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  1. Article ; Online: Subcellular quantitative imaging of metabolites at the organelle level.

    Siuzdak, Gary

    Nature metabolism

    2023  Volume 5, Issue 9, Page(s) 1446–1448

    MeSH term(s) Organelles
    Language English
    Publishing date 2023-09-07
    Publishing country Germany
    Document type Journal Article
    ISSN 2522-5812
    ISSN (online) 2522-5812
    DOI 10.1038/s42255-023-00882-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book: Mass spectrometry for biotechnology

    Siuzdak, Gary

    1996  

    Author's details Gary Siuzdak
    Keywords Nucleic Acids / analysis ; Proteins / analysis ; Biotechnology / methods ; Spectrum Analysis, Mass ; Massenspektrometrie
    Subject Massenspektrographie ; Massenspektroskopie
    Language English
    Size XVI, 161 S. : Ill., graph. Darst.
    Publisher Acad. Press
    Publishing place San Diego u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT007233514
    ISBN 0-12-647471-0 ; 978-0-12-647471-8
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    1996 A 5872 order for loan Magazin

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  3. Article ; Online: Metabolite discovery: Biochemistry's scientific driver.

    Giera, Martin / Yanes, Oscar / Siuzdak, Gary

    Cell metabolism

    2022  Volume 34, Issue 1, Page(s) 21–34

    Abstract: Metabolite identification represents a major challenge, and opportunity, for biochemistry. The collective characterization and quantification of metabolites in living organisms, with its many successes, represents a major biochemical knowledgebase and ... ...

    Abstract Metabolite identification represents a major challenge, and opportunity, for biochemistry. The collective characterization and quantification of metabolites in living organisms, with its many successes, represents a major biochemical knowledgebase and the foundation of metabolism's rebirth in the 21
    MeSH term(s) Artificial Intelligence ; Magnetic Resonance Spectroscopy/methods ; Mass Spectrometry/methods ; Metabolomics/methods
    Language English
    Publishing date 2022-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2176834-1
    ISSN 1932-7420 ; 1550-4131
    ISSN (online) 1932-7420
    ISSN 1550-4131
    DOI 10.1016/j.cmet.2021.11.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Metabolomics Data Processing Using XCMS.

    Domingo-Almenara, Xavier / Siuzdak, Gary

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2104, Page(s) 11–24

    Abstract: XCMS is one of the most used software for liquid chromatography-mass spectrometry (LC-MS) data processing and it exists both as an R package and as a cloud-based platform known as XCMS Online. In this chapter, we first overview the nature of LC-MS data ... ...

    Abstract XCMS is one of the most used software for liquid chromatography-mass spectrometry (LC-MS) data processing and it exists both as an R package and as a cloud-based platform known as XCMS Online. In this chapter, we first overview the nature of LC-MS data to contextualize the need for data processing software. Next, we describe the algorithms used by XCMS and the role that the different user-defined parameters play in the data processing. Finally, we describe the extended capabilities of XCMS Online.
    MeSH term(s) Algorithms ; Chromatography, Liquid ; Computational Biology/methods ; Data Interpretation, Statistical ; Mass Spectrometry ; Metabolomics/methods ; Online Systems ; Software ; User-Computer Interface ; Workflow
    Language English
    Publishing date 2020-01-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0239-3_2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: The Anodization of Thin Titania Layers as a Facile Process towards Semitransparent and Ordered Electrode Material.

    Kouao, Dujearic-Stephane / Grochowska, Katarzyna / Siuzdak, Katarzyna

    Nanomaterials (Basel, Switzerland)

    2022  Volume 12, Issue 7

    Abstract: ... by anodic oxidation are being widely investigated as a low-cost alternative to silicon-based materials, e.g., in solar ...

    Abstract Photoanodes consisting of titania nanotubes (TNTs) grown on transparent conductive oxides (TCO) by anodic oxidation are being widely investigated as a low-cost alternative to silicon-based materials, e.g., in solar light-harvesting applications. Intending to enhance the optical properties of those photoanodes, the modification of the surface chemistry or control of the geometrical characteristics of developed TNTs has been explored. In this review, the recent advancement in light-harvesting properties of transparent anodic TNTs formed onto TCO is summarized. The physical deposition methods such as magnetron sputtering, pulsed laser deposition and electron beam evaporation are the most reported for the deposition of Ti film onto TCO, which are subsequently anodized. A concise description of methods utilized to improve the adhesion of the deposited film and achieve TNT layers without cracks and delamination after the anodization is outlined. Then, the different models describing the formation mechanism of anodic TNTs are discussed with particular focus on the impact of the deposited Ti film thickness on the adhesion of TNTs. Finally, the effects of the modifications of both the surface chemistry and morphological features of materials on their photocatalyst and photovoltaic performances are discussed. For each section, experimental results obtained by different research groups are evoked.
    Language English
    Publishing date 2022-03-29
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662255-5
    ISSN 2079-4991
    ISSN 2079-4991
    DOI 10.3390/nano12071131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: METLIN: A Tandem Mass Spectral Library of Standards.

    Montenegro-Burke, J Rafael / Guijas, Carlos / Siuzdak, Gary

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2104, Page(s) 149–163

    Abstract: ... as the tools (e.g., Fragment Similarity Search and Neutral Loss Search) used to query the database and ...

    Abstract Untargeted mass spectrometry metabolomics studies rely on accurate databases for the identification of metabolic features. Leveraging unique fragmentation patterns as well as characteristic dissociation routes allows for structural information to be gained for specific metabolites and molecular classes, respectively. Here we describe the evolution of METLIN as a resource for small molecule analysis as well as the tools (e.g., Fragment Similarity Search and Neutral Loss Search) used to query the database and their workflows for the identification of molecular entities. Additionally, we will discuss the functionalities of isoMETLIN, a database of isotopic metabolites, and the latest addition to the METLIN family, METLIN-MRM, which facilitates the analysis of quantitative mass spectrometry data generated with triple quadrupole instrumentation.
    MeSH term(s) Databases, Factual ; Metabolome ; Metabolomics/methods ; Metabolomics/standards ; Software ; Tandem Mass Spectrometry/methods ; Workflow
    Language English
    Publishing date 2020-01-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0239-3_9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Modeling of transmission characteristics in step-index polymer optical fiber using the matrix exponential method.

    Stepniak, Grzegorz / Siuzdak, Jerzy

    Applied optics

    2018  Volume 57, Issue 31, Page(s) 9203–9207

    Abstract: In this paper, we propose to calculate the impulse and frequency response of step-index polymer optical fiber in the presence of mode coupling using the matrix exponential method. The computation time in this method is independent of the fiber length and ...

    Abstract In this paper, we propose to calculate the impulse and frequency response of step-index polymer optical fiber in the presence of mode coupling using the matrix exponential method. The computation time in this method is independent of the fiber length and is typically 2 orders of magnitude shortened compared with the standard numerical procedures involving finite difference methods. Results obtained with our method are compared with those of known cases, where an analytical solution for the time-dependent power flow equation exists, and with a finite difference method. We also investigate the impact of mode coupling and differential modal attenuation on impulse response duration and shape.
    Language English
    Publishing date 2018-11-21
    Publishing country United States
    Document type Journal Article
    ISSN 1539-4522
    ISSN (online) 1539-4522
    DOI 10.1364/AO.57.009203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Reply to Comment on METLIN: A Technology Platform for Identifying Knowns and Unknowns.

    Guijas, Carlos / Siuzdak, Gary

    Analytical chemistry

    2018  Volume 90, Issue 21, Page(s) 13128–13129

    Language English
    Publishing date 2018-10-18
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.8b04081
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  9. Article ; Online: The Anodization of Thin Titania Layers as a Facile Process towards Semitransparent and Ordered Electrode Material

    Dujearic-Stephane Kouao / Katarzyna Grochowska / Katarzyna Siuzdak

    Nanomaterials, Vol 12, Iss 1131, p

    2022  Volume 1131

    Abstract: ... by anodic oxidation are being widely investigated as a low-cost alternative to silicon-based materials, e.g., in solar ...

    Abstract Photoanodes consisting of titania nanotubes (TNTs) grown on transparent conductive oxides (TCO) by anodic oxidation are being widely investigated as a low-cost alternative to silicon-based materials, e.g., in solar light-harvesting applications. Intending to enhance the optical properties of those photoanodes, the modification of the surface chemistry or control of the geometrical characteristics of developed TNTs has been explored. In this review, the recent advancement in light-harvesting properties of transparent anodic TNTs formed onto TCO is summarized. The physical deposition methods such as magnetron sputtering, pulsed laser deposition and electron beam evaporation are the most reported for the deposition of Ti film onto TCO, which are subsequently anodized. A concise description of methods utilized to improve the adhesion of the deposited film and achieve TNT layers without cracks and delamination after the anodization is outlined. Then, the different models describing the formation mechanism of anodic TNTs are discussed with particular focus on the impact of the deposited Ti film thickness on the adhesion of TNTs. Finally, the effects of the modifications of both the surface chemistry and morphological features of materials on their photocatalyst and photovoltaic performances are discussed. For each section, experimental results obtained by different research groups are evoked.
    Keywords Ti film ; transparent conductive oxides ; electrochemical anodization ; interfacial adhesion ; titania nanotubes ; semitransparent photoelectrode ; Chemistry ; QD1-999
    Subject code 620
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Tandem Mass Spectrometry across Platforms.

    Hoang, Corey / Uritboonthai, Winnie / Hoang, Linh / Billings, Elizabeth M / Aisporna, Aries / Nia, Farshad A / Derks, Rico J E / Williamson, James R / Giera, Martin / Siuzdak, Gary

    Analytical chemistry

    2024  Volume 96, Issue 14, Page(s) 5478–5488

    Abstract: PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous fields including metabolism, pharmaceuticals, toxicology, cosmetics, agriculture, and ... ...

    Abstract PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous fields including metabolism, pharmaceuticals, toxicology, cosmetics, agriculture, and many more. Rapid identification of these small molecules increasingly relies on electrospray ionization (ESI) paired with tandem mass spectrometry (MS/MS), particularly by comparison to genuine standard MS/MS data sets. Despite its widespread application, achieving consistency in MS/MS data across various analytical platforms remains an unaddressed concern. This study evaluated MS/MS data derived from one hundred molecular standards utilizing instruments from five manufacturers, inclusive of quadrupole time-of-flight (QTOF) and quadrupole orbitrap "exactive" (QE) mass spectrometers by Agilent (QTOF), Bruker (QTOF), SCIEX (QTOF), Waters (QTOF), and Thermo QE. We assessed fragment ion variations at multiple collisional energies (0, 10, 20, and 40 eV) using the cosine scoring algorithm for comparisons and the number of fragments observed. A parallel visual analysis of the MS/MS spectra across instruments was conducted, consistent with a standard procedure that is used to circumvent the still prevalent issue of mischaracterizations as shown for dimethyl sphingosine and C20 sphingosine. Our analysis revealed a notable consistency in MS/MS data and identifications, with fragment ions'
    MeSH term(s) Tandem Mass Spectrometry/methods ; Sphingosine ; Spectrometry, Mass, Electrospray Ionization/methods ; Gas Chromatography-Mass Spectrometry ; Ions
    Chemical Substances Sphingosine (NGZ37HRE42) ; Ions
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c05576
    Database MEDical Literature Analysis and Retrieval System OnLINE

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