Creation of a Plant Metabolite Spectral Library for Untargeted and Targeted Metabolomics

Li, Yangyang; Zhu, Wei; Xiang, Qingyuan; Kim, Jeongim; Dufresne, Craig; Liu, Yufeng; Li, Tianlai; Chen, Sixue

doi:10.3390/ijms24032249

Cited by 8 publications

(6 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The data acquired during DDA-CNL/MS 3 analysis is well-suited for DNA adduct identification through our recently completed DNA adduct mass spectral database . Our database is available for manual examination and downloading in the .MSP (NIST format) and .db (mzVault format, Thermo Scientific) formats at the DNA Adduct Portal Web site (https://sites.google.com/umn.edu/dnaadductportal). The .MSP format is highly flexible and can be used directly with open-source tools such as NIST MS Search and MS-DIAL .…”

Section: Resultsmentioning

confidence: 99%

Screening DNA Damage in the Rat Kidney and Liver by Untargeted DNA Adductomics

Ragi,

Walmsley,

Jacobs

et al. 2024

Chem. Res. Toxicol.

View full text Add to dashboard Cite

Air pollution, tobacco smoke, and red meat are associated with renal cell cancer (RCC) risk in the United States and Western Europe; however, the chemicals that form DNA adducts and initiate RCC are mainly unknown. Aristolochia herbaceous plants are used for medicinal purposes in Asia and worldwide. They are a significant risk factor for upper tract urothelial carcinoma (UTUC) and RCC to a lesser extent. The aristolochic acid (AA) 8-methoxy-6-nitrophenanthro-[3,4-d]-1,3dioxolo-5-carboxylic acid (AA-I), a component of Aristolochia herbs, contributes to UTUC in Asian cohorts and in Croatia, where AA-I exposure occurs from ingesting contaminated wheat flour. The DNA adduct of AA-I, 7-(2′-deoxyadenosin-N 6 -yl)-aristolactam I, is often detected in patients with UTUC, and its characteristic A:T-to-T:A mutational signature occurs in oncogenes and tumor suppressor genes in AA-associated UTUC. Identifying DNA adducts in the renal parenchyma and pelvis caused by other chemicals is crucial to gaining insights into unknown RCC and UTUC etiologies. We employed untargeted screening with wide-selected ion monitoring tandem mass spectrometry (wide-SIM/MS 2 ) with nanoflow liquid chromatography/Orbitrap mass spectrometry to detect DNA adducts formed in rat kidneys and liver from a mixture of 13 environmental, tobacco, and dietary carcinogens that may contribute to RCC. Twenty DNA adducts were detected. DNA adducts of 3-nitrobenzanthrone (3-NBA), an atmospheric pollutant, and AA-I were the most abundant. The nitrophenanthrene moieties of 3-NBA and AA-I undergo reduction to their N-hydroxy intermediates to form 2′-deoxyguanosine (dG) and 2′deoxyadenosine (dA) adducts. We also discovered a 2′-deoxycytidine AA-I adduct and dA and dG adducts of 10-methoxy-6-nitrophenanthro-[3,4-d]-1,3-dioxolo-5-carboxylic acid (AA-III), an AA-I isomer and minor component of the herbal extract assayed, signifying AA-III is a potent kidney DNA-damaging agent. The roles of AA-III, other nitrophenanthrenes, and nitroarenes in renal DNA damage and human RCC warrant further study. Wide-SIM/MS 2 is a powerful scanning technology in DNA adduct discovery and cancer etiology characterization.

show abstract

Section: Resultsmentioning

confidence: 99%

Screening DNA Damage in the Rat Kidney and Liver by Untargeted DNA Adductomics

Ragi,

Walmsley,

Jacobs

et al. 2024

Chem. Res. Toxicol.

View full text Add to dashboard Cite

show abstract

“…Additionally, a flavonoid (40) was found whose aglycone is quercetin that has substituents at positions C-3 and C-7 in the form of hexose sugars, which we were unable to identify. Among derivatives of kaempferol, the following glycosides Analysis of our data allowed us to identify isoflavones and flavans in the extract, for which the following structural interpretation was proposed: iridin (44), glycitein (64), and auriculoside (59). Flavanones are represented by prunin (58), flavones by luteolin (54) and nobiletin (63), and glucosides by cirsimarin (60) and gossypin (42), which contain glucopyranose as a sugar residue.…”

Section: Flavonoidsmentioning

confidence: 93%

“…Several mzVaults were used in the mzVault Search node: Creation of a Plant Metabolite Spectral Library for Untargeted and targeted Metabolomics.db [59], Negative ion mode_Jan2021.db, Positive ion mode_Jan2021.db (https://more.bham.ac.uk/bamcg/resources/; last accessed 5 November 2023), and MS2_library.db (https://doi.org/10.1016/j.jchromb.2020.122105, last accessed 27 November 2023).…”

Section: Lc-hrms Analysis Of Metabolites In the A Macrophylla Extractsmentioning

confidence: 99%

Chemical Composition of Methanol Extracts from Leaves and Flowers of Anemonopsis macrophylla (Ranunculaceae)

Kostikova,

Petrova,

Chernonosov

et al. 2024

IJMS

View full text Add to dashboard Cite

Anemonopsis Siebold et Zucc. is an unstudied single-species genus belonging to the tribe Cimicifugeae (Ranunculaceae). The only species of this genus—Anemonopsis macrophylla Siebold and Zucc.—is endemic to Japan. There are no data on its chemical composition. This work is the first to determine (with liquid chromatography–high-resolution mass spectrometry, LC-HRMS) the chemical composition of methanol extracts of leaves and flowers of A. macrophylla. More than 100 compounds were identified. In this plant, the classes of substances are coumarins (13 compounds), furocoumarins (3), furochromones (2), phenolic acids (21), flavonoids (27), and fatty acids and their derivatives (15 compounds). Isoferulic acid (detected in extracts from this plant) brings this species closer to plants of the genus Cimicifuga, one of the few genera containing this acid and ferulic acid at the same time. Isoferulic acid is regarded as a reference component of a quality indicator of Cimicifuga raw materials. The determined profiles of substances are identical between the leaf and flower methanol extracts. Differences in levels of some identified substances were revealed between the leaf and flower extracts of A. macrophylla; these differences may have a substantial impact on the manifestation of the biological and pharmacological effects of the extracts in question.

show abstract

“…Moreover, this approach is using MS data for semi-quantitation (relative quantitation) [ 22 ]. Interestingly, Li et al have used the same approach of creating a plant metabolite spectral library using 544 authentic standards, which increased the efficiency of identification for untargeted metabolomic studies, but they called the approach a pseudo-targeted method [ 53 ]. A multi-platform (2D LC-MS/MS and NMR) protocol was also used for the aim of identification of natural compounds of the Mediterranean marine sponge Crambe crambe .…”

Section: Simultaneous Quantitation and Discovery (Squad) Analysismentioning

confidence: 99%

Simultaneous Quantitation and Discovery (SQUAD) Analysis: Combining the Best of Targeted and Untargeted Mass Spectrometry-Based Metabolomics

2023

View full text Add to dashboard Cite

Untargeted and targeted approaches are the traditional metabolomics workflows acquired for a wider understanding of the metabolome under focus. Both approaches have their strengths and weaknesses. The untargeted, for example, is maximizing the detection and accurate identification of thousands of metabolites, while the targeted is maximizing the linear dynamic range and quantification sensitivity. These workflows, however, are acquired separately, so researchers compromise either a low-accuracy overview of total molecular changes (i.e., untargeted analysis) or a detailed yet blinkered snapshot of a selected group of metabolites (i.e., targeted analysis) by selecting one of the workflows over the other. In this review, we present a novel single injection simultaneous quantitation and discovery (SQUAD) metabolomics that combines targeted and untargeted workflows. It is used to identify and accurately quantify a targeted set of metabolites. It also allows data retro-mining to look for global metabolic changes that were not part of the original focus. This offers a way to strike the balance between targeted and untargeted approaches in one single experiment and address the two approaches’ limitations. This simultaneous acquisition of hypothesis-led and discovery-led datasets allows scientists to gain more knowledge about biological systems in a single experiment.

show abstract

Creation of a Plant Metabolite Spectral Library for Untargeted and Targeted Metabolomics

Cited by 8 publications

References 50 publications

Screening DNA Damage in the Rat Kidney and Liver by Untargeted DNA Adductomics

Screening DNA Damage in the Rat Kidney and Liver by Untargeted DNA Adductomics

Chemical Composition of Methanol Extracts from Leaves and Flowers of Anemonopsis macrophylla (Ranunculaceae)

Simultaneous Quantitation and Discovery (SQUAD) Analysis: Combining the Best of Targeted and Untargeted Mass Spectrometry-Based Metabolomics

Contact Info

Product

Resources

About