CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry

Nikolić, Dejan

doi:10.1016/j.phytol.2017.01.006

Cited by 12 publications

(10 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another approach showed the combined use of high-resolution MS/MS data and use of the metabolic in-silico network expansion database (MINE) for the discovery of novel methylated epi-metabolites including N-methyl-UMP [ 45 ]. Natural products can be manually annotated with high success rates [ 182 ], but such approaches require deep mass spectral knowledge. In the future, such manual approaches must be translated into practical expert-algorithms and software that allows non-experts to perform such complicated analysis to a certain degree [ 27 ].…”

Section: Compound Identification: Hybrid and Orthogonal Approachesmentioning

confidence: 99%

“…The CASMI (critical assessment of small molecule identification) contest ( ) has been held since 2012 as a worldwide scientific competition to determine the best approaches for identifying small molecule structures directly from mass spectra [ 183 , 184 ]. The competitions are commonly structured into different categories, including best natural product determination [ 96 , 182 , 185 ], best molecular formula determination [ 186 ] and unknown compound determination. More recently, categories that allow for in silico fragmentation software only [ 187 ] and a category that allows for all meta-data use were included [ 85 ].…”

Section: Critical Assessment Of Small Molecule Analysis (Casmi)mentioning

confidence: 99%

See 1 more Smart Citation

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

et al. 2018

View full text Add to dashboard Cite

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

show abstract

Section: Compound Identification: Hybrid and Orthogonal Approachesmentioning

confidence: 99%

Section: Critical Assessment Of Small Molecule Analysis (Casmi)mentioning

confidence: 99%

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The raw data obtained from the LC-HR-ESI-MS analysis were analyzed using MS-DIAL version 3.20 [34]. Multiple reference mass spectral libraries were used for querying the unknown metabolites, including MassBank [35], RIKEN tandem mass spectral database for phytochemicals (ReSpect) (), the Global Natural Product Social Molecular Networking system (GNPS) (), the Critical Assessment of Small Molecule Identification (CASMI) 2016 library [36], the Fiehn lab hydrophilic interaction liquid chromatography (HILIC) MS/MS library (available at ), the Bruker MetaboBASE plant library (), RIKEN PlaSMA (), and Karolinska Institute and Gunma (GIAR) zic-HILIC deconvoluted MS2 spectra in data independent acquisition [37]. Tentative compound identification was based on the weighted similarity score of accurate mass, isotope ratio, and MS/MS spectra with a cut-off value set at 80.…”

Section: Methodsmentioning

confidence: 99%

Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill.

Wilson

Tian

2019

Molecules

View full text Add to dashboard Cite

Although the evolutionary significance of the early-diverging flowering plant Amborella (Amborella trichopoda Baill.) is widely recognized, its metabolic landscape, particularly specialized metabolites, is currently underexplored. In this work, we analyzed the metabolomes of Amborella tissues using liquid chromatography high-resolution electrospray ionization mass spectrometry (LC-HR-ESI-MS). By matching the mass spectra of Amborella metabolites with those of authentic phytochemical standards in the publicly accessible libraries, 63, 39, and 21 compounds were tentatively identified in leaves, stems, and roots, respectively. Free amino acids, organic acids, simple sugars, cofactors, as well as abundant glycosylated and/or methylated phenolic specialized metabolites were observed in Amborella leaves. Diverse metabolites were also detected in stems and roots, including those that were not identified in leaves. To understand the biosynthesis of specialized metabolites with glycosyl and methyl modifications, families of small molecule UDP-dependent glycosyltransferases (UGTs) and O-methyltransferases (OMTs) were identified in the Amborella genome and the InterPro database based on conserved functional domains. Of the 17 phylogenetic groups of plant UGTs (A–Q) defined to date, Amborella UGTs are absent from groups B, N, and P, but they are highly abundant in group L. Among the 25 Amborella OMTs, 7 cluster with caffeoyl-coenzyme A (CCoA) OMTs involved in lignin and phenolic metabolism, whereas 18 form a clade with plant OMTs that methylate hydroxycinnamic acids, flavonoids, or alkaloids. Overall, this first report of metabolomes and candidate metabolic genes in Amborella provides a starting point to a better understanding of specialized metabolites and biosynthetic enzymes in this basal lineage of flowering plants.

show abstract

“…Metfrag and CFM-ID are silico fragmentation tools that utilize known compounds from structure databases to calculate fragments that are matched to experimentally obtained spectra (Blaženović et al 2018). In addition to these automated approaches, we have also performed a manual dereplication approach on the data obtained from UIC to compare and verify the metabolites of interest from ASRC, as described in previous publications (Gödecke et al 2009;Nikolić et al 2012Nikolić et al , 2015Nikolić et al , 2017, some of which contain extensive analysis of fragmentation spectra of benzylisoquinoline alkaloids (BIA). Tandem mass spectra of BIAs and other metabolites identified in this study were compared to those stored in our in-house library and public databases (MoNA, Horai et al 2010;GNPS, Wang et al 2016).…”

Section: Cuttings Of Rafflesia Lagascae-infected Tetrastigma Loherimentioning

confidence: 99%

Living with a giant, flowering parasite: metabolic differences between Tetrastigma loheri Gagnep. (Vitaceae) shoots uninfected and infected with Rafflesia (Rafflesiaceae) and potential applications for propagation

Molina

Nikolić

Jeevarathanam

et al. 2021

Planta

View full text Add to dashboard Cite

Main conclusion Metabolites in Rafflesia-infected and non-infected Tetrastigma were compared which may have applications in Rafflesia propagation. Benzylisoquinoline alkaloids, here reported for the first time in Vitaceae, were abundant in non-infected shoots and may be a form of defense. In Rafflesia-infected shoots, oxylipins, which mediate immune response, were elevated. Abstract Endemic to the forests of Southeast Asia, Rafflesia (Rafflesiaceae) is a genus of holoparasitic plants producing the largest flowers in the world, yet completely dependent on its host, the tropical grape vine, Tetrastigma. Rafflesia species are threatened with extinction, making them an iconic symbol of plant conservation. Thus far, propagation has proved challenging, greatly decreasing efficacy of conservation efforts. This study compared the metabolites in the shoots of Rafflesia-infected and non-infected Tetrastigma loheri to examine how Rafflesia infection affects host metabolomics and elucidate the Rafflesia infection process. Results from LC–MS-based untargeted metabolomics analysis showed benzylisoquinoline alkaloids were naturally more abundant in non-infected shoots and are here reported for the first time in the genus Tetrastigma, and in the grape family, Vitaceae. These metabolites have been implicated in plant defense mechanisms and may prevent a Rafflesia infection. In Rafflesia-infected shoots, oxygenated fatty acids, or oxylipins, and a flavonoid, previously shown involved in plant immune response, were significantly elevated. This study provides a preliminary assessment of metabolites that differ between Rafflesia-infected and non-infected Tetrastigma hosts and may have applications in Rafflesia propagation to meet conservation goals.

show abstract

CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry

Cited by 12 publications

References 22 publications

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill.

Living with a giant, flowering parasite: metabolic differences between Tetrastigma loheri Gagnep. (Vitaceae) shoots uninfected and infected with Rafflesia (Rafflesiaceae) and potential applications for propagation

Contact Info

Product

Resources

About