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Redox proteomics DIALRP to study MND response in DU145 cells

ABSTRACT: In this study, we developed a label-free redox proteomics method using data-independent acquisition mass spectrometry (DIA-MS), termed DIALRP, to comprehensively analyze cysteine oxidative modifications in the prostate cancer cell line DU145 under oxidative stress induced by menadione (MND).

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Masaki Matsumoto

PROVIDER: PXD057921 | JPOST Repository | Thu Jul 31 00:00:00 BST 2025

REPOSITORIES: jPOST

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			Action	DRS
	20240607_DU145_1_DIC0_Mena0_All.raw	Raw
	20240607_DU145_1_DIC0_Mena0_Oxi.raw	Raw
	20240607_DU145_1_DIC0_Mena50_All.raw	Raw
	20240607_DU145_1_DIC0_Mena50_Oxi.raw	Raw
	20240607_DU145_2_DIC0_Mena0_All.raw	Raw

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Publications

Data-Independent Acquisition (DIA)-Based Label-Free Redox Proteomics (DIALRP) Identifies Prominent Cysteine Oxidations in Translation Machinery in Prostate Cancer Cells Under Oxidative Stress.

Kobayashi Daiki D Takami Tomoyo T Matsumoto Masaki M

Journal of proteome research 20250731 9

Oxidative stress is a key factor in numerous physiological and pathological processes, including aging, cancer, and neurodegenerative diseases. Protein cysteine residues are particularly susceptible to oxidative stress-induced modifications that can alter their structure and function, thereby affecting intracellular signaling pathways. In this study, we performed a data-independent acquisition mass spectrometry (DIA-MS)-based label-free redox proteomics method, termed DIALRP, to comprehensively ...[more]

PMID: 40740030

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SP3-enabled rapid and high coverage chemoproteomic identification of redox-sensitive cysteines

Project description:Cysteine residues undergo various oxidative modifications, acting as key sensors of reactive oxygen species (ROS) and reactive nitrogen species (RNS). Given that ROS and RNS have known roles in many pathophysiological processes, numerous proteome-wide strategies to profile cysteine oxidation state have emerged in the last decade. Recent advancements to traditional redox profiling methods include incorporation of costly isotopic labeling reagents to allow for more quantitative assessment of oxidation states. These methods are typically carried out by using sequential thiol capping and reduction steps in order to label redox-sensitive cysteines, often found in di-cysteine motifs (‘CXXC’ or ‘CXXXC’). Tailored, pricy algorithms are commonly used to analyze redox-profiling datasets, the majority of which cannot accurately quantify site-of-labeling in redox-motifs; moreover, accurate quantification is confounded by excess labeling reagents during sample preparation. Here, we present a low-cost redox-profiling workflow using newly synthesized isotopic reagents compatible with SP3-bead technology, termed SP3-ROx, that allows for high throughput, rapid identification of redox-sensitive cysteines. We optimize cysteine labeling quantification using the FragPipe suite, an open source GUI for MSfragger-based search algorithm. Application of SP3-ROx to naive and activated T cells identifies redox-senstive cysteines, showcasing the utility of this workflow to study biological processes.

2022-03-02 | PXD031647 | Pride

SP3-enabled rapid and high coverage chemoproteomic identification of redox-sensitive cysteines

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Beyond Glucose: The Crucial Role of Redox Signaling in β-Cell Metabolic Adaptation

Project description:Objective: Redox signaling mediated by reversible oxidative cysteine thiol modifications is crucial for driving cellular adaptation to dynamic environmental changes, maintaining homeostasis, and ensuring proper function. This is particularly critical in pancreatic β-cells, which are highly metabolically active and play a specialized role in whole organism glucose homeostasis. Glucose stimulation in β-cells triggers signals leading to insulin secretion, including changes in ATP/ADP ratio and intracellular calcium levels. Additionally, lipid metabolism and reactive oxygen species (ROS) signaling are essential for β-cell function and health. Methods: We employed IodoTMT isobaric labeling combined with tandem mass spectrometry to elucidate redox signaling pathways in pancreatic β-cells. Results: Glucose stimulation significantly increases ROS levels in β-cells, leading to targeted reversible oxidation of proteins involved in key metabolic pathways such as glycolysis, the tricarboxylic acid (TCA) cycle, pyruvate metabolism, oxidative phosphorylation, protein processing in the endoplasmic reticulum (ER), and insulin secretion. Furthermore, the glucose-induced increase in reversible cysteine oxidation correlates with the presence of other post-translational modifications, including acetylation and phosphorylation. Conclusions: Proper functioning of pancreatic β-cell metabolism relies on fine-tuned regulation, achieved through a sophisticated system of diverse post-translational modifications that modulate protein functions. Our findings demonstrate that glucose induces the production of ROS in pancreatic β-cells, leading to targeted reversible oxidative modifications of proteins. Furthermore, protein activity is modulated by acetylation and phosphorylation, highlighting the complexity of the regulatory mechanisms in β-cell function.

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Characterization of the redox proteome in Drosophila melanogaster aging eyes.

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Divergent downstream biosynthetic pathways are supported by L-cysteine synthases of Mycobacterium tuberculosis

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Profiling oxidative stress in Saccharomyces cerevisiae by oxidation of transcription factor Swi6p

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