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Native top-down proteomics enables discovery in endocrine-resistant breast cancer

Native top-down proteomics reveals epidermal growth factor receptor–estrogen receptor-alpha (EGFR–ER) signaling crosstalk in breast cancer cells and dissociation of nuclear transport factor 2 (NUTF2) dimers to modulate ER signaling and cell growth.

Fabio P. Gomes
Kenneth R. Durbin
John R. Yates III
Research04 Apr 2025
Nature Chemical Biology

Volume: 21, P: 1205-1213
Using in vivo intact structure for system-wide quantitative analysis of changes in proteins

This study introduces an in vivo protein footprinting method, revealing structural changes in proteome during progressing AD. It demonstrates these changes occur before expression alterations, advancing understanding of protein misfolding mechanisms.

Ahrum Son
Hyunsoo Kim
John R. Yates
ResearchOpen Access29 Oct 2024
Nature Communications

Volume: 15, P: 1-17
Click-generated triazole ureas as ultrapotent in vivo–active serine hydrolase inhibitors

Investigations of serine hydrolases have been frustrated by a lack of selective chemical inhibitors. Profiling of synthetically accessible 1,2,3-triazole ureas in cells and mice now identifies several effective compounds, application of which yields new insights into N-acetylation by APEH.

Alexander Adibekian
Brent R Martin
Benjamin F Cravatt
Research15 May 2011
Nature Chemical Biology

Volume: 7, P: 469-478
Quantitative analysis of global protein stability rates in tissues

Daniel B. McClatchy
Salvador Martínez-Bartolomé
John R. Yates III
ResearchOpen Access29 Sept 2020
Scientific Reports

Volume: 10, P: 1-12
Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy

Priscilla D. Negraes
Cleber A. Trujillo
Alysson R. Muotri
ResearchOpen Access22 Apr 2021
Molecular Psychiatry

Volume: 26, P: 7047-7068
Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death

Ling Huang
Daniel B. McClatchy
Antonio Currais
ResearchOpen Access06 Oct 2020
Cell Death & Disease

Volume: 11, P: 1-13
Quantitative analysis of newly synthesized proteins

This protocol describes a proteomics approach for quantifying newly synthesized proteins (NSPs). NSPs are pulse-labeled with the methionine analog AHA or a heavy-isotope version of it, followed by AHA-peptide enrichment and LC-MS/MS analysis.

Yuanhui Ma
Daniel B. McClatchy
John R. Yates III
Protocols23 Jul 2018
Nature Protocols

Volume: 13, P: 1744-1762

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Native top-down proteomics enables discovery in endocrine-resistant breast cancer

Using in vivo intact structure for system-wide quantitative analysis of changes in proteins

Click-generated triazole ureas as ultrapotent in vivo–active serine hydrolase inhibitors

Quantitative analysis of global protein stability rates in tissues

Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death

Quantitative analysis of newly synthesized proteins

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