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  1. AU="Kohler, Devon"
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  1. Article ; Online: MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments.

    Kohler, Devon / Kaza, Maanasa / Pasi, Cristina / Huang, Ting / Staniak, Mateusz / Mohandas, Dhaval / Sabido, Eduard / Choi, Meena / Vitek, Olga

    Journal of proteome research

    2023  Volume 22, Issue 2, Page(s) 551–556

    Abstract: Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is a versatile technology for identifying and quantifying proteins in complex biological mixtures. Postidentification, analysis of changes in protein abundances ... ...

    Abstract Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is a versatile technology for identifying and quantifying proteins in complex biological mixtures. Postidentification, analysis of changes in protein abundances between conditions requires increasingly complex and specialized statistical methods. Many of these methods, in particular the family of open-source Bioconductor packages
    MeSH term(s) Software ; Proteomics/methods ; Chromatography, Liquid/methods ; Tandem Mass Spectrometry/methods ; Proteins/analysis
    Chemical Substances Proteins
    Language English
    Publishing date 2023-01-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00603
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
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  2. Article ; Online: MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics.

    Kohler, Devon / Tsai, Tsung-Heng / Verschueren, Erik / Huang, Ting / Hinkle, Trent / Phu, Lilian / Choi, Meena / Vitek, Olga

    Molecular & cellular proteomics : MCP

    2022  Volume 22, Issue 1, Page(s) 100477

    Abstract: Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is increasingly used to detect changes in posttranslational modifications (PTMs) in samples from different conditions. Analysis of data from such experiments faces ...

    Abstract Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is increasingly used to detect changes in posttranslational modifications (PTMs) in samples from different conditions. Analysis of data from such experiments faces numerous statistical challenges. These include the low abundance of modified proteoforms, the small number of observed peptides that span modification sites, and confounding between changes in the abundance of PTM and the overall changes in the protein abundance. Therefore, statistical approaches for detecting differential PTM abundance must integrate all the available information pertaining to a PTM site and consider all the relevant sources of confounding and variation. In this manuscript, we propose such a statistical framework, which is versatile, accurate, and leads to reproducible results. The framework requires an experimental design, which quantifies, for each sample, both peptides with PTMs and peptides from the same proteins with no modification sites. The proposed framework supports both label-free and tandem mass tag-based LC-MS/MS acquisitions. The statistical methodology separately summarizes the abundances of peptides with and without the modification sites, by fitting separate linear mixed effects models appropriate for the experimental design. Next, model-based inferences regarding the PTM and the protein-level abundances are combined to account for the confounding between these two sources. Evaluations on computer simulations, a spike-in experiment with known ground truth, and three biological experiments with different organisms, modification types, and data acquisition types demonstrate the improved fold change estimation and detection of differential PTM abundance, as compared to currently used approaches. The proposed framework is implemented in the free and open-source R/Bioconductor package MSstatsPTM.
    MeSH term(s) Proteomics/methods ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Protein Processing, Post-Translational ; Proteins ; Peptides/chemistry
    Chemical Substances Proteins ; Peptides
    Language English
    Publishing date 2022-12-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2075924-1
    ISSN 1535-9484 ; 1535-9476
    ISSN (online) 1535-9484
    ISSN 1535-9476
    DOI 10.1016/j.mcpro.2022.100477
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  3. Article ; Online: MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.

    Kohler, Devon / Staniak, Mateusz / Tsai, Tsung-Heng / Huang, Ting / Shulman, Nicholas / Bernhardt, Oliver M / MacLean, Brendan X / Nesvizhskii, Alexey I / Reiter, Lukas / Sabido, Eduard / Choi, Meena / Vitek, Olga

    Journal of proteome research

    2023  Volume 22, Issue 5, Page(s) 1466–1482

    Abstract: ... ...

    Abstract The
    MeSH term(s) Proteomics/methods ; Research Design ; Software ; Mass Spectrometry/methods ; Chromatography, Liquid/methods
    Language English
    Publishing date 2023-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; 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.2c00834
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
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  4. Article ; Online: Author Correction: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.

    Malinovska, Liliana / Cappelletti, Valentina / Kohler, Devon / Piazza, Ilaria / Tsai, Tsung-Heng / Pepelnjak, Monika / Stalder, Patrick / Dörig, Christian / Sesterhenn, Fabian / Elsässer, Franziska / Kralickova, Lucie / Beaton, Nigel / Reiter, Lukas / de Souza, Natalie / Vitek, Olga / Picotti, Paola

    Nature protocols

    2023  Volume 18, Issue 6, Page(s) 1979

    Language English
    Publishing date 2023-01-17
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-023-00808-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.

    Malinovska, Liliana / Cappelletti, Valentina / Kohler, Devon / Piazza, Ilaria / Tsai, Tsung-Heng / Pepelnjak, Monika / Stalder, Patrick / Dörig, Christian / Sesterhenn, Fabian / Elsässer, Franziska / Kralickova, Lucie / Beaton, Nigel / Reiter, Lukas / de Souza, Natalie / Vitek, Olga / Picotti, Paola

    Nature protocols

    2022  Volume 18, Issue 3, Page(s) 659–682

    Abstract: Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to a perturbation, protein structure may be altered by various molecular events, such as post-translational modifications, ... ...

    Abstract Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to a perturbation, protein structure may be altered by various molecular events, such as post-translational modifications, protein-protein interactions, aggregation, allostery or binding to other molecules. The ability to probe these structural changes in thousands of proteins simultaneously in cells or tissues can provide valuable information about the functional state of biological processes and pathways. Here, we present an updated protocol for LiP-MS, a proteomics technique combining limited proteolysis with mass spectrometry, to detect protein structural alterations in complex backgrounds and on a proteome-wide scale. In LiP-MS, proteins undergo a brief proteolysis in native conditions followed by complete digestion in denaturing conditions, to generate structurally informative proteolytic fragments that are analyzed by mass spectrometry. We describe advances in the throughput and robustness of the LiP-MS workflow and implementation of data-independent acquisition-based mass spectrometry, which together achieve high reproducibility and sensitivity, even on large sample sizes. We introduce MSstatsLiP, an R package dedicated to the analysis of LiP-MS data for the identification of structurally altered peptides and differentially abundant proteins. The experimental procedures take 3 d, mass spectrometric measurement time and data processing depend on sample number and statistical analysis typically requires ~1 d. These improvements expand the adaptability of LiP-MS and enable wide use in functional proteomics and translational applications.
    MeSH term(s) Proteolysis ; Proteome/analysis ; Reproducibility of Results ; Mass Spectrometry/methods ; Protein Processing, Post-Translational
    Chemical Substances Proteome
    Language English
    Publishing date 2022-12-16
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-022-00771-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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