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Article ; Online: Weighting Low-Intensity MS/MS Ions and

Engler Hart, Chloe / Kind, Tobias / Dorrestein, Pieter C / Healey, David / Domingo-Fernández, Daniel

Journal of the American Society for Mass Spectrometry

2024 Volume 35, Issue 2, Page(s) 266–274

Abstract: Calculating spectral similarity is a fundamental step in MS/MS data analysis in untargeted metabolomics experiments, as it facilitates the identification of related spectra and the annotation of compounds. To improve matching accuracy when querying an ... ...

Abstract	Calculating spectral similarity is a fundamental step in MS/MS data analysis in untargeted metabolomics experiments, as it facilitates the identification of related spectra and the annotation of compounds. To improve matching accuracy when querying an experimental mass spectrum against a spectral library, previous approaches have proposed increasing peak intensities for high
MeSH term(s)	Tandem Mass Spectrometry ; Metabolomics/methods ; Ions
Chemical Substances	Ions
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00353
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Zs.A 4618: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 241: Show issues

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Article ; Online: The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases.

Fogelson, Kelly A / Dorrestein, Pieter C / Zarrinpar, Amir / Knight, Rob

Gastroenterology

2023 Volume 164, Issue 7, Page(s) 1069–1085

Abstract: The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we ...

Abstract	The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we focused on the rapidly expanding information about the bile acid repertoire produced by the gut microbiome, including the impacts of bile acids on a wide range of host physiological processes and diseases, and discussed the role of short-chain fatty acids and other important gut microbiome-derived metabolites. Of particular note is the action of gut microbiome-derived metabolites throughout the body, which impact processes ranging from obesity to aging to disorders traditionally thought of as diseases of the nervous system, but that are now recognized as being strongly influenced by the gut microbiome and the metabolites it produces. We also highlighted the emerging role for modifying the gut microbiome to improve health or to treat disease, including the "engineered native bacteria'' approach that takes bacterial strains from a patient, modifies them to alter metabolism, and reintroduces them. Taken together, study of the metabolites derived from the gut microbiome provided insights into a wide range of physiological and pathophysiological processes, and has substantial potential for new approaches to diagnostics and therapeutics of disease of, or involving, the gastrointestinal tract.
MeSH term(s)	Humans ; Gastrointestinal Microbiome/physiology ; Bile Acids and Salts/metabolism ; Microbiota ; Metabolome ; Microorganisms, Genetically-Modified ; Fatty Acids, Volatile
Chemical Substances	Bile Acids and Salts ; Fatty Acids, Volatile
Language	English
Publishing date	2023-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	80112-4
ISSN	1528-0012 ; 0016-5085
ISSN (online)	1528-0012
ISSN	0016-5085
DOI	10.1053/j.gastro.2023.02.022
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Ui V Zs.44: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MO 572: Show issues

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Article ; Online: The critical role that spectral libraries play in capturing the metabolomics community knowledge.

Bittremieux, Wout / Wang, Mingxun / Dorrestein, Pieter C

Metabolomics : Official journal of the Metabolomic Society

2022 Volume 18, Issue 12, Page(s) 94

Abstract: Background: Spectral library searching is currently the most common approach for compound annotation in untargeted metabolomics. Spectral libraries applicable to liquid chromatography mass spectrometry have grown in size over the past decade to include ... ...

Abstract	Background: Spectral library searching is currently the most common approach for compound annotation in untargeted metabolomics. Spectral libraries applicable to liquid chromatography mass spectrometry have grown in size over the past decade to include hundreds of thousands to millions of mass spectra and tens of thousands of compounds, forming an essential knowledge base for the interpretation of metabolomics experiments. Aim of review: We describe existing spectral library resources, highlight different strategies for compiling spectral libraries, and discuss quality considerations that should be taken into account when interpreting spectral library searching results. Finally, we describe how spectral libraries are empowering the next generation of machine learning tools in computational metabolomics, and discuss several opportunities for using increasingly accessible large spectral libraries. Key scientific concepts of review: This review focuses on the current state of spectral libraries for untargeted LC-MS/MS based metabolomics. We show how the number of entries in publicly accessible spectral libraries has increased more than 60-fold in the past eight years to aid molecular interpretation and we discuss how the role of spectral libraries in untargeted metabolomics will evolve in the near future.
MeSH term(s)	Metabolomics/methods ; Chromatography, Liquid/methods ; Tandem Mass Spectrometry/methods
Language	English
Publishing date	2022-11-19
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2250617-2
ISSN	1573-3890 ; 1573-3882
ISSN (online)	1573-3890
ISSN	1573-3882
DOI	10.1007/s11306-022-01947-y
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Zs.A 6361: Show issues

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Article ; Online: The changing metabolic landscape of bile acids - keys to metabolism and immune regulation.

Mohanty, Ipsita / Allaband, Celeste / Mannochio-Russo, Helena / El Abiead, Yasin / Hagey, Lee R / Knight, Rob / Dorrestein, Pieter C

Nature reviews. Gastroenterology & hepatology

2024

Abstract: Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The ... ...

Abstract	Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The observation that there are hundreds of bile acids, especially many amidated bile acids, necessitates a revision of many of the classical descriptions of bile acids and bile acid enzyme functions. For example, bile salt hydrolases also have transferase activity. There are now hundreds of known modifications to bile acids and thousands of bile acid-associated genes, especially when including the microbiome, distributed throughout the human body (for example, there are >2,400 bile salt hydrolases alone). The fact that so much of our genetic and small-molecule repertoire, in both amount and diversity, is dedicated to bile acid function highlights the centrality of bile acids as key regulators of metabolism and immune homeostasis, which is, in large part, communicated via the gut microbiome.
Language	English
Publishing date	2024-04-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2493722-8
ISSN	1759-5053 ; 1759-5045
ISSN (online)	1759-5053
ISSN	1759-5045
DOI	10.1038/s41575-024-00914-3
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Zs.MG 97: Show issues

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Article ; Online: Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis.

P Gomes, Paulo Wender / Mannochio-Russo, Helena / Mao, Junhong / Zhao, Haoqi Nina / Ancira, Jacob / Tipton, Craig D / Dorrestein, Pieter C / Li, Min

mSystems

2024 Volume 9, Issue 3, Page(s) e0111923

Abstract: Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the ... ...

Abstract	Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence.
MeSH term(s)	Adult ; Humans ; Dermatitis, Atopic/drug therapy ; Staphylococcus aureus/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Metabolome ; Bacteria/genetics ; Dipeptides/therapeutic use
Chemical Substances	RNA, Ribosomal, 16S ; Dipeptides
Language	English
Publishing date	2024-02-06
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.01119-23
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Article ; Online: Urine Excretion, Organ Distribution, and Placental Transfer of 6PPD and 6PPD-Quinone in Mice and Potential Developmental Toxicity through Nuclear Receptor Pathways.

Zhao, Haoqi Nina / Thomas, Sydney P / Zylka, Mark J / Dorrestein, Pieter C / Hu, Wenxin

Environmental science & technology

2023 Volume 57, Issue 36, Page(s) 13429–13438

Abstract: The rubber antioxidant 6PPD has gained significant attention due to its highly toxic transformation product, 6PPD-quinone (6PPDQ). Despite their detection in urines of pregnant women, the placental transfer and developmental toxicity of 6PPD and 6PPDQ ... ...

Abstract	The rubber antioxidant 6PPD has gained significant attention due to its highly toxic transformation product, 6PPD-quinone (6PPDQ). Despite their detection in urines of pregnant women, the placental transfer and developmental toxicity of 6PPD and 6PPDQ are unknown. Here, we treated C57Bl/6 mice with 4 mg/kg 6PPD or 6PPDQ to investigate their urine excretion and placental transfer. Female and male mice exhibited sex difference in excretion profiles of 6PPD and 6PPDQ. Urine concentrations of 6PPDQ were one order of magnitude lower than those of 6PPD, suggesting lower excretion and higher bioaccumulation of 6PPDQ. In pregnant mice treated with 6PPD or 6PPDQ from embryonic day 11.5 to 15.5, 6PPDQ showed ∼1.5-8 times higher concentrations than 6PPD in placenta, embryo body, and embryo brain, suggesting higher placental transfer of 6PPDQ. Using in vitro dual-luciferase reporter assays, we revealed that 6PPDQ activated the human retinoic acid receptor α (RARα) and retinoid X receptor α (RXRα) at concentrations as low as 0.3 μM, which was ∼10-fold higher than the concentrations detected in human urines. 6PPD activated the RXRα at concentrations as low as 1.2 μM. These results demonstrate the exposure risks of 6PPD and 6PPDQ during pregnancy and emphasize the need for further toxicological and epidemiological investigations.
MeSH term(s)	Animals ; Female ; Humans ; Male ; Mice ; Pregnancy ; Benzoquinones/metabolism ; Benzoquinones/toxicity ; Benzoquinones/urine ; Placenta/metabolism ; Phenylenediamines/metabolism ; Phenylenediamines/toxicity ; Phenylenediamines/urine ; Mice, Inbred C57BL ; Tissue Distribution ; Sex Factors ; Embryonic Development/drug effects ; HEK293 Cells ; Retinoic Acid Receptor alpha/metabolism ; Retinoid X Receptor alpha/metabolism
Chemical Substances	Benzoquinones ; N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone ; Phenylenediamines ; N-(1,3-dimethylbutyl)-N'-phenyl-1,4-phenylenediamine (HJD0U67PS1) ; Retinoic Acid Receptor alpha ; Retinoid X Receptor alpha
Language	English
Publishing date	2023-08-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.3c05026
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Article ; Online: Editorial: Mass spectrometry of small molecules and natural products.

Dorrestein, Pieter C

Natural product reports

2014 Volume 31, Issue 6, Page(s) 704–705

MeSH term(s)	Biological Products/analysis ; Biological Products/chemistry ; Nuclear Magnetic Resonance, Biomolecular/methods
Chemical Substances	Biological Products
Language	English
Publishing date	2014-06
Publishing country	England
Document type	Editorial ; Introductory Journal Article
ZDB-ID	2002546-4
ISSN	1460-4752 ; 0265-0568
ISSN (online)	1460-4752
ISSN	0265-0568
DOI	10.1039/c4np90016b
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Article ; Online: Chemical signaling at the eukaryotic/prokaryotic interface.

Dorrestein, Pieter C / Balskus, Emily P

Chemical Society reviews

2018 Volume 47, Issue 5, Page(s) 1572–1573

MeSH term(s)	Eukaryota/chemistry ; Eukaryota/metabolism ; Humans ; Prokaryotic Cells/chemistry ; Prokaryotic Cells/metabolism ; Signal Transduction
Language	English
Publishing date	2018--05
Publishing country	England
Document type	Editorial ; Introductory Journal Article
ZDB-ID	1472875-8
ISSN	1460-4744 ; 0306-0012
ISSN (online)	1460-4744
ISSN	0306-0012
DOI	10.1039/c8cs90021c
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Article ; Online: foodMASST a mass spectrometry search tool for foods and beverages.

West, Kiana A / Schmid, Robin / Gauglitz, Julia M / Wang, Mingxun / Dorrestein, Pieter C

NPJ science of food

2022 Volume 6, Issue 1, Page(s) 22

Abstract: There is a growing interest in unraveling the chemical complexity of our diets. To help the scientific community gain insight into the molecules present in foods and beverages that we ingest, we created foodMASST, a search tool for MS/MS spectra (of both ...

Abstract	There is a growing interest in unraveling the chemical complexity of our diets. To help the scientific community gain insight into the molecules present in foods and beverages that we ingest, we created foodMASST, a search tool for MS/MS spectra (of both known and unknown molecules) against a growing metabolomics food and beverage reference database. We envision foodMASST will become valuable for nutrition research and to assess the potential uniqueness of dietary biomarkers to represent specific foods or food classes.
Language	English
Publishing date	2022-04-20
Publishing country	England
Document type	Journal Article
ISSN	2396-8370
ISSN (online)	2396-8370
DOI	10.1038/s41538-022-00137-3
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Article ; Online: Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.

Bittremieux, Wout / Laukens, Kris / Noble, William Stafford / Dorrestein, Pieter C

Rapid communications in mass spectrometry : RCM

2021 , Page(s) e9153

Abstract: Rationale: Advanced algorithmic solutions are necessary to process the ever-increasing amounts of mass spectrometry data that are being generated. In this study, we describe the falcon spectrum clustering tool for efficient clustering of millions of MS/ ... ...

Abstract	Rationale: Advanced algorithmic solutions are necessary to process the ever-increasing amounts of mass spectrometry data that are being generated. In this study, we describe the falcon spectrum clustering tool for efficient clustering of millions of MS/MS spectra. Methods: falcon succeeds in efficiently clustering large amounts of mass spectral data using advanced techniques for fast spectrum similarity searching. First, high-resolution spectra are binned and converted to low-dimensional vectors using feature hashing. Next, the spectrum vectors are used to construct nearest neighbor indexes for fast similarity searching. The nearest neighbor indexes are used to efficiently compute a sparse pairwise distance matrix without having to exhaustively perform all pairwise spectrum comparisons within the relevant precursor mass tolerance. Finally, density-based clustering is performed to group similar spectra into clusters. Results: Several state-of-the-art spectrum clustering tools were evaluated using a large draft human proteome data set consisting of 25 million spectra, indicating that alternative tools produce clustering results with different characteristics. Notably, falcon generates larger highly pure clusters than alternative tools, leading to a larger reduction in data volume without the loss of relevant information for more efficient downstream processing. Conclusions: falcon is a highly efficient spectrum clustering tool, which is publicly available as an open source under the permissive BSD license at https://github.com/bittremieux/falcon.
Language	English
Publishing date	2021-06-25
Publishing country	England
Document type	Journal Article
ZDB-ID	58731-x
ISSN	1097-0231 ; 0951-4198
ISSN (online)	1097-0231
ISSN	0951-4198
DOI	10.1002/rcm.9153
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Zs.A 3461: Show issues

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