LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 5 of total 5

Search options

  1. Article ; Online: Experimental and data analysis advances in thermal proteome profiling.

    Figueroa-Navedo, Amanda M / Ivanov, Alexander R

    Cell reports methods

    2024  Volume 4, Issue 2, Page(s) 100717

    Abstract: Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of ... ...

    Abstract Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.
    MeSH term(s) Proteome/analysis ; Proteomics/methods ; Ligands ; Mass Spectrometry/methods ; Data Analysis
    Chemical Substances Proteome ; Ligands
    Language English
    Publishing date 2024-02-26
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2667-2375
    ISSN (online) 2667-2375
    DOI 10.1016/j.crmeth.2024.100717
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling.

    Huang, Ting / Staniak, Mateusz / Veiga Leprevost, Felipe da / Figueroa-Navedo, Amanda M / Ivanov, Alexander R / Nesvizhskii, Alexey I / Choi, Meena / Vitek, Olga

    Journal of proteome research

    2023  Volume 22, Issue 8, Page(s) 2641–2659

    Abstract: Repeated measures experimental designs, which quantify proteins in biological subjects repeatedly over multiple experimental conditions or times, are commonly used in mass spectrometry-based proteomics. Such designs distinguish the biological variation ... ...

    Abstract Repeated measures experimental designs, which quantify proteins in biological subjects repeatedly over multiple experimental conditions or times, are commonly used in mass spectrometry-based proteomics. Such designs distinguish the biological variation within and between the subjects and increase the statistical power of detecting within-subject changes in protein abundance. Meanwhile, proteomics experiments increasingly incorporate tandem mass tag (TMT) labeling, a multiplexing strategy that gains both relative protein quantification accuracy and sample throughput. However, combining repeated measures and TMT multiplexing in a large-scale investigation presents statistical challenges due to unique interplays of between-mixture, within-mixture, between-subject, and within-subject variation. This manuscript proposes a family of linear mixed-effects models for differential analysis of proteomics experiments with repeated measures and TMT multiplexing. These models decompose the variation in the data into the contributions from its sources as appropriate for the specifics of each experiment, enable statistical inference of differential protein abundance, and recognize a difference in the uncertainty of between-subject versus within-subject comparisons. The proposed family of models is implemented in the R/Bioconductor package MSstatsTMT v2.2.0. Evaluations of four simulated datasets and four investigations answering diverse biological questions demonstrated the value of this approach as compared to the existing general-purpose approaches and implementations.
    MeSH term(s) Humans ; Tandem Mass Spectrometry ; Research Design ; Proteome/analysis
    Chemical Substances Proteome
    Language English
    Publishing date 2023-07-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00155
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Xanthommatin-Based Electrochromic Displays Inspired by Nature.

    Kumar, Amrita / Williams, Thomas L / Martin, Camille A / Figueroa-Navedo, Amanda M / Deravi, Leila F

    ACS applied materials & interfaces

    2018  Volume 10, Issue 49, Page(s) 43177–43183

    Abstract: Color is a signature visual feature in nature; however, the ability to trigger color change in the presence of different environmental stimuli is unique to only a handful of species in the animal kingdom. We exploit the natural color-changing properties ... ...

    Abstract Color is a signature visual feature in nature; however, the ability to trigger color change in the presence of different environmental stimuli is unique to only a handful of species in the animal kingdom. We exploit the natural color-changing properties of the predominant pigment in arthropods and cephalopods-xanthommatin (Xa)-and describe its utility as a new broad-spectrum electrochromic material. To accomplish this goal, we explored the spectroelectrochemical properties of Xa adsorbed to an indium-doped tin oxide-coated substrate chemically modified with poly(3,4-ethylene dioxythiophene) doped with poly(styrenesulfonate) (PEDOT:PSS). We identified a synergistic role between PEDOT:PSS and Xa that contributed to its absorption profile, which could be modulated across multiple cycles. By varying the ratio of the two electroactive components, we also altered the perceived visible color of Xa-based devices, which cycled from different shades of red to yellow under reducing and oxidizing potentials, respectively. Together, our data illustrate the utility of Xa-based devices as new broad-spectrum electrochromic materials.
    Language English
    Publishing date 2018-12-03
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.8b14123
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Standoff detection of highly energetic materials using laser-induced thermal excitation of infrared emission.

    Galán-Freyle, Nataly J / Pacheco-Londoño, Leonardo C / Figueroa-Navedo, Amanda M / Hernandez-Rivera, Samuel P

    Applied spectroscopy

    2015  Volume 69, Issue 5, Page(s) 535–544

    Abstract: A laser-mediated methodology for standoff infrared detection of threat chemicals is described in this article. Laser-induced thermal emissions (LITE) from vibrationally excited residue of highly energetic material (HEM) deposited on substrates were ... ...

    Abstract A laser-mediated methodology for standoff infrared detection of threat chemicals is described in this article. Laser-induced thermal emissions (LITE) from vibrationally excited residue of highly energetic material (HEM) deposited on substrates were detected remotely. Telescope-based Fourier transform infrared (FT-IR) spectroscopy measurements were carried out on substrates containing small amounts of HEM at surface concentrations of 5-200 μg/cm(2). Target substrates of various thicknesses were heated remotely using a carbon dioxide laser, and their mid-infrared (mid-IR), thermally stimulated emission spectra were recorded after heating. The telescope was configured from reflective optical elements to minimize emission losses in the mid-IR frequencies. Spectral replicas were acquired at distances from 4 to 64 m using an FT-IR interferometer at 4 cm(-1) resolution. The laser power, laser exposure times, and acquisition time of the FT-IR interferometer were adjusted to improve the detection and identification of samples. The advantages of increasing the thermal emission were easily observed in the results. The signal intensities were proportional to the thickness of the coated surface (a function of the surface concentration) as well as the laser power and laser exposure time. The limits of detection obtained for the HEM studied were 140-21 μg/cm(2) at 4 m. Detection was achieved at 64 m for a surface concentration of 200 μg/cm(2).
    Language English
    Publishing date 2015-05
    Publishing country United States
    Document type Journal Article
    ISSN 1943-3530
    ISSN (online) 1943-3530
    DOI 10.1366/14-07501
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Optical Properties of β-RDX Thin Films Deposited on Gold and Stainless Steel Substrates Calculated from Reflection-Absorption Infrared Spectra.

    Ruiz-Caballero, José L / Aparicio-Bolaño, Joaquín A / Figueroa-Navedo, Amanda M / Pacheco-Londoño, Leonardo C / Hernandez-Rivera, Samuel P

    Applied spectroscopy

    2017  Volume 71, Issue 8, Page(s) 1990–2000

    Abstract: The optical properties for crystalline films of the highly energetic material (HEM) hexahydro-1,3,5-trinitro-s-triazine, which is also known as RDX, deposited on gold (Au) and stainless steel (SS) substrates are presented. RDX has two important stable ... ...

    Abstract The optical properties for crystalline films of the highly energetic material (HEM) hexahydro-1,3,5-trinitro-s-triazine, which is also known as RDX, deposited on gold (Au) and stainless steel (SS) substrates are presented. RDX has two important stable conformational polymorphs at room temperature: α-RDX and β-RDX. The optical properties obtained in the present work correspond to thin film samples of predominantly β-RDX polymorph. The infrared spectroscopic intensities measured showed significant differences in the β-RDX crystalline films deposited on the two substrates with respect to the calculated real part of refractive index. The β-RDX/Au crystalline films have a high dynamic response, which is characterized by the asymmetric stretching mode of the axial nitro groups, whereas for the β-RDX/SS crystalline films, the dynamic response was mediated by the -N-NO
    Language English
    Publishing date 2017-08
    Publishing country United States
    Document type Journal Article
    ISSN 1943-3530
    ISSN (online) 1943-3530
    DOI 10.1177/0003702817710248
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top