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  1. Article: Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline.

    Mitchell, Joshua M / Chi, Yuanye / Thapa, Maheshwor / Pang, Zhiqiang / Xia, Jianguo / Li, Shuzhao

    bioRxiv : the preprint server for biology

    2024  

    Abstract: To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data ...

    Abstract To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics.
    Language English
    Publishing date 2024-02-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.13.580048
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  2. Article: Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier Transform Mass Spectrometry Experiments.

    Flight, Robert M / Mitchell, Joshua M / Moseley, Hunter N B

    Metabolites

    2022  Volume 12, Issue 6

    Abstract: We present a novel, scan-centric method for characterizing peaks from direct injection multi-scan Fourier transform mass spectra of complex samples that utilizes frequency values derived directly from the spacing of ... ...

    Abstract We present a novel, scan-centric method for characterizing peaks from direct injection multi-scan Fourier transform mass spectra of complex samples that utilizes frequency values derived directly from the spacing of raw
    Language English
    Publishing date 2022-06-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo12060515
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  3. Article: Untargeted Lipidomics of Non-Small Cell Lung Carcinoma Demonstrates Differentially Abundant Lipid Classes in Cancer vs. Non-Cancer Tissue.

    Mitchell, Joshua M / Flight, Robert M / Moseley, Hunter N B

    Metabolites

    2021  Volume 11, Issue 11

    Abstract: Lung cancer remains the leading cause of cancer death worldwide and non-small cell lung carcinoma (NSCLC) represents 85% of newly diagnosed lung cancers. In this study, we utilized our untargeted assignment tool Small Molecule Isotope Resolved Formula ... ...

    Abstract Lung cancer remains the leading cause of cancer death worldwide and non-small cell lung carcinoma (NSCLC) represents 85% of newly diagnosed lung cancers. In this study, we utilized our untargeted assignment tool Small Molecule Isotope Resolved Formula Enumerator (SMIRFE) and ultra-high-resolution Fourier transform mass spectrometry to examine lipid profile differences between paired cancerous and non-cancerous lung tissue samples from 86 patients with suspected stage I or IIA primary NSCLC. Correlation and co-occurrence analysis revealed significant lipid profile differences between cancer and non-cancer samples. Further analysis of machine-learned lipid categories for the differentially abundant molecular formulas identified a high abundance sterol, high abundance and high m/z sphingolipid, and low abundance glycerophospholipid metabolic phenotype across the NSCLC samples. At the class level, higher abundances of sterol esters and lower abundances of cardiolipins were observed suggesting altered stearoyl-CoA desaturase 1 (SCD1) or acetyl-CoA acetyltransferase (ACAT1) activity and altered human cardiolipin synthase 1 or lysocardiolipin acyltransferase activity respectively, the latter of which is known to confer apoptotic resistance. The presence of a shared metabolic phenotype across a variety of genetically distinct NSCLC subtypes suggests that this phenotype is necessary for NSCLC development and may result from multiple distinct genetic lesions. Thus, targeting the shared affected pathways may be beneficial for a variety of genetically distinct NSCLC subtypes.
    Language English
    Publishing date 2021-10-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo11110740
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  4. Article: Deriving Lipid Classification Based on Molecular Formulas.

    Mitchell, Joshua M / Flight, Robert M / Moseley, Hunter N B

    Metabolites

    2020  Volume 10, Issue 3

    Abstract: Despite instrument and algorithmic improvements, the untargeted and accurate assignment of metabolites remains an unsolved problem in metabolomics. New assignment methods such as our SMIRFE algorithm can assign elemental molecular formulas to observed ... ...

    Abstract Despite instrument and algorithmic improvements, the untargeted and accurate assignment of metabolites remains an unsolved problem in metabolomics. New assignment methods such as our SMIRFE algorithm can assign elemental molecular formulas to observed spectral features in a highly untargeted manner without orthogonal information from tandem MS or chromatography. However, for many lipidomics applications, it is necessary to know at least the lipid category or class that is associated with a detected spectral feature to derive a biochemical interpretation. Our goal is to develop a method for robustly classifying elemental molecular formula assignments into lipid categories for an application to SMIRFE-generated assignments. Using a Random Forest machine learning approach, we developed a method that can predict lipid category and class from SMIRFE non-adducted molecular formula assignments. Our methods achieve high average predictive accuracy (>90%) and precision (>83%) across all eight of the lipid categories in the LIPIDMAPS database. Classification performance was evaluated using sets of theoretical, data-derived, and artifactual molecular formulas. Our methods enable the lipid classification of non-adducted molecular formula assignments generated by SMIRFE without orthogonal information, facilitating the biochemical interpretation of untargeted lipidomics experiments. This lipid classification appears insufficient for validating single-spectrum assignments, but could be useful in cross-spectrum assignment validation.
    Language English
    Publishing date 2020-03-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo10030122
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  5. Article: Atom Identifiers Generated by a Neighborhood-Specific Graph Coloring Method Enable Compound Harmonization across Metabolic Databases.

    Jin, Huan / Mitchell, Joshua M / Moseley, Hunter N B

    Metabolites

    2020  Volume 10, Issue 9

    Abstract: Metabolic flux analysis requires both a reliable metabolic model and reliable metabolic profiles in characterizing metabolic reprogramming. Advances in analytic methodologies enable production of high-quality metabolomics datasets capturing isotopic flux. ...

    Abstract Metabolic flux analysis requires both a reliable metabolic model and reliable metabolic profiles in characterizing metabolic reprogramming. Advances in analytic methodologies enable production of high-quality metabolomics datasets capturing isotopic flux. However, useful metabolic models can be difficult to derive due to the lack of relatively complete atom-resolved metabolic networks for a variety of organisms, including human. Here, we developed a neighborhood-specific graph coloring method that creates unique identifiers for each atom in a compound facilitating construction of an atom-resolved metabolic network. What is more, this method is guaranteed to generate the same identifier for symmetric atoms, enabling automatic identification of possible additional mappings caused by molecular symmetry. Furthermore, a compound coloring identifier derived from the corresponding atom coloring identifiers can be used for compound harmonization across various metabolic network databases, which is an essential first step in network integration. With the compound coloring identifiers, 8865 correspondences between KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc compounds are detected, with 5451 of them confirmed by other identifiers provided by the two databases. In addition, we found that the Enzyme Commission numbers (EC) of reactions can be used to validate possible correspondence pairs, with 1848 unconfirmed pairs validated by commonality in reaction ECs. Moreover, we were able to detect various issues and errors with compound representation in KEGG and MetaCyc databases by compound coloring identifiers, demonstrating the usefulness of this methodology for database curation.
    Language English
    Publishing date 2020-09-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo10090368
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  6. Article: Iodide uptake by forest soils is principally related to the activity of extracellular oxidases.

    Grandbois, Russell M / Santschi, Peter H / Xu, Chen / Mitchell, Joshua M / Kaplan, Daniel I / Yeager, Chris M

    Frontiers in chemistry

    2023  Volume 11, Page(s) 1105641

    Abstract: ... ...

    Abstract 129
    Language English
    Publishing date 2023-03-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2023.1105641
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  7. Article ; Online: Small Molecule Isotope Resolved Formula Enumeration: A Methodology for Assigning Isotopologues and Metabolite Formulas in Fourier Transform Mass Spectra.

    Mitchell, Joshua M / Flight, Robert M / Moseley, Hunter N B

    Analytical chemistry

    2019  Volume 91, Issue 14, Page(s) 8933–8940

    Abstract: Improvements in Fourier transform mass spectrometry (FT-MS) enable increasingly more complex experiments in the field of metabolomics. What is directly detected in FT-MS spectra are spectral features (peaks) that correspond to sets of adducted and ... ...

    Abstract Improvements in Fourier transform mass spectrometry (FT-MS) enable increasingly more complex experiments in the field of metabolomics. What is directly detected in FT-MS spectra are spectral features (peaks) that correspond to sets of adducted and charged forms of specific molecules in the sample. The robust assignment of these features is an essential step for MS-based metabolomics experiments, but the sheer complexity of what is detected and a variety of analytically introduced variance, errors, and artifacts has hindered the systematic analysis of complex patterns of observed peaks with respect to isotope content. We have developed a method called SMIRFE that detects small biomolecules and determines their elemental molecular formula (EMF) using detected sets of isotopologue peaks sharing the same EMF. SMIRFE does not use a database of known metabolite formulas; instead a nearly comprehensive search space of all isotopologues within a mass range is constructed and used for assignment. This search space can be tailored for different isotope labeling patterns expected in different stable isotope tracing experiments. Using consumer-level computing equipment, a large search space of 2000 Da was constructed, and assignment performance was evaluated and validated using verified assignments on a pair of peak lists derived from spectra containing unlabeled and
    MeSH term(s) Algorithms ; Amino Acids/analysis ; Carbon Isotopes/analysis ; Fourier Analysis ; Isotope Labeling/methods ; Mass Spectrometry/methods ; Metabolomics/methods ; Nitrogen Isotopes/analysis
    Chemical Substances Amino Acids ; Carbon Isotopes ; Nitrogen Isotopes
    Language English
    Publishing date 2019-07-01
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.9b00748
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    Zs.A 4033: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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  8. Article ; Online: Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40.

    Mitchell, Joshua M / June, Cynthia M / Baggett, Vincent L / Lowe, Beth C / Ruble, James F / Bonomo, Robert A / Leonard, David A / Powers, Rachel A

    The Journal of biological chemistry

    2022  Volume 298, Issue 7, Page(s) 102127

    Abstract: The evolution of multidrug resistance in Acinetobacter spp. increases the risk of our best antibiotics losing their efficacy. From a clinical perspective, the carbapenem-hydrolyzing class D β-lactamase subfamily present in Acinetobacter spp. is ... ...

    Abstract The evolution of multidrug resistance in Acinetobacter spp. increases the risk of our best antibiotics losing their efficacy. From a clinical perspective, the carbapenem-hydrolyzing class D β-lactamase subfamily present in Acinetobacter spp. is particularly concerning because of its ability to confer resistance to carbapenems. The kinetic profiles of class D β-lactamases exhibit variability in carbapenem hydrolysis, suggesting functional differences. To better understand the structure-function relationship between the carbapenem-hydrolyzing class D β-lactamase OXA-24/40 found in Acinetobacter baumannii and carbapenem substrates, we analyzed steady-state kinetics with the carbapenem antibiotics meropenem and ertapenem and determined the structures of complexes of OXA-24/40 bound to imipenem, meropenem, doripenem, and ertapenem, as well as the expanded-spectrum cephalosporin cefotaxime, using X-ray crystallography. We show that OXA-24/40 exhibits a preference for ertapenem compared with meropenem, imipenem, and doripenem, with an increase in catalytic efficiency of up to fourfold. We suggest that superposition of the nine OXA-24/40 complexes will better inform future inhibitor design efforts by providing insight into the complicated and varying ways in which carbapenems are selected and bound by class D β-lactamases.
    MeSH term(s) Acinetobacter baumannii/enzymology ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Carbapenems/chemistry ; Carbapenems/metabolism ; Hydrolysis ; Microbial Sensitivity Tests ; Protein Conformation ; Substrate Specificity ; beta-Lactamases/chemistry ; beta-Lactamases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Carbapenems ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase OXA-24 (EC 3.5.2.6) ; beta-lactamase OXA-40, Acinetobacter baumannii (EC 3.5.2.6)
    Language English
    Publishing date 2022-06-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.102127
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  9. Article ; Online: Common clinical substitutions enhance the carbapenemase activity of OXA-51-like class D β-lactamases from Acinetobacter spp.

    Mitchell, Joshua M / Leonard, David A

    Antimicrobial agents and chemotherapy

    2014  Volume 58, Issue 11, Page(s) 7015–7016

    MeSH term(s) Acinetobacter/drug effects ; Acinetobacter/enzymology ; Acinetobacter/genetics ; Acinetobacter Infections/drug therapy ; Acinetobacter Infections/microbiology ; Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Carbapenems/metabolism ; Carbapenems/pharmacology ; Catalytic Domain ; Cross Infection/drug therapy ; Cross Infection/microbiology ; Humans ; Protein Folding ; beta-Lactamases/genetics ; beta-Lactamases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Carbapenems ; Ampicillin (7C782967RD) ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase OXA-51, Acinetobacter baumannii (EC 3.5.2.6) ; carbapenemase (EC 3.5.2.6)
    Language English
    Publishing date 2014-08-25
    Publishing country United States
    Document type Letter
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/AAC.03651-14
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  10. Article: Small Molecule Isotope Resolved Formula Enumeration: A Methodology for Assigning Isotopologues and Metabolite Formulas in Fourier Transform Mass Spectra

    Mitchell, Joshua M / Flight, Robert M / Moseley, Hunter N. B

    Analytical chemistry. 2019 June 20, v. 91, no. 14

    2019  

    Abstract: Improvements in Fourier transform mass spectrometry (FT-MS) enable increasingly more complex experiments in the field of metabolomics. What is directly detected in FT-MS spectra are spectral features (peaks) that correspond to sets of adducted and ... ...

    Abstract Improvements in Fourier transform mass spectrometry (FT-MS) enable increasingly more complex experiments in the field of metabolomics. What is directly detected in FT-MS spectra are spectral features (peaks) that correspond to sets of adducted and charged forms of specific molecules in the sample. The robust assignment of these features is an essential step for MS-based metabolomics experiments, but the sheer complexity of what is detected and a variety of analytically introduced variance, errors, and artifacts has hindered the systematic analysis of complex patterns of observed peaks with respect to isotope content. We have developed a method called SMIRFE that detects small biomolecules and determines their elemental molecular formula (EMF) using detected sets of isotopologue peaks sharing the same EMF. SMIRFE does not use a database of known metabolite formulas; instead a nearly comprehensive search space of all isotopologues within a mass range is constructed and used for assignment. This search space can be tailored for different isotope labeling patterns expected in different stable isotope tracing experiments. Using consumer-level computing equipment, a large search space of 2000 Da was constructed, and assignment performance was evaluated and validated using verified assignments on a pair of peak lists derived from spectra containing unlabeled and 15N-labeled versions of amino acids derivatized using ethylchloroformate. SMIRFE identified 18 of 18 predicted derivatized EMFs, and each assignment was evaluated statistically and assigned an e-value representing the probability to occur by chance.
    Keywords amino acids ; databases ; equipment ; isotope labeling ; mass spectrometry ; metabolites ; metabolomics ; probability ; stable isotopes ; variance
    Language English
    Dates of publication 2019-0620
    Size p. 8933-8940.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.9b00748
    Database NAL-Catalogue (AGRICOLA)

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