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Page 1
Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Nat Protoc. 2023 Mar;18(3):659-682. doi: 10.1038/s41596-022-00771-x. Epub 2022 Dec 16.
Nat Protoc. 2023.
PMID: 36526727
Review.
An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing.
Kohler D, Staniak M, Yu F, Nesvizhskii AI, Vitek O.
Kohler D, et al.
Nat Protoc. 2024 May 20. doi: 10.1038/s41596-024-01000-3. Online ahead of print.
Nat Protoc. 2024.
PMID: 38769142
Review.
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MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments.
Kohler D, Kaza M, Pasi C, Huang T, Staniak M, Mohandas D, Sabido E, Choi M, Vitek O.
Kohler D, et al.
J Proteome Res. 2023 Feb 3;22(2):551-556. doi: 10.1021/acs.jproteome.2c00603. Epub 2023 Jan 9.
J Proteome Res. 2023.
PMID: 36622173
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MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics.
Kohler D, Tsai TH, Verschueren E, Huang T, Hinkle T, Phu L, Choi M, Vitek O.
Kohler D, et al.
Mol Cell Proteomics. 2023 Jan;22(1):100477. doi: 10.1016/j.mcpro.2022.100477. Epub 2022 Dec 8.
Mol Cell Proteomics. 2023.
PMID: 36496144
Free PMC article.
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Author Correction: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Malinovska L, Cappelletti V, Kohler D, Piazza I, Tsai TH, Pepelnjak M, Stalder P, Dörig C, Sesterhenn F, Elsässer F, Kralickova L, Beaton N, Reiter L, de Souza N, Vitek O, Picotti P.
Malinovska L, et al. Among authors: kohler d.
Nat Protoc. 2023 Jun;18(6):1979. doi: 10.1038/s41596-023-00808-9.
Nat Protoc. 2023.
PMID: 36653529
No abstract available.
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MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.
Kohler D, Staniak M, Tsai TH, Huang T, Shulman N, Bernhardt OM, MacLean BX, Nesvizhskii AI, Reiter L, Sabido E, Choi M, Vitek O.
Kohler D, et al.
J Proteome Res. 2023 May 5;22(5):1466-1482. doi: 10.1021/acs.jproteome.2c00834. Epub 2023 Apr 5.
J Proteome Res. 2023.
PMID: 37018319
Free PMC article.
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