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1. Correction: Investigation of plasma metabolomics and neurotransmitter dysfunction in the process of Alzheimer’s disease rat induced by amyloid beta 25-35

Author:
Wei, Mengying; Liu, Yuanyuan; Pi, Zifeng; Yue, Kexin; Li, Shizhe; Hu, Mingxin; Liu, Zhiqiang; Song, Fengrui; Liu, Zhongying
Source:
RSC advances 2021 v.11 no.13 pp. 7416
ISSN:
2046-2069
Subject:
metabolomics,   etc   ; amyloid; neurotransmitters; rats;     Show all 4 Subjects
Abstract:
... Correction for ‘Investigation of plasma metabolomics and neurotransmitter dysfunction in the process of Alzheimer’s disease rat induced by amyloid beta 25-35’ by Mengying Wei et al., RSC Adv., 2019, 9, 18308–18319. DOI: 10.1039/C9RA00302A. ...
DOI:
10.1039/d1ra90081a

2. Retraction: A high-throughput metabolomics strategy for discovering the influence of differential metabolites and metabolic pathways of huaxian capsules on sepsis-associated Qi deficiency and blood stasis syndrome

Author:
Fisher, Laura
Source:
RSC advances 2021 v.11 no.11 pp. 6235
ISSN:
2046-2069
Subject:
metabolomics,   etc   ; blood stasis; metabolites;     Show all 3 Subjects
Abstract:
... Retraction of ‘A high-throughput metabolomics strategy for discovering the influence of differential metabolites and metabolic pathways of huaxian capsules on sepsis-associated Qi deficiency and blood stasis syndrome’ by Qun Liang et al., RSC Adv., 2019, 9, 30868–30878, DOI: 10.1039/C9RA06679A. ...
DOI:
10.1039/d1ra90055b

3. Correction: The metabolomic analysis of five Mentha species: cytotoxicity, anti-Helicobacter assessment, and the development of polymeric micelles for enhancing the anti-Helicobacter activity

Author:
Bakr, Riham O.; Tawfike, Ahmed F.; El-Gizawy, Heba A.; Tawfik, Nashwa; Abdelmohsen, Usama Ramadan; Abdelwahab, Miada F.; Alshareef, Walaa A.; Fayez, Sahar M.; El-Mancy, Shereen M. S.; El-Fishawy, Ahlam M.; Abdelkawy, Mostafa A.; Fayed, Marwa A. A.
Source:
RSC advances 2021 v.11 no.15 pp. 8916
ISSN:
2046-2069
Subject:
metabolomics,   etc   ; Mentha; cytotoxicity; micelles; polymers;     Show all 5 Subjects
Abstract:
... Correction for ‘The metabolomic analysis of five Mentha species: cytotoxicity, anti-Helicobacter assessment, and the development of polymeric micelles for enhancing the anti-Helicobacter activity’ by Riham O. Bakr et al., RSC Adv., 2021, 11, 7318–7330, DOI: 10.1039/D0RA09334C. ...
DOI:
10.1039/d1ra90085d

4. A Practical Guide to Metabolomics Software Development

Author:
Chang, Hui-Yin; Colby, Sean M.; Du, Xiuxia; Gomez, Javier D.; Helf, Maximilian J.; Kechris, Katerina; Kirkpatrick, Christine R.; Li, Shuzhao; Patti, Gary J.; Renslow, Ryan S.; Subramaniam, Shankar; Verma, Mukesh; Xia, Jianguo; Young, Jamey D.
Source:
Analytical chemistry 2021 v.93 no.4 pp. 1912-1923
ISSN:
1520-6882
Subject:
metabolomics,   etc   ; analytical chemistry; computer software;     Show all 3 Subjects
Abstract:
... A growing number of software tools have been developed for metabolomics data processing and analysis. Many new tools are contributed by metabolomics practitioners who have limited prior experience with software development, and the tools are subsequently implemented by users with expertise that ranges from basic point-and-click data analysis to advanced coding. This Perspective is intended to intr ...
DOI:
10.1021/acs.analchem.0c03581

5. Towards superior plant-based foods using metabolomics

Author:
Jacobs, Doris M; van den Berg, Marco A; Hall, Robert D
Source:
Current opinion in biotechnology 2021 v.70 pp. 23-28
ISSN:
0958-1669
Subject:
metabolomics,   etc   ; agronomy; biotechnology; chemometrics; food production; nutrition;     Show all 6 Subjects
Abstract:
... Metabolomics is proving a useful approach for many of the main future goals in agronomy and food production such as sustainability/crop resilience, food quality, safety, storage, and nutrition. Targeted and/or untargeted small-molecule analysis, coupled to chemometric analysis, has already unveiled a great deal of the complexity of plant-based foods, but there is still ‘dark matter’ to be discover ...
DOI:
10.1016/j.copbio.2020.08.010

6. Simultaneous UHPLC/MS quantitative analysis and comparison of Saposhnikoviae radix constituents in cultivated, wild and commercial products

Author:
Fuchino, Hiroyuki; Murase, Sayaka; Hishida, Atsuyuki; Kawahara, Nobuo
Source:
Natural medicines 2021 v.75 no.3 pp. 499-519
ISSN:
1340-3443
Subject:
metabolomics,   etc   ; Japan; drugs; glycosides; quantitative analysis; China;     Show all 6 Subjects
Abstract:
... Differences in the components of the crude drug Saposhnikoviae radix, both wild and cultivated, and the cultivation duration were examined by UHPLC/MS. As a result, there was no significant difference in composition depending on the region in China where the drug was produced. The most abundant components in all samples were prim-O-glucosylcimifugin, 4′-O-glucosyl-5-O-methylvisamminol, 3′-O-acetyl ...
DOI:
10.1007/s11418-021-01486-1

7. Sparse PLS-Based Method for Overlapping Metabolite Set Enrichment Analysis

Author:
Deng, Lingli; Ma, Lei; Cheng, Kian-Kai; Xu, Xiangnan; Raftery, Daniel; Dong, Jiyang
Source:
Journal of proteome research 2021 v.20 no.6 pp. 3204-3213
ISSN:
1535-3907
Subject:
metabolomics,   etc   ; data collection; metabolites; models; proteome; research;     Show all 6 Subjects
Abstract:
... Metabolite set enrichment analysis (MSEA) has gained increasing research interest for identification of perturbed metabolic pathways in metabolomics. The method incorporates predefined metabolic pathways information in the analysis where metabolite sets are typically assumed to be mutually exclusive to each other. However, metabolic pathways are known to contain common metabolites and intermediate ...
DOI:
10.1021/acs.jproteome.1c00064

8. Global and Simultaneous Hypothesis Testing for High-Dimensional Logistic Regression Models

Author:
Ma, Rong; Tony Cai, T.; Li, Hongzhe
Source:
Journal of the American Statistical Association 2021 v.116 no.534 pp. 984-998
ISSN:
1537-274X
Subject:
metabolomics,   etc   ; data collection; metabolites; regression analysis;     Show all 4 Subjects
Abstract:
... High-dimensional logistic regression is widely used in analyzing data with binary outcomes. In this article, global testing and large-scale multiple testing for the regression coefficients are considered in both single- and two-regression settings. A test statistic for testing the global null hypothesis is constructed using a generalized low-dimensional projection for bias correction and its asymp ...
DOI:
10.1080/01621459.2019.1699421

9. metabCombiner: Paired Untargeted LC-HRMS Metabolomics Feature Matching and Concatenation of Disparately Acquired Data Sets

Author:
Habra, Hani; Kachman, Maureen; Bullock, Kevin; Clish, Clary; Evans, Charles R.; Karnovsky, Alla
Source:
Analytical chemistry 2021 v.93 no.12 pp. 5028-5036
ISSN:
1520-6882
Subject:
metabolomics,   etc   ; analytical chemistry; meta-analysis; prediction; urine;     Show all 5 Subjects
Abstract:
... LC-HRMS experiments detect thousands of compounds, with only a small fraction of them identified in most studies. Traditional data processing pipelines contain an alignment step to assemble the measurements of overlapping features across samples into a unified table. However, data sets acquired under nonidentical conditions are not amenable to this process, mostly due to significant alterations in ...
DOI:
10.1021/acs.analchem.0c03693

10. leapR: An R Package for Multiomic Pathway Analysis

Author:
Danna, Vincent; Mitchell, Hugh; Anderson, Lindsey; Godinez, Iobani; Gosline, Sara J. C.; Teeguarden, Justin; McDermott, Jason E.
Source:
Journal of proteome research 2021 v.20 no.4 pp. 2116-2121
ISSN:
1535-3907
Subject:
metabolomics,   etc   ; genomics; proteome; proteomics; research; transcriptomics;     Show all 6 Subjects
Abstract:
... A generalized goal of many high-throughput data studies is to identify functional mechanisms that underlie observed biological phenomena, whether they be disease outcomes or metabolic output. Increasingly, studies that rely on multiple sources of high-throughput data (genomic, transcriptomic, proteomic, metabolomic) are faced with a challenge of summarizing the data to generate testable hypotheses ...
DOI:
10.1021/acs.jproteome.0c00963

11. Targeted Isolation of Saalfelduracin B–D from Amycolatopsis saalfeldensis Using LC-MS/MS-Based Molecular Networking

Author:
Um, Soohyun; Seibel, Elena; Schalk, Felix; Balluff, Sven; Beemelmanns, Christine
Source:
Journal of natural products 2021 v.84 no.4 pp. 1002-1011
ISSN:
1520-6025
Subject:
metabolomics,   etc   ; Amycolatopsis; tandem mass spectrometry; Germany;     Show all 4 Subjects
Abstract:
... High-resolution tandem mass spectrometry (HR-MS²)-based metabolomic studies of Amycolatopsis saalfeldensis, isolated from the “Saalfelder Feengrotten” caves in Germany, led to the isolation of three ribosomally synthesized and post-translationally modified type II thiopeptides, saalfelduracin B–D (1–3) and the known saalfelduracin A (4). The structures of all four compounds were determined by comp ...
DOI:
10.1021/acs.jnatprod.0c01027

12. Retraction: High-throughput metabolomics identifies serum metabolic signatures in acute kidney injury using LC-MS combined with pattern recognition approach

Author:
Fisher, Laura
Source:
RSC advances 2021 v.11 no.10 pp. 5722
ISSN:
2046-2069
Subject:
metabolomics,   etc   ; acute kidney injury; blood serum;     Show all 3 Subjects
Abstract:
... Retraction of ‘High-throughput metabolomics identifies serum metabolic signatures in acute kidney injury using LC-MS combined with pattern recognition approach’ by Hai-Hong Li et al., RSC Adv., 2018, 8, 14838–14847, DOI: 10.1039/C8RA01749B ...
DOI:
10.1039/d1ra90062e

13. CE‐MS for metabolomics: Developments and applications in the period 2018–2020

Author:
Zhang, Wei; Ramautar, Rawi
Source:
Electrophoresis 2021 v.42 no.4 pp. 381-401
ISSN:
0173-0835
Subject:
metabolomics,   etc   ; capillary electrophoresis; mass spectrometry; metabolites;     Show all 4 Subjects
Abstract:
... Capillary electrophoresis‐mass spectrometry (CE‐MS) is now a mature analytical technique in metabolomics, notably for the efficient profiling of polar and charged metabolites. Over the past few years, (further) progress has been made in the design of improved interfacing techniques for coupling CE to MS; also, in the development of CE‐MS approaches for profiling metabolites in volume‐restricted sa ...
DOI:
10.1002/elps.202000203

14. Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks

Author:
Kanazawa, Shinji; Noda, Akira; Ito, Arisa; Hashimoto, Kyoko; Kunisawa, Akihiro; Nakanishi, Tsuyoshi; Kajihara, Shigeki; Mukai, Norio; Iida, Junko; Fukusaki, Eiichiro; Matsuda, Fumio
Source:
Journal of bioscience and bioengineering 2021 v.131 no.2 pp. 207-212
ISSN:
1389-1723
Subject:
metabolomics,   etc   ; biotechnology; chromatography; computer software; metabolome;     Show all 5 Subjects
Abstract:
... Finding peaks in chromatograms and determining their start and end points (peak picking) is a core task in chromatography based biotechnology. Construction of peak-picking neural networks by deep learning was, however, hampered from the preparation of exact peak-picked or “labeled” chromatograms since the exact start and end points were often unclear in overlapping peaks in real chromatograms. We ...
DOI:
10.1016/j.jbiosc.2020.09.013

15. Capillary ultrahigh-pressure liquid chromatography-mass spectrometry for fast and high resolution metabolomics separations

Author:
Sorensen, Matthew J.; Kennedy, Robert T.
Source:
Journal of chromatography 2021 v.1635 pp. 461706
ISSN:
0021-9673
Subject:
metabolomics,   etc   ; mass spectrometry; metabolites; particle size;     Show all 4 Subjects
Abstract:
... LC-MS is an important tool for metabolomics due its high sensitivity and broad metabolite coverage. The goal of improving resolution and decreasing analysis time in HPLC has led to the use of 5 – 15 cm long columns packed with 1.7 – 1.9 µm particles requiring pressures of 8 – 12 kpsi. We report on the potential for capillary LC-MS based metabolomics utilizing porous C18 particles down to 1.1 µm di ...
DOI:
10.1016/j.chroma.2020.461706

16. Numerical Representations of Metabolic Systems

Author:
Smilde, Age K.; Hankemeier, Thomas
Source:
Analytical chemistry 2020 v.92 no.20 pp. 13614-13621
ISSN:
1520-6882
Subject:
metabolomics,   etc   ; analytical chemistry; proteomics;     Show all 3 Subjects
Abstract:
... Metabolomics is becoming a mature part of analytical chemistry as evidenced by the growing number of publications and attendees of international conferences dedicated to this topic. Yet, a systematic treatment of the fundamental structure and properties of metabolomics data is lagging behind. We want to fill this gap by introducing two fundamental theories concerning metabolomics data: data theory ...
DOI:
10.1021/acs.analchem.9b05613

17. Diversity of antioxidant ingredients among Echinacea species

Author:
Fu, Rao; Zhang, Pingyu; Deng, Zongbi; Jin, Ge; Guo, Yiran; Zhang, Yang
Source:
Industrial crops and products 2021 v.170 pp. 113699
ISSN:
0926-6690
Subject:
metabolomics,   etc   ; antioxidants; biosynthesis; caftaric acid; pharmaceutical industry; quantitative analysis; therapeutics;     Show all 7 Subjects
Abstract:
... Echinacea species are important medicinal plants with significant therapeutic potential and are widely used in the pharmaceutical industry. Different Echinacea species exhibit various chemical compositions and bioactivities. In the present study, the chemical differences, antioxidant ingredients, and diversity mechanisms of Echinacea species were studied. The aerial parts and roots of six differen ...
DOI:
10.1016/j.indcrop.2021.113699

18. Data sharing in PredRet for accurate prediction of retention time: Application to plant food bioactive compounds

Author:
Low, Dorrain Yanwen; Micheau, Pierre; Koistinen, Ville Mikael; Hanhineva, Kati; Abrankó, László; Rodriguez-Mateos, Ana; da Silva, Andreia Bento; van Poucke, Christof; Almeida, Conceição; Andres-Lacueva, Cristina; Rai, Dilip K.; Capanoglu, Esra; Tomás Barberán, Francisco A.; Mattivi, Fulvio; Schmidt, Gesine; Gürdeniz, Gözde; Valentová, Kateřina; Bresciani, Letizia; Petrásková, Lucie; Dragsted, Lars Ove; Philo, Mark; Ulaszewska, Marynka; Mena, Pedro; González-Domínguez, Raúl; Garcia-Villalba, Rocío; Kamiloglu, Senem; de Pascual-Teresa, Sonia; Durand, Stéphanie; Wiczkowski, Wieslaw; Bronze, Maria Rosário; Stanstrup, Jan; Manach, Claudine
Source:
Food chemistry 2021 v.357 pp. 129757
ISSN:
0308-8146
Subject:
metabolomics,   etc   ; accuracy; chromatography; food chemistry; metabolites; prediction; shape; width;     Show all 8 Subjects
Abstract:
... Prediction of retention times (RTs) is increasingly considered in untargeted metabolomics to complement MS/MS matching for annotation of unidentified peaks. We tested the performance of PredRet (http://predret.org/) to predict RTs for plant food bioactive metabolites in a data sharing initiative containing entry sets of 29–103 compounds (totalling 467 compounds, >30 families) across 24 chromatogra ...
DOI:
10.1016/j.foodchem.2021.129757

19. Future perspectives on in-vitro diagnosis of drug allergy by the lymphocyte transformation test

Author:
Fatangare, Amol; Glässner, Andreas; Sachs, Bernhardt; Sickmann, Albert
Source:
Journal of immunological methods 2021 v.495 pp. 113072
ISSN:
0022-1759
Subject:
metabolomics,   etc   ; drugs; flow cytometry; hypersensitivity; lymphocyte proliferation; proteomics; transcriptomics;     Show all 7 Subjects
Abstract:
... This article aims to envisage future perspectives of the lymphocyte transformation test (LTT). We describe the select innovative techniques, which can be integrated at different stages of the LTT to potentially improve the sensitivity, specificity, or practicability of the LTT. We first focus upon the cell sorting techniques comprising immunomagnetic cell separation and flow cytometry, which can b ...
DOI:
10.1016/j.jim.2021.113072

20. Metabolomics and molecular docking to compare of the efficacies of wild-simulated and transplanted Astragali Radix based on its compatibility with Angelicae Sinensis Radix against blood deficiency

Author:
Liu, YueTao; Wang, ZiYing; Qin, XueMei
Source:
Journal of chromatography 2021 v.1173 pp. 122682
ISSN:
1570-0232
Subject:
metabolomics,   etc   ; Angelica sinensis; blood serum; chromatography; databases; markets; metabolites; China;     Show all 8 Subjects
Abstract:
... Astragali Radix (AR) has been widely used as bulk medicines in China. Currently, there are mainly two types in the market, wild-simulated AR (WAR) and transplanted AR (TAR). The present work was designed to compare their effects in treatment of blood deficiency with its compatibility with Angelicae Sinensis Radix, a classical formula Danggui Buxue decoction (DBD). UHPLC-Q-Exactive-MS-based serum m ...
DOI:
10.1016/j.jchromb.2021.122682