Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies DOI Creative Commons
Amit Kumar Dey, Reema Banarjee, Mozhgan Boroumand

et al.

Biology, Journal Year: 2023, Volume and Issue: 12(10), P. 1301 - 1301

Published: Oct. 2, 2023

Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies chronic inflammation, type 2 diabetes, cancer, neurodegeneration. Targeted removal senescent cells in preclinical models promotes health longevity, suggesting that selective elimination promising therapeutic approach for mitigating myriad age-related humans. However, moving senescence-targeting drugs (senotherapeutics) into clinic will require targets biomarkers, fueled by an improved understanding complex dynamic biology populations their molecular profiles, as well mechanisms underlying emergence maintenance SASP. Advances mass spectrometry-based proteomic technologies workflows have potential address these needs. Here, we review translational research how approaches added our knowledge date. Further, lay out roadmap from fundamental biological discovery clinical translation senotherapeutic through development application emerging technologies, targeted untargeted approaches, bottom-up top-down methods, stability proteomics, surfaceomics. These are integral probing cellular composition dynamics and, ultimately, senotype-specific biomarkers senotherapeutics (senolytics senomorphics). This aims highlight areas applications proteomics aid exploring new future senotherapeutics.

Language: Английский

Bottom-Up Proteomics: Advancements in Sample Preparation DOI Open Access
Van‐An Duong, Hookeun Lee

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(6), P. 5350 - 5350

Published: March 10, 2023

Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist the following three major steps: sample preparation, LC–MS/MS analysis, data analysis. analysis techniques have been intensively developed, whereas laborious process, remains difficult task main challenge in different applications. Sample preparation crucial stage that affects overall efficiency study; however, it prone to errors has low reproducibility throughput. In-solution digestion filter-aided are typical widely used methods. In past decade, novel methods improve facilitate entire process or integrate fractionation reported reduce time, increase throughput, reproducibility. this review, we outlined current proteomics, including on-membrane digestion, bead-based immobilized enzymatic suspension trapping. Additionally, summarized discussed devices integrating steps peptide fractionation.

Language: Английский

Citations

70
Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry DOI Creative Commons
Yuming Jiang, Rex Devasahayam Arokia Balaya, Dina Schuster

et al.

ACS Measurement Science Au, Journal Year: 2024, Volume and Issue: 4(4), P. 338 - 417

Published: June 4, 2024

Proteomics is the large scale study of protein structure and function from biological systems through identification quantification."Shotgun proteomics" or "bottom-up prevailing strategy, in which proteins are hydrolyzed into peptides that analyzed by mass spectrometry.Proteomics studies can be applied to diverse ranging simple proteoforms, protein-protein interactions, structural alterations, absolute relative quantification, post-translational modifications, stability.To enable this range different experiments, there strategies for proteome analysis.The nuances how proteomic workflows differ may challenging understand new practitioners.Here, we provide a comprehensive overview proteomics methods.We cover biochemistry basics extraction interpretation orthogonal validation.We expect Review will serve as handbook researchers who field bottom-up proteomics.

Language: Английский

Citations

30
Top-down proteomics DOI
David S. Roberts, Joseph A. Loo, Yury O. Tsybin

et al.

Nature Reviews Methods Primers, Journal Year: 2024, Volume and Issue: 4(1)

Published: June 13, 2024

Language: Английский

Citations

22
Proteomics: An In‐Depth Review on Recent Technical Advances and Their Applications in Biomedicine DOI Open Access
Jing Liang, Jun Tian,

Huadong Zhang

et al.

Medicinal Research Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

ABSTRACT Proteins hold pivotal importance since many diseases manifest changes in protein activity. Proteomics techniques provide a comprehensive exploration of structure, abundance, and function biological samples, enabling the holistic characterization overall organisms. Nowadays, breadth emerging methodologies proteomics is unprecedentedly vast, with constant optimization technologies sample processing, data collection, analysis, its scope application steadily transitioning from bench to clinic. Here, we offer an insightful review technical developments applications biomedicine over past 5 years. We focus on profound contributions profiling disease spectra, discovering new biomarkers, identifying promising drug targets, deciphering alterations conformation, unearthing protein–protein interactions. Moreover, summarize cutting‐edge potential breakthroughs pipeline principal challenges proteomics. Based these, aspire broaden applicability inspire researchers enhance our understanding complex systems by utilizing such techniques.

Language: Английский

Citations

2
High sensitivity top–down proteomics captures single muscle cell heterogeneity in large proteoforms DOI Creative Commons
Jake A. Melby, Kyle A. Brown, Zachery R. Gregorich

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(19)

Published: May 1, 2023

Single-cell proteomics has emerged as a powerful method to characterize cellular phenotypic heterogeneity and the cell-specific functional networks underlying biological processes. However, significant challenges remain in single-cell for analysis of proteoforms arising from genetic mutations, alternative splicing, post-translational modifications. Herein, we have developed highly sensitive functionally integrated top–down comprehensive single cells. We applied this muscle fibers (SMFs) resolve their heterogeneous proteomic properties at level. Notably, detected large (>200 kDa) SMFs. Using SMFs obtained three distinct muscles, found fiber-to-fiber among sarcomeric which can be related heterogeneity. Importantly, multiple isoforms myosin heavy chain (~223 kDa), motor protein that drives contraction, with high reproducibility enable classification individual fiber types. This study reveals cell establishes direct relationship between types, highlighting potential uncovering molecular underpinnings cell-to-cell variation complex systems.

Language: Английский

Citations

39
Chitosan functionalized two-dimensional covalent organic framework nanosheets with high hydrophilicity for efficient glycopeptide enrichment DOI

Zhuo Mi,

Wenkang Zhang, Han Wang

et al.

Journal of Chromatography B, Journal Year: 2025, Volume and Issue: 1252, P. 124461 - 124461

Published: Jan. 10, 2025

Language: Английский

Citations

1
Development of Top-Down Mass Spectrometry Strategies in the Chromatographic Time Scale (LC-TD-MS) for the Extended Characterization of an Anti-EGFR Single-Domain Antibody-Drug Conjugate in Both Reduced and Nonreduced Forms DOI
Rania Benazza,

Léa Letissier,

Greg Papadakos

et al.

Analytical Chemistry, Journal Year: 2025, Volume and Issue: 97(5), P. 2639 - 2647

Published: Jan. 31, 2025

Even though mAbs have attracted the biggest interest in development of therapeutic proteins, next-generation therapeutics such as single-domain antibodies (sdAb) are propelling increasing attention new alternatives with appealing applications different clinical areas. These constructs small proteins formed by a variable domain heavy chain an antibody multiple and production benefits compared their mAb counterparts. can be subjected to bioconjugation processes form antibody-drug conjugates (sdADCs) hence increase potency, akin other nanobodies related products require dedicated analytical strategies fully characterize primary structure prior release market. In this study, we report for first time extensive sequence characterization conjugated anti-EGFR 14 kDa sdADC using state-of-the-art top-down mass spectrometry combination liquid chromatography (LC-TD-MS). Mass analysis revealed highly homogeneous sample one molecule. Subsequently, reduced was submitted fragmentation techniques, namely, higher-energy collisional dissociation, electron-transfer collision allowing unambiguously assess conjugation site 24 diagnostic fragment ions 85% global coverage. The coverage nonreduced protein significantly lower (around 16%); however, spectra corroborated presence intramolecular disulfide bridge along localization site. Altogether, our results pinpoint difficulties challenges associated sdAb-derived formats LC scale due remarkable stability consequence bridge. However, use complementary activation techniques identification specific ion fragments allows improved coverage, bond, unambiguous

Language: Английский

Citations

1
Monitoring Functional Posttranslational Modifications Using a Data‐Driven Proteome Informatic Pipeline DOI Creative Commons
Payman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie

et al.

PROTEOMICS, Journal Year: 2025, Volume and Issue: unknown

Published: March 18, 2025

ABSTRACT Posttranslational modifications (PTMs) are of significant interest in molecular biomedicine due to their crucial role signal transduction across various cellular and organismal processes. Characterizing PTMs, distinguishing between functional inert modifications, quantifying occupancies, understanding PTM crosstalk challenging tasks any biosystem. Studying each often requires a specific, labor‐intensive experimental design. Here, we present PTM‐centric proteome informatic pipeline for predicting relevant PTMs mass spectrometry‐based proteomics data without prior information. Once predicted, these silico identified can be incorporated into refined database search compared measured data. As practical application, demonstrate how this used study glycoproteomics oral squamous cell carcinoma based on the profile primary tumors. Subsequently, experimentally proteins that differentially expressed cells treated with multikinase inhibitors dasatinib staurosporine using proteomics. Computational enrichment analysis was then employed determine potential induced by both drugs. Finally, conducted an additional round predicted PTMs. Our successfully analyzed enriched detected not initial search. findings support effectiveness searching MS computational analysis, propose integrating approach future engines.

Language: Английский

Citations

1
Ultraviolet Photodissociation Permits Comprehensive Characterization of O-Glycopeptides Cleaved with O-Glycoprotease IMPa DOI
Amanda Helms, Edwin E. Escobar, Saulius Vainauskas

et al.

Analytical Chemistry, Journal Year: 2023, Volume and Issue: 95(24), P. 9280 - 9287

Published: June 8, 2023

Complete O-glycosite characterization, including identification of the peptides, localization glycosites, and mapping glycans, has been a persistent challenge in O-glycoproteomics owing to technical challenges surrounding O-glycan analysis. Multi-glycosylated peptides pose an even greater their potential heterogeneity. Ultraviolet photodissociation (UVPD) can localize multiple post-translational modifications is well-suited for characterization glycans. Three glycoproteins were assessed based on strategy combining use O-glycoprotease IMPa HCD-triggered UVPD complete O-glycopeptides. This approach localized adjacent or proximal O-glycosites individual glycopeptides identified previously unknown glycosite etanercept at S218. Nine different glycoforms characterized as multi-glycosylated peptide from etanercept. The performance was compared that HCD EThcD constituent

Language: Английский

Citations

14
Self-assembly of hydrazide-linked porous organic polymers rich in titanium for efficient enrichment of glycopeptides and phosphopeptides from human serum DOI
Danni Wang,

Quanshou Feng,

Yiting Luo

et al.

The Analyst, Journal Year: 2023, Volume and Issue: 148(14), P. 3392 - 3402

Published: Jan. 1, 2023

The mechanism of selective enrichment by hydrazide-POPs-Ti 4+ .

Language: Английский

Citations

14