Daniel J. Hermanson

Thermo Fisher Scientific (United States)

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Lawrence J. Marnett

Vanderbilt University

Hamish Stewart

Thermo Fisher Scientific (Germany)

Eugen Damoc

Thermo Fisher Scientific (Germany)

Alexander Makarov

Engelhardt Institute of Molecular Biology

Christian Hock

Thermo Fisher Scientific (Germany)

Tabiwang N. Arrey

Thermo Fisher Scientific (Germany)

Anna Pashkova

Thermo Fisher Scientific (Germany)

Vlad Zabrouskov

Thermo Fisher Scientific (United States)

Amelia C. Peterson

Thermo Fisher Scientific (Germany)

J. Petzoldt

Thermo Fisher Scientific (Germany)

Cooperative Institutions

Thermo Fisher Scientific (Canada)

Thermo Fisher Scientific (Germany)

Vanderbilt University

Vanderbilt University Medical Center

University of Wisconsin–Madison

Scripps Research Institute

The University of Texas MD Anderson Cancer Center

Duke University Hospital

Duke Medical Center

University of Copenhagen

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Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

Nature Biotechnology (2024)

Ulises H. Guzmán Ana Martínez-Val Zilu Ye Eugen Damoc Tabiwang N. Arrey

Abstract Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th isolation windows, dissolving the differences between data-dependent and -independent methods. This is achieved by pairing a quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer which provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. The nDIA strategy enables profiling of >100 full yeast proteomes per day, or 48 human proteomes per day at the depth of ~10,000 human protein groups in half-an-hour or ~7,000 proteins in 5 min, representing 3× higher coverage compared with current state-of-the-art MS. Multi-shot acquisition of offline fractionated samples provides comprehensive coverage of human proteomes in ~3 h. High quantitative precision and accuracy are demonstrated in a three-species proteome mixture, quantifying 14,000+ protein groups in a single half-an-hour run.

Proteome

Tandem mass tag

Orbitrap

10.1038/s41587-023-02099-7

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The One Hour Human Proteome

Molecular & Cellular Proteomics (2024)

Lia R. Serrano Trenton M. Peters-Clarke Tabiwang N. Arrey Eugen Damoc Margaret Lea Robinson

We describe deep analysis of the human proteome in less than one hour. We achieve this expedited proteome characterization by leveraging state-of-the-art sample preparation, chromatographic separations, data analysis tools, and by using the new Orbitrap Astral mass spectrometer equipped with a quadrupole mass filter, a high-field Orbitrap mass analyzer, and an asymmetric track lossless (Astral) mass analyzer. The system offers high MS/MS acquisition speed of 200 Hz and detects hundreds of peptide sequences per second within data independent- or data-dependent acquisition modes of operation. The fast-switching capabilities of the new quadrupole complement the sensitivity and fast ion scanning of the Astral analyzer to enable narrow-bin data-independent analysis (DIA) methods. Over a 30-minute active chromatographic method consuming a total analysis time of 56 minutes, the Q-Orbitrap-Astral hybrid MS collects an average of 4,319 MS1 scans and 438,062 MS/MS scans per run, producing 235,916 peptide sequences (1% false discovery rate (FDR)). On average, each 30-minute analysis achieved detection of 10,411 protein groups (1% FDR). We conclude, with these results and alongside other recent reports, that the one-hour human proteome is within reach.

Proteome

Human proteome project

10.1016/j.mcpro.2024.100760

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Citations (16)

Chemical Proteomics Identifies SLC25A20 as a Functional Target of the Ingenol Class of Actinic Keratosis Drugs

ACS Central Science (2017)

Christopher G. Parker Christian A. Kuttruff Andrea Galmozzi Lars Jørgensen Chien‐Hung Yeh

The diterpenoid ester ingenol mebutate (IngMeb) is the active ingredient in the topical drug Picato, a first-in-class treatment for the precancerous skin condition actinic keratosis. IngMeb is proposed to exert its therapeutic effects through a dual mode of action involving (i) induction of cell death that is associated with mitochondrial dysfunction followed by (ii) stimulation of a local inflammatory response, at least partially driven by protein kinase C (PKC) activation. Although this therapeutic model has been well characterized, the complete set of molecular targets responsible for mediating IngMeb activity remains ill-defined. Here, we have synthesized a photoreactive, clickable analogue of IngMeb and used this probe in quantitative proteomic experiments to map several protein targets of IngMeb in human cancer cell lines and primary human keratinocytes. Prominent among these targets was the mitochondrial carnitine-acylcarnitine translocase SLC25A20, which we show is inhibited in cells by IngMeb and the more stable analogue ingenol disoxate (IngDsx), but not by the canonical PKC agonist 12-O-tetradecanoylphorbol-13-acetate (TPA). SLC25A20 blockade by IngMeb and IngDsx leads to a buildup of cellular acylcarnitines and blockade of fatty acid oxidation (FAO), pointing to a possible mechanism for IngMeb-mediated perturbations in mitochondrial function.

Actinic keratosis

Mechanism of Action

10.1021/acscentsci.7b00420

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Citations (59)

Crystal Structure of Ovine Cyclooxygenase-1 Complex with Meloxicam

S. Xu Daniel J. Hermanson S. S. Banerjee Kebreab Ghebreselasie Gina M. Clayton

Meloxicam

10.2210/pdb4o1z/pdb

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Citations (2)

Structure of (R)-flurbiprofen bound to mCOX-2

Kelsey C. Duggan Daniel J. Hermanson Joel Musee Jeffery J. Prusakiewicz Jami L. Scheib

Flurbiprofen

10.2210/pdb3rr3/pdb

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Substrate-selective COX-2 inhibition decreases anxiety via endocannabinoid activation

Nature Neuroscience (2013)

Daniel J. Hermanson Nolan D. Hartley Joyonna Gamble‐George Naoko Brown Brian C. Shonesy

10.1038/nn.3480

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Citations (116)

Oxidative Metabolites of Endocannabinoids Formed by Cyclooxygenase-2

Elsevier eBooks (2014)

Lawrence J. Marnett Philip J. Kingsley Daniel J. Hermanson

10.1016/b978-0-12-420126-2.00004-3

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Corticotropin-Releasing Hormone Drives Anandamide Hydrolysis in the Amygdala to Promote Anxiety

Journal of Neuroscience (2015)

Jennifer M. Gray Haley A. Vecchiarelli Maria Morena Tiffany T.-Y. Lee Daniel J. Hermanson

Corticotropin-releasing hormone (CRH) is a central integrator in the brain of endocrine and behavioral stress responses, whereas activation of the endocannabinoid CB1 receptor suppresses these responses. Although these systems regulate overlapping functions, few studies have investigated whether these systems interact. Here we demonstrate a novel mechanism of CRH-induced anxiety that relies on modulation of endocannabinoids. Specifically, we found that CRH, through activation of the CRH receptor type 1 (CRHR1), evokes a rapid induction of the enzyme fatty acid amide hydrolase (FAAH), which causes a reduction in the endocannabinoid anandamide (AEA), within the amygdala. Similarly, the ability of acute stress to modulate amygdala FAAH and AEA in both rats and mice is also mediated through CRHR1 activation. This interaction occurs specifically in amygdala pyramidal neurons and represents a novel mechanism of endocannabinoid–CRH interactions in regulating amygdala output. Functionally, we found that CRH signaling in the amygdala promotes an anxious phenotype that is prevented by FAAH inhibition. Together, this work suggests that rapid reductions in amygdala AEA signaling following stress may prime the amygdala and facilitate the generation of downstream stress-linked behaviors. Given that endocannabinoid signaling is thought to exert “tonic” regulation on stress and anxiety responses, these data suggest that CRH signaling coordinates a disruption of tonic AEA activity to promote a state of anxiety, which in turn may represent an endogenous mechanism by which stress enhances anxiety. These data suggest that FAAH inhibitors may represent a novel class of anxiolytics that specifically target stress-induced anxiety.

Anandamide

10.1523/jneurosci.2737-14.2015

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Citations (215)

Central anandamide deficiency predicts stress-induced anxiety: behavioral reversal through endocannabinoid augmentation

Translational Psychiatry (2014)

Rebecca J. Bluett Joyonna Gamble‐George Daniel J. Hermanson Nolan D. Hartley Lawrence J. Marnett

Stress is a major risk factor for the development of mood and anxiety disorders; elucidation of novel approaches to mitigate the deleterious effects of stress could have broad clinical applications. Pharmacological augmentation of central endogenous cannabinoid (eCB) signaling may be an effective therapeutic strategy to mitigate the adverse behavioral and physiological consequences of stress. Here we show that acute foot-shock stress induces a transient anxiety state measured 24 h later using the light-dark box assay and novelty-induced hypophagia test. Acute pharmacological inhibition of the anandamide-degrading enzyme, fatty acid amide hydrolase (FAAH), reverses the stress-induced anxiety state in a cannabinoid receptor-dependent manner. FAAH inhibition does not significantly affect anxiety-like behaviors in non-stressed mice. Moreover, whole brain anandamide levels are reduced 24 h after acute foot-shock stress and are negatively correlated with anxiety-like behavioral measures in the light-dark box test. These data indicate that central anandamide levels predict acute stress-induced anxiety, and that reversal of stress-induced anandamide deficiency is a key mechanism subserving the therapeutic effects of FAAH inhibition. These studies provide further support that eCB-augmentation is a viable pharmacological strategy for the treatment of stress-related neuropsychiatric disorders.

Anandamide

10.1038/tp.2014.53

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Citations (136)

Structure of (R)-naproxen bound to mCOX-2.

Kelsey C. Duggan Daniel J. Hermanson Joel Musee Jeffery J. Prusakiewicz Jami L. Scheib

10.2210/pdb3q7d/pdb

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Citations (0)