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Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Interpreting untargeted mass spectrometry (MS) data is challenging due to incomplete reference libraries. Here, the authors created the nearest neighbor suspect spectral library from largescale public MS data, significantly enhancing the ability to hypothesize structures for unknown mass spectra.

Wout Bittremieux
Nicole E. Avalon
Pieter C. Dorrestein
ResearchOpen Access20 Dec 2023
Nature Communications

Volume: 14, P: 1-15
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.

Smruthi Karthikeyan
Joshua I. Levy
Rob Knight
ResearchOpen Access07 Jul 2022
Nature

Volume: 609, P: 101-108
ReDU: a framework to find and reanalyze public mass spectrometry data

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.

Alan K. Jarmusch
Mingxun Wang
Pieter C. Dorrestein
Research17 Aug 2020
Nature Methods

Volume: 17, P: 901-904
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation

Julia M. Gauglitz
Kiana A. West
Pieter C. Dorrestein
Amendments and Corrections18 Oct 2023
Nature Biotechnology

Volume: 41, P: 1656
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

The outbreak.info genomic reports provides comprehensive and detailed information about SARS-CoV-2 lineages and mutations worldwide, which facilitates near real-time genomic surveillance.

Karthik Gangavarapu
Alaa Abdel Latif
Laura D. Hughes
Research23 Feb 2023
Nature Methods

Volume: 20, P: 512-522
Enhancing untargeted metabolomics using metadata-based source annotation

Metabolomics is improved by using a reference library of both known and unknown molecules.

Julia M. Gauglitz
Kiana A. West
Pieter C. Dorrestein
Research07 Jul 2022
Nature Biotechnology

Volume: 40, P: 1774-1779
Mass spectrometry searches using MASST

Mingxun Wang
Alan K. Jarmusch
Pieter C. Dorrestein
Correspondence01 Jan 2020
Nature Biotechnology

Volume: 38, P: 23-26
Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Global Natural Product Social Molecular Networking (GNPS) is an online tandem mass spectrometry (MS²) data curation and analysis infrastructure. This protocol describes how to use GNPS to explore uploaded metabolomics data.

Allegra T. Aron
Emily C. Gentry
Pieter C. Dorrestein
Protocols13 May 2020
Nature Protocols

Volume: 15, P: 1954-1991
30-day morbidity and mortality of sleeve gastrectomy, Roux-en-Y gastric bypass and one anastomosis gastric bypass: a propensity score-matched analysis of the GENEVA data

Rishi Singhal
Victor Roth Cardoso
Mehmet Saydam
ResearchOpen Access15 Dec 2021
International Journal of Obesity

Volume: 46, P: 750-757

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