Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification

Wang, Xusheng; Jones, Drew R.; Shaw, Timothy I.; Cho, Ji-Hoon; Wang, Yuanyuan; Tan, Haidong; Xie, Boer; Zhou, Suiping; Li, Yuxin; Peng, Junmin

doi:10.1021/acs.jproteome.8b00019

Cited by 41 publications

(25 citation statements)

References 43 publications

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“…It is also worth noting that the estimation of false discovery rates, has been a historical goal 17 and recent focus for small molecule identification. 18,19 However, these tools are not presently in mainstream use and do not exist in the software used for this study. The mzCloud library does possess a sophisticated scoring mechanism for quality of MS/MS spectra as shown in Figure 1B for the amino acid asparagine, but the other libraries rely on MS1 mass accuracy alone.…”

Section: Resultsmentioning

confidence: 99%

Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

Jenkins

Orsburn²

2019

Preprint

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GraphicAbstract Food fraud and drug counterfeiting are of increasingly large concern to both global economics and to public health and safety. Simple medicinal products consisting of single synthesized or purified compounds can be tested for purity and authenticity rapidly with established assays such as chromatography and UV absorbance. Drugs derived from natural sources may contain hundreds or thousands of distinct chemical compounds and require correspondingly complex analytical methods. In this study we explore the use of methods developed for global metabolic profiling toward the identification of unknown complex medicinal products. By utilizing rapid solvent extraction followed by ultrahigh pressure high performance liquid chromatography (UHPLC) coupled to high resolution accurate mass spectrometry (HRAM-MS/MS), we can reliably obtain a profile of the sample's molecular makeup. After profiling plant material to the depth of over 1,000 distinct molecules identified and quantified, we utilize these profiles to identify separately prepared and individually assayed blinded samples. We conclude that once a comprehensive library of small molecules has been acquired for each sample, identical preparations of products of unknown origin may be identified using simple statistical tools such as principal component analysis. We also conclude that these tools will be a valuable resource in affordably identified contaminated, adulterated and counterfeit products. .

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Section: Resultsmentioning

confidence: 99%

Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

Jenkins

Orsburn²

2019

Preprint

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“…Tandem mass spectra were obtained using collision-induced dissociation in a data-dependent manner. Raw mass spectral data files were converted to Mascot generic format and were analyzed using SearchGUI (35). Spectra were searched against a database of BTV proteins concatenated with the cRAP database (36).…”

Section: Methodsmentioning

confidence: 99%

The Interaction of Bluetongue Virus VP6 and Genomic RNA Is Essential for Genome Packaging

Sung

Vaughan

Rahman

et al. 2019

J Virol

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The genomes of the Reoviridae, including the animal pathogen bluetongue virus (BTV), are multisegmented double-stranded RNA (dsRNA). During replication, single-stranded (ss) positive-sense RNA segments are packaged into the assembling virus capsid, triggering genomic dsRNA synthesis. However, exactly how this packaging event occurs is not clear. A minor capsid protein, VP6, unique for the orbiviruses, has been proposed to be involved in the RNA-packaging process. In this study, we sought to characterize the RNA binding activity of VP6 and its functional relevance. A novel proteomic approach was utilized to map the ssRNA/dsRNA binding sites of a purified recombinant protein and the genomic dsRNA binding sites of the capsid-associated VP6. The data revealed that each VP6 protein has multiple distinct RNA-binding regions and that only one region is shared between recombinant and capsid-associated VP6. A combination of targeted mutagenesis and reverse genetics identified the RNA-binding region that is essential for virus replication. Using an in vitro RNA-binding competition assay, a unique cell-free assembly assay, and an in vivo single-cycle replication assay, it was possible to identify a motif within the shared binding region that binds BTV ssRNA preferentially in a manner consistent with specific RNA recruitment during capsid assembly. These data highlight the critical roles that this unique protein plays in orbivirus genome packaging and replication. IMPORTANCE Genome packaging is a critical stage during virus replication. For viruses with segmented genomes, the genome segments need to be correctly packaged into a newly formed capsid. However, the detailed mechanism of this packaging is unclear. Here we focus on VP6, a minor viral protein of bluetongue virus, which is critical for genome packaging. We used multiple approaches, including a robust RNA-protein fingerprinting assay, to map the ssRNA binding sites of recombinant VP6 and the genomic dsRNA binding sites of capsid-associated VP6. By these means, together with virological and biochemical methods, we identify the viral RNA-packaging motif of a segmented dsRNA virus for the first time.

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“…However, appropriately modeling this error, as well as the error associated with experimental measurements, enables significant downselection to candidate lists amenable to verification by authentic standards. Further, by leveraging libraries of much broader chemical space coverage, putative matches carry better approximations of false discovery, an until recently ignored metric among the metabolomics community with potentially problematic ramifications (Scheubert et al, 2017 ; Wang et al, 2018 ).…”

Section: Standards-free Metabolomics and Computational Library Buildimentioning

confidence: 99%

Who Is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them

Couvillion

Agrawal

Colby

et al. 2020

Front. Cell. Infect. Microbiol.

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Even as the field of microbiome research has made huge strides in mapping microbial community composition in a variety of environments and organisms, explaining the phenotypic influences on the host by microbial taxa—both known and unknown—and their specific functions still remain major challenges. A pressing need is the ability to assign specific functions in terms of enzymes and small molecules to specific taxa or groups of taxa in the community. This knowledge will be crucial for advancing personalized therapies based on the targeted modulation of microbes or metabolites that have predictable outcomes to benefit the human host. This perspective article advocates for the combined use of standards-free metabolomics and activity-based protein profiling strategies to address this gap in functional knowledge in microbiome research via the identification of novel biomolecules and the attribution of their production to specific microbial taxa.

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Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification

Cited by 41 publications

References 43 publications

Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

The Interaction of Bluetongue Virus VP6 and Genomic RNA Is Essential for Genome Packaging

Who Is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them

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