GNPS LC-MS/MS DDA Method Optimization Natural Products
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Unknown Species
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000088732 | GNPS | Wed Jan 26 00:25:00 GMT 2022
REPOSITORIES: GNPS
Similar Datasets
Project description:Untargeted-metabolomics LC-MS/MS analysis of commercial natural products pool, analyzed with different DDA settings with the objective to find the best one.
2022-01-26 | MSV000088732 | MassIVE
Project description:DDA untargeted metabolomics of 3 different complex samples coming from river, ocean, and soil sources was used to obtain the best optimization setting.
2022-03-01 | MSV000088937 | MassIVE
Project description:DDA untargeted metabolomics of 3 different complex samples coming from river, ocean, and soil sources was used to obtain the best optimization setting.
2022-03-01 | MSV000088937 | GNPS
Project description:Introduction Stable isotope tracer studies are increasingly applied to explore metabolism from the detailed analysis of tracer incorporation into metabolites. Untargeted LC/MS approaches have recently emerged and provide potent methods for expanding the dimension and complexity of the metabolic networks that can be investigated. A number of software tools have been developed to process the highly complex MS data collected in such studies; however, a method to optimize the extraction of valuable isotopic data is lacking. Objectives To develop and validate a method to optimize automated data processing for untargeted MS-based isotopic tracing investigations of metabolism. Methods The method is based on the application of a suitable reference material to rationally perform parameter optimization throughout the complete data processing workflow. It was applied in the context of 13C-labelling experiments and with two different software, namely geoRge and X13CMS. It was illustrated with the study of a E. coli mutant impaired for central metabolism. Results The optimization methodology provided significant gain in the number and quality of extracted isotopic data, independently of the software considered. Pascal triangle samples are well suited for such purpose since they allow both the identification of analytical issues and optimization of data processing at the same time. Conclusion The proposed method maximizes the biological value of untargeted MS-based isotopic tracing investigations by revealing the full metabolic information that is encoded in the labelling patterns of metabolites. Supplementary Information The online version contains supplementary material available at 10.1007/s11306-022-01897-5.
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Project description:In this study, a multi-residue analysis was developed for 32 compounds, including pesticides and metabolites, in five meat products using gas chromatography-tandem mass spectrometry (GC-MS/MS). The validation of the developed analytical method was also evaluated in accordance with Codex Alimentarius guidelines. Aminopropyl (NH2), C18, and florisil solid phase extraction (SPE) cartridges were used to evaluate and optimize the cleanup procedure of the tested samples prior to GC-MS/MS analysis. Based on the analytical performance, the C18 SPE cartridge was deemed to be the most suitable among the examined SPE cartridges. The optimized method demonstrated that 29 out of 32 tested compounds acquired good linearity (R2 ≥ 0.99), and 25 tested compounds displayed the method limit of quantification (MLOQ) ≤ 0.01 mg/kg. Out of the 32 tested compounds, only 21 compounds met the acceptable analytical criteria for the lard and tallow samples, compared to 27 compounds in the beef, pork, and chicken samples that falls within the acceptable standards for recovery (70–120%) and analytical precision (relative standard deviation RSD ≤ 20%). The average matrix effect was widely varied (20.1–64.8%) in the studied meat samples that were affected by either ion enhancement or suppression. In particular, in the lard sample, 13 compounds showed poor recovery and analytical precision due to ion suppression. Thus, the matrix effect (ME) was considered a critical factor during multi-residue pesticide analysis in different meat products. In conclusion, this developed analytical method can be used as a routine monitoring system for residual pesticide analysis in livestock products with acceptable analytical standards. Further meticulous analytical studies should be optimized and validated for multi-residue pesticide analysis in diversified meat products.
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Project description:An effective analytical method was optimized for residues including chlorpyrifos-methyl, deltamethrin, fenoxanil, thiobencarb and fludioxonil in mealworms, the larval form of Tenebrio molitor. They are listed for pest control during wheat cultivation and can be found in wheat-bran feed for growing mealworms in South Korea. Analytes were extracted using acetonitrile and salt packet. Four clean-up methods ((1) MgSO4 + 25 mg PSA + 25 mg C18; (2) MgSO4 + 50 mg PSA + 50 mg C18; (3) EMR-lipidTM tube; and (4) 10 mL n-hexane) were investigated and the method (1) was selected due to its robustness. Low-temperature precipitation of fat and proteins improved the recoveries. Recoveries from the Method (1) were satisfying with 70-120% with <20% relative SD at a spiking level of 0.01 mg/kg. With the simultaneous sample preparation, fenoxanil, thiobencarb and fludioxonil were analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) and chlorpyrifos-methyl and deltamethrin by gas chromatography tandem mass spectrometry (GC-MS/MS). Quantification limits for LC-MS/MS and GC-MS/MS were 0.5 and 2.5 μg/L, respectively. No pesticides of interest were detected in 30 real samples collected across the nation. However, the data can be provided for establishing maximum residue limits for the pesticides in mealworms in response to the positive list system.
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Project description:Cas12a CRISPR technology, unlike Cas9, allows for multiplexing guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results to those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and we provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.
2023-05-09 | GSE231789 | GEO
Project description:Cas12a CRISPR technology, unlike Cas9, allows for multiplexing guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results to those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and we provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.
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