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  1. No Access

    Chapter

    METLIN Tandem Mass Spectrometry and Neutral Loss Databases for the Identification of Microbial Natural Products and Other Chemical Entities

    In this section the principles of the METLIN tandem mass spectrometry (MS/MS or MS2) and neutral loss (NL) databases will be outlined.

    Wilasinee Heim, Aries Aisporna, Linh Hoang… in A Practical Guide to Metabolomics Applicat… (2023)

  2. Article

    Open Access

    Accelerated lysine metabolism conveys kidney protection in salt-sensitive hypertension

    Hypertension and kidney disease have been repeatedly associated with genomic variants and alterations of lysine metabolism. Here, we combined stable isotope labeling with untargeted metabolomics to investigate...

    Markus M. Rinschen, Oleg Palygin, Ashraf El-Meanawy… in Nature Communications (2022)

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  3. No Access

    Article

    Cognitive analysis of metabolomics data for systems biology

    Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms hel** researchers to efficiently search and...

    Erica L.-W. Majumder, Elizabeth M. Billings, H. Paul Benton… in Nature Protocols (2021)

  4. No Access

    Article

    METLIN MS2 molecular standards database: a broad chemical and biological resource

    **gchuan Xue, Carlos Guijas, H. Paul Benton, Benedikt Warth… in Nature Methods (2020)

  5. Article

    Open Access

    The METLIN small molecule dataset for machine learning-based retention time prediction

    Machine learning has been extensively applied in small molecule analysis to predict a wide range of molecular properties and processes including mass spectrometry fragmentation or chromatographic retention tim...

    Xavier Domingo-Almenara, Carlos Guijas, Elizabeth Billings… in Nature Communications (2019)

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  6. No Access

    Article

    XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

    We report XCMS-MRM and METLIN-MRM (http://xcmsonline-mrm.scripps.edu/ and http://metlin.scripps.edu/), a cloud-based data-analysis platform and a public multiple-reaction monitoring (MRM) transition repository fo...

    Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Julijana Ivanisevic… in Nature Methods (2018)

  7. No Access

    Article

    Data processing, multi-omic pathway map**, and metabolite activity analysis using XCMS Online

    This protocol describes XCMS Online, a web-based systems biology platform for processing of metabolomics data, pathway map** and integration with genomics and proteomics data.

    Erica M Forsberg, Tao Huan, Duane Rinehart, H Paul Benton… in Nature Protocols (2018)

  8. No Access

    Article

    Systems biology guided by XCMS Online metabolomics

    Tao Huan, Erica M Forsberg, Duane Rinehart, Caroline H Johnson… in Nature Methods (2017)

  9. Article

    Open Access

    Global metabolomics reveals metabolic dysregulation in ischemic retinopathy

    Proliferative diabetic retinopathy (PDR) is the most severe form of diabetic retinopathy and, along with diabetic macular edema, is responsible for the majority of blindness in adults below the age of 65. Ther...

    Liliana P. Paris, Caroline H. Johnson, Edith Aguilar, Yoshihiko Usui… in Metabolomics (2015)

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  10. No Access

    Article

    An interactive cluster heat map to visualize and explore multidimensional metabolomic data

    Heat maps are a commonly used visualization tool for metabolomic data where the relative abundance of ions detected in each sample is represented with color intensity. A limitation of applying heat maps to glo...

    Julijana Ivanisevic, H. Paul Benton, Duane Rinehart, Adrian Epstein… in Metabolomics (2015)

  11. No Access

    Article

    Metabolomic data streaming for biology-dependent data acquisition

    Duane Rinehart, Caroline H Johnson, Thomas Nguyen… in Nature Biotechnology (2014)

  12. No Access

    Article

    Metabolic oxidation regulates embryonic stem cell differentiation

    Metabolomics analysis of stem cells and differentiated cells points to chemical unsaturation as a key feature of stem cell metabolites. Manipulation of these metabolites' concentrations directly influences ste...

    Oscar Yanes, Julie Clark, Diana M Wong, Gary J Patti… in Nature Chemical Biology (2010)