Mass spectrometry searches using MASST

Mingxun Wang^{1

2}, Alan K Jarmusch¹, Fernando Vargas^{1

3}, Alexander A Aksenov¹, Julia M Gauglitz¹, Kelly Weldon^{1

4}, Daniel Petras¹, Ricardo da Silva¹, Robert Quinn^{1

5}, Alexey V Melnik¹, Justin J J van der Hooft^{1

6}, Andrés Mauricio Caraballo-Rodríguez¹, Louis Felix Nothias¹, Christine M Aceves¹, Morgan Panitchpakdi¹, Elizabeth Brown¹, Francesca Di Ottavio⁷, Nicole Sikora¹, Emmanuel O Elijah¹, Lara Labarta-Bajo³, Emily C Gentry¹, Shabnam Shalapour⁸, Kathleen E Kyle⁹, Sara P Puckett¹⁰, Jeramie D Watrous¹¹, Carolina S Carpenter⁴, Amina Bouslimani¹, Madeleine Ernst¹, Austin D Swafford⁴, Elina I Zúñiga³, Marcy J Balunas¹⁰, Jonathan L Klassen⁹, Rohit Loomba^{4

12}, Rob Knight^{4

13

14}, Nuno Bandeira^{4

14

15}, Pieter C Dorrestein^{16

17

18

19}

Affiliations

¹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
² Ometa Labs LLC, San Diego, CA, USA.
³ Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
⁴ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁵ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
⁶ Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
⁷ Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, Teramo, TE, Italy.
⁸ Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
⁹ Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
¹⁰ Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA.
¹¹ Department of Medicine, University of California San Diego, San Diego, California, USA.
¹² Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA.
¹³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
¹⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
¹⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
¹⁶ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
¹⁷ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
¹⁸ Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
¹⁹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.

PMID: 31894142
PMCID: PMC7236533
DOI: 10.1038/s41587-019-0375-9

Mass spectrometry searches using MASST

Mingxun Wang et al. Nat Biotechnol. 2020 Jan.

. 2020 Jan;38(1):23-26.

doi: 10.1038/s41587-019-0375-9.

Authors

Affiliations

¹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
² Ometa Labs LLC, San Diego, CA, USA.
³ Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
⁴ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁵ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
⁶ Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
⁷ Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, Teramo, TE, Italy.
⁸ Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
⁹ Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
¹⁰ Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA.
¹¹ Department of Medicine, University of California San Diego, San Diego, California, USA.
¹² Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA.
¹³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
¹⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
¹⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
¹⁶ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
¹⁷ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
¹⁸ Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
¹⁹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.

PMID: 31894142
PMCID: PMC7236533
DOI: 10.1038/s41587-019-0375-9

No abstract available

PubMed Disclaimer

Conflict of interest statement

Competing interest: Mingxun Wang is the founder of Ometa and consults for Sirenas and Pieter C. Dorrestein is on the scientific advisory board of Sirenas.

Figures

**Figure 1.. MASST search, reporting and match visualization.**
a. Overview of MASST query procedure. MASST queries MS/MS spectra against all public metabolomics data, including spectra deposited in GNPS, Metabolomics Workbench and Metabolights. Combining these matches with sample information provides users with a report containing MS/MS compound annotation and MS/MS sample information (metadata). Once a MASST search is completed at https://proteosafe-extensions.ucsd.edu/masst/, the results can be found in the user’s job tab or using a link provided over email. b. The opening page is shown. There are two options (2 and 3) for inspecting the data and additional options for cloning a job (1). Clicking (2) will reveal all MS/MS spectral matches within the user defined settings. There can be none, one, or more than one match for a given input spectrum. c. Clicking (3) will reveal all data sets that contain an MS/MS spectrum that has a match to the input spectrum and any associated metadata. d. clicking on “View Mirror Match” (4) shows the mirror match between the input spectrum and the merged MS/MS spectrum enabling manual inspection of a match; “View MSV0000…..” (5) brings the user to the data set: all uploaded information associated with this data set can be found or is linked in this location. (6) Opens up the file information window and tabulated metadata. (7) shows the files where MS/MS matches are found and (8) Links-out to full sample information for the file. (9) Displays the abbreviated (and filterable) sample information associated with the files. If no sample information has been uploaded with the original data, then this field will be blank. The MASST_GNPS job link for this search to enable the reader to navigate the same results can be found here. https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=bac3d3788e704af59e4a15a5146e4d6b

See this image and copyright information in PMC

Comment in

Mass Spectrometry Search Tool (MASST).
Singh A. Singh A. Nat Methods. 2020 Feb;17(2):128. doi: 10.1038/s41592-020-0743-x. Nat Methods. 2020. PMID: 32020093 No abstract available.

References

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Mass spectrometry searches using MASST

Affiliations

Mass spectrometry searches using MASST

Authors

Affiliations

Conflict of interest statement

Figures

Comment in

References

Publication types

MeSH terms

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LinkOut - more resources

Full Text Sources