metAlignID: A high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data

Lommen, Arjen; Kamp, Henk J. van der; Kools, Harrie J.; Lee, Martijn K. van der; Weg, G. van der; Mol, Hans

doi:10.1016/j.chroma.2012.09.056

Cited by 20 publications

(7 citation statements)

References 19 publications

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“…We identified this novel compound through recently improved data processing that could annotate unknown VOCs. These developments include database analysis tools, such as BinBase Database 21 , AMDIS 22 , SpectConnect ( http://spectconnect.mit.edu ), MZmine 23 , TagFinder 24 , MetAligh 3.0, and MetAlignID 25 , 26 . For this study, we used BinBase; this tool can be assessed by the public at http://vocBinBase.fiehnlab.ucdavis.edu.…”

Section: Discussionmentioning

confidence: 99%

Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis

Shahid

Lee

Yeon

et al. 2018

Sci Rep

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Chronic inflammation is a potential systemic risk factor for many bladder dysfunctions, including interstitial cystitis (IC). However, the underlying mechanism through which a healthy bladder protects itself from inflammatory triggers remains unknown. In this study, we identified odor compounds in urine obtained from IC patients and healthy controls. Using comprehensive solid-phase microextraction-gas chromatography-time-of-flight-mass spectrometry (SPME-GC-TOF-MS) profiling and bioinformatics, we found that levels of urinary volatile metabolites, such as menthol, were significantly reduced in IC patients, compared to healthy controls. In an attempt to understand the mechanistic meaning of our volatile metabolites data and the role of menthol in the immune system, we performed two independent experiments: (a) cytokine profiling, and (b) DNA microarray. Our findings suggest that lipopolysaccharide (LPS)-stimulated inflammatory events, such as the production and secretion of inflammatory cytokines (e.g., TNF-α, IL-6, and IL-1β) and the activation of NF-κB and associated proteins within a large signaling network (e.g., Akt, TLR1, TNFAIP3, and NF-κB), are suppressed by the presence of menthol. These findings broaden our knowledge on the role of urinary menthol in suppressing inflammatory events and provide potential new strategies for alleviating both the odor and inflammation associated with IC.

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Section: Discussionmentioning

confidence: 99%

Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis

Shahid

Lee

Yeon

et al. 2018

Sci Rep

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“…Exhaustive data set generated from above high throughput tools are processed through data processing platforms like MET-COFEA, Met-Align, ChromaTOF, MET-XAlign, etc., ( Pegasus, 2007 ; Lommen et al, 2012 ; Kessler et al, 2014 ; Zhang et al, 2014 , 2015 ; Ma et al, 2016 ; Misra and van der Hooft, 2016 ; de Souza et al, 2017 ). This basically includes baseline correction, alignment, separation of co-eluting peaks (deconvolution), normalization, etc.…”

Section: Analytical Tools For Metabolomic Studiesmentioning

confidence: 99%

Metabolomics for Plant Improvement: Status and Prospects

et al. 2017

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Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

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“…MetAlign [91,92] and MSClust [93] software were employed to perform mass spectra alignment, baseline correction, and mass signal clustering, as described by Scalabrin et al [15]. Available online libraries (Metlin, HMDB, Dictionary of Natural Products, LIPID MAPS Structure Database) and literature were used to achieve metabolite identification, on the basis of the monoisotopic mass, the most probable molecular formula, and molecular fragmentation.…”

Section: Data Treatment and Metabolite Identificationmentioning

confidence: 99%

Effects of Water Deficit and Heat Stress on Nicotiana langsdorffii Metabolomic Pattern Modified by Insertion of rolD Gene from Agrobacterium rhizogenes

2020

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Abiotic stresses are major factors that negatively affect plant growth and productivity. Plants have developed complex strategies to ensure their survival and reproduction under adverse conditions, activating mechanisms that involve changes at different metabolic levels. In order to select stress-resistant species, research has focused on molecular studies and genetic engineering, showing promising results. In this work, the insertion of the rolD gene from Agrobacterium rhizogenes into Nicotiana langsdorffii plants is investigated, in order to assess the potential of this genetic modification towards mitigating water and heat stresses. Different approaches were combined: a high-throughput metabolomics and ionomics study was performed, together with the determination of important plant phytohormones. The aim was to identify the influence of abiotic stresses on plants and to highlight the effects of the rolD genetic modification on plant stress response. The most relevant compounds for each kind of stress were identified, belonging mainly to the classes of lipids, acyl sugars, glycosides, and amino acid derivatives. Water stress (WS) determined a decrease of elements and secondary metabolites, while amino acids and their derivatives increased, proving to be key molecules in this type of stress. RolD plants exposed to high temperature stress (HS) presented higher dry weight levels than controls, as well as increased amounts of K and adenosine and lower levels of damage-associated metabolites, suggesting the increased resistance of rolD-modified plants toward HS.

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metAlignID: A high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data

Cited by 20 publications

References 19 publications

Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis

Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis

Metabolomics for Plant Improvement: Status and Prospects

Effects of Water Deficit and Heat Stress on Nicotiana langsdorffii Metabolomic Pattern Modified by Insertion of rolD Gene from Agrobacterium rhizogenes

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