berkeley National Lab. One Cyclotron Road. Berkeley, CA, 94720, Berkeley, California, United States
Christopher J. Brown
13Mass Spectrometry Center of Expertise, Regulatory and Stewardship, Mass Spectrometry Center of Expertise, Regulatory and Stewardship, Corteva Agriscences, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States
Fernanda O. Chagas
10Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
Kenneth D. Clevenger
14Biologicals and Natural Products, Crop Protection R & D, Corteva Agriscences, Indianapolis, United States
Mario S. P. Correia
15Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
William J. Crandall
16Clinical Biomarkers Laboratory, School of Medicine, Emory University, Atlanta, GA, 30332, United States
Max Crüsemann
17Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, Bonn, 53115, Germany
Tito Damiani
18Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Praha 6, 160 00, Czech Republic
Oliver Fiehn
19Department of Chemistry, University of California Davis, Davis, United States
Neha Garg
20School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
William H Gerwick
21Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Jeffrey R. Gilbert
13Mass Spectrometry Center of Expertise, Regulatory and Stewardship, Mass Spectrometry Center of Expertise, Regulatory and Stewardship, Corteva Agriscences, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States
Daniel Globisch
15Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Paulo Wender P. Gomes
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Steffen Heuckeroth
22Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, Münster, 48149, Germany
C. Andrew James
23Center for Urban Waters, University of Washington, Tacoma, United States
Scott A. Jarmusch
24Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kongens Lyngby, Denmark
Sarvar A. Kakhkhorov
25Laboratory of Physical and Chemical Methods of Research, Center for Advanced Technologies, Tashkent, 100174, Uzbekistan
Kyo Bin Kang
26College of Pharmacy, Sookmyung Women’s University, Seoul, Republic of Korea
Roland D Kersten
27Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, 428 Church Street, Ann Arbor, MI, 48104, United States
Hyunwoo Kim
28College of Pharmacy, Dongguk University, 32 Dongguk-ro, Goyang, 10326, Republic of Korea
Riley D. Kirk
29College of Pharmacy, University of Rhode Island, Kingston, RI, 02881, United States
Oliver Kohlbacher
30Applied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen; Institute for Bioinformatics and Medical Informatics, University of Tuebingen; Institute for Translational Bioinformatics, University Hospital Tuebingen, Tübingen, 72076, Germany
Eftychia E. Kontou
31The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, building 220, Kongens Lyngby, 2800, Denmark
Ken Liu
16Clinical Biomarkers Laboratory, School of Medicine, Emory University, Atlanta, GA, 30332, United States
Itzel Lizama-Chamu
32Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, United States
Gordon T. Luu
32Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, United States
Tal Luzzatto Knaan
33Department of Marine Biology, The Leon H. Cherney School of Marine Sciences, University of Haifa, 199 Aba Koushy Ave, Haifa, 3498838, Israel
Michael T. Marty
34Department of Chemstry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, AZ, 85721, United States
Andrew C. McAvoy
35School of Chemistry and Biochemistry,, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
Laura-Isobel McCall
36Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, United States
Osama G. Mohamed
37Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el-Aini St., Cairo, 11562, Egypt
38Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
Omri Nahor
33Department of Marine Biology, The Leon H. Cherney School of Marine Sciences, University of Haifa, 199 Aba Koushy Ave, Haifa, 3498838, Israel
Timo H.J. Niedermeyer
39Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, Halle (Saale), 06114, Germany
Trent R. Northen
40Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, United States
41The Joint Genome Institute, Lawrence Berkeley National Lab. One Cyclotron Road. Berkeley, CA, 94720, Berkeley, United States
Kirsten E. Overdahl
42Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health
Tomáš Pluskal
18Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Praha 6, 160 00, Czech Republic
Johannes Rainer
43Institute for Biomedicine (Affiliated to the University of Lübeck), Eurac Research, Bolzano, 39100, Italy
Raphael Reher
39Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, Halle (Saale), 06114, Germany
Elys Rodriguez
19Department of Chemistry, University of California Davis, Davis, United States
Timo T. Sachsenberg
44Applied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen, Tübingen, Germany
Laura M. Sanchez
32Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, United States
Robin Schmid
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Cole Stevens
45Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States
Zhenyu Tian
46Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, United States
Ashootosh Tripathi
38Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
47Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, United States
Hiroshi Tsugawa
48Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo, 184-8588, Japan
49RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
50RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
Kozo Nishida
48Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo, 184-8588, Japan
Yuki Matsuzawa
48Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo, 184-8588, Japan
Justin J.J. van der Hooft
51Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
52Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
Andrea Vicini
43Institute for Biomedicine (Affiliated to the University of Lübeck), Eurac Research, Bolzano, 39100, Italy
Axel Walter
44Applied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen, Tübingen, Germany
Tilmann Weber
53The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, Kongens Lyngby, 2800, Denmark
Quanbo Xiong
54Crop Protection R & D, Corteva Agriscences, 9330 Zionsville Road, Indianapolis, IN, 46268, United States
Tao Xu
55Data Science and Bioinformatics, Corteva Agriscences, Dublin, United States
Haoqi Nina Zhao
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Pieter C. Dorrestein
2Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
Mingxun Wang
56Department of Computer Science, University of California Riverside, Riverside, CA, 92521, United States
Abstract
Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.
Competing Interest Statement
PCD is an advisor to Cybele and a Co-founder and scientific advisor to Ometa and Enveda with prior approval by UC San Diego. MW is a co-founder of Ometa Labs LLC. TRN. is an advisor of Brightseed Bio. JJJvdH is a member of the Scientific Advisory Board of NAICONS Srl., Milano, Italy.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Posted August 07, 2022.
A Universal Language for Finding Mass Spectrometry Data Patterns
Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Tito Damiani, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, Kyo Bin Kang, Roland D Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, Michael T. Marty, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Timo H.J. Niedermeyer, Trent R. Northen, Kirsten E. Overdahl, Tomáš Pluskal, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Kozo Nishida, Yuki Matsuzawa, Justin J.J. van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Haoqi Nina Zhao, Pieter C. Dorrestein, Mingxun Wang
bioRxiv 2022.08.06.503000; doi: https://doi.org/10.1101/2022.08.06.503000
A Universal Language for Finding Mass Spectrometry Data Patterns
Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Tito Damiani, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, Kyo Bin Kang, Roland D Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, Michael T. Marty, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Timo H.J. Niedermeyer, Trent R. Northen, Kirsten E. Overdahl, Tomáš Pluskal, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Kozo Nishida, Yuki Matsuzawa, Justin J.J. van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Haoqi Nina Zhao, Pieter C. Dorrestein, Mingxun Wang
bioRxiv 2022.08.06.503000; doi: https://doi.org/10.1101/2022.08.06.503000
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