Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis DOI Creative Commons
Svitlana Tretiak, Teresa Mendes Maia, Delphi Van Haver

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 15, 2025

Analysis of the blood proteome allows identification proteins related to changes upon certain physiological conditions. The pathophysiology necrotic enteritis (NE) has been extensively studied. While intestinal have very well documented, data addressing NE-induced alterations in are scant, although these might merit diagnostics. In light recent technological advancements proteomics and pressing need for tools access gut health, current study employs mass-spectrometry (MS)-based identify biomarkers gastrointestinal health chickens. Here, we report findings an untargeted investigation conducted on plasma chickens under NE challenge. Two MS-strategies were used analysis: conventional dependent acquisition coupled standard nanoflow liquid chromatography (LC) (nano-DDA) recently-developed independent Evosep One LC system (Evo-DIA). Despite superior completeness quantification Evo-DIA-acquired data, high degree agreement was observed between both approaches. Additionally, identified 15 differentially expressed (shared by nano-DDA Evo-DIA) that represent responses animals infection may serve as potential biomarkers. Experimental validation through ELISA immunoassays targeted MS selected regulated (CFD, HPS5, MASP2) confirmed medium-to-high levels inter-protein correlation. A GSEA analysis revealed enrichment a number processes adaptive humoral immunity, immune activation response infected animals. Data available via ProteomeXchange with identifiers PXD050461, PXD050473, PXD061607.

Language: Английский

Proteomics of prostate cancer serum and plasma using low and high throughput approaches DOI Creative Commons
Ghaith M. Hamza, Rekha Raghunathan,

Stephanie Kay Ashenden

et al.

Clinical Proteomics, Journal Year: 2024, Volume and Issue: 21(1)

Published: March 12, 2024

Abstract Despite progress, MS-based proteomics in biofluids, especially blood, faces challenges such as dynamic range and throughput limitations biomarker disease studies. In this work, we used cutting-edge technologies to construct label-based label-free workflows, capable of quantifying approximately 2,000 proteins biofluids. With 70µL blood a single depletion strategy, conducted an analysis homogenous cohort ( n = 32), comparing medium-grade prostate cancer patients (Gleason score: 7(3 + 4); TNM stage: T2cN0M0, stage IIB) healthy donors. The results revealed dozens differentially expressed both plasma serum. We identified the upregulation Prostate Specific Antigen (PSA), well-known for cancer, serum cohort. Further bioinformatics highlighted noteworthy which appear be secreted into bloodstream, making them good candidates further exploration.

Language: Английский

Citations

5
Advances in aqueous humor proteomics for biomarker discovery and disease mechanisms exploration: a spotlight on primary open angle glaucoma DOI Creative Commons
Vanessa M. Beutgen, Johannes Graumann

Frontiers in Molecular Neuroscience, Journal Year: 2024, Volume and Issue: 17

Published: April 24, 2024

Altered protein levels in the aqueous humor (AH) may be a valuable source of novel biomarkers neurodegenerative retinal disease. The proximity this body fluid to disease focus, and its corresponding enrichment for tissue specific proteins, renders it an excellent matrix study underlying molecular mechanisms. Novel proteomic methods accordingly hold large potential insight into pathologies based on composition AH proteome, including primary open angle glaucoma (POAG). Recent mass spectrometry-based studies use approaches tackle challenges arising from combination low available sample volume concentration, thereby increasing proteome coverage. But despite significant improvements spectrometry (MS), different class technologies is poised majorly impact analysis ocular biofluids. Affinity workflows, having become commercially recently, have started complement data obtained by MS likely will grow crucial tool ophthalmological biomarker research. This review highlights discusses recent findings alterations POAG.

Language: Английский

Citations

5
Integrating Artificial Intelligence for Advancing Multiple Cancer Early Detection via Serum Biomarkers: A Narrative Review DOI Open Access
Hsin‐Yao Wang, Wan-Ying Lin, Chenfei Zhou

et al.

Published: Jan. 3, 2024

The concept and policies of multiple early cancer detection (MCED) have gained significant attention from governments worldwide in recent years. In the era burgeoning artificial intelligence (AI) technology, integration MCED with AI has become a prevailing trend, giving rise to plethora products. However, due heterogeneity both targets technologies, overall diversity products remains considerable. types encompass protein biomarkers, cell-free DNA, or combinations these biomarkers. development models, different model training approaches are employed, including datasets case-control researches real-world screening datasets. Various validation techniques, such as cross-validation, location-wise validation, time-wise used. All factors show impacts on predictive efficacy AIs. After completion development, deploying AIs clinical practice presents numerous challenges, presenting reports, identifying potential locations tumor, addressing cancer-related information follow-up treatment. This study reviews several mature currently available market, detecting their composing serum biomarkers detection, training/validation, application. review illuminates challenges encountered by existing across stages, offering insights into continued obstacles within field AI.

Language: Английский

Citations

4
Mass spectrometry-based proteomics data from thousands of HeLa control samples DOI Creative Commons
Henry Webel, Yasset Pérez‐Riverol,

Annelaura Bach Nielsen

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Jan. 23, 2024

Here we provide a curated, large scale, label free mass spectrometry-based proteomics data set derived from HeLa cell lines for general purpose machine learning and analysis. Data access filtering is tedious task, which takes up considerable amounts of time researchers. Therefore based metadata easy selection overview along the 7,444 raw files MaxQuant search output. For convenience, three filtered aggregated development datasets on protein groups, peptides precursors level. Next to providing training data, SDRF file annotating each with instrument settings allowing automated reprocessing. We encourage others enlarge this by runs further samples different types our workflows analysis scripts.

Language: Английский

Citations

4
Heparin-enriched plasma proteome is significantly altered in Alzheimer’s disease DOI Creative Commons
Qi Guo, Lingyan Ping, Eric B. Dammer

et al.

Molecular Neurodegeneration, Journal Year: 2024, Volume and Issue: 19(1)

Published: Oct. 8, 2024

Heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to β-amyloid (Aβ) and tau pathology Alzheimer's disease (AD) brain cerebrospinal fluid (CSF). However, it remains challenging detect these plasma using standard mass spectrometry-based proteomic approaches.

Language: Английский

Citations

4
The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends DOI Creative Commons
Philipp E. Geyer, Daniel Hornburg, Maria Pernemalm

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 31, 2024

Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest using these novel methods for studying the circulating proteome, as blood offers accessible window into health. However, every methodological innovation and analytical progress calls reassessing existing approaches routines ensure that new data will add value greater biomedical research community avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present 2024 survey current community, including latest build PeptideAtlas now comprises 4608 proteins detected 113 sets. We then discuss updates established methods, emerging technologies, investigations proteoforms, protein networks, extracellualr vesicles, antibodies microsamples. Finally, provide a prospective view tools studies proteins.

Language: Английский

Citations

4
Comparative evaluation of peptide vs. protein-based calibration for quantification of cardiac troponin I using ID-LC-MS/MS DOI
Meltem Asicioglu, Claudia Swart, Evren Saban

et al.

Clinical Chemistry and Laboratory Medicine (CCLM), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

An analytical protocol based on isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS), which includes a peptide-based calibration strategy, was developed and validated for the determination of cardiac troponin I (cTnI) levels in clinical samples. Additionally, method compared with protein-based using cTnI serving as model low-abundant proteins. The aim is to evaluate new approaches protein quantification complex matrices, supporting metrology community implementing methods developing fit-for-purpose SI- traceable peptide or primary calibrators.

Language: Английский

Citations

0
Omics and rare diseases: challenges, applications, and future perspectives DOI
Daniela Braconi, Haidara Nadwa, Giulia Bernardini

et al.

Expert Review of Proteomics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 16, 2025

Introduction Rare diseases (RDs) are a heterogeneous group of recognized as relevant global health priority but posing aspects complexity such as: geographical scattering affected individuals, improper/late diagnosis, limited awareness, difficult surveillance and monitoring, understanding natural history, lack treatment. Usually, RDs have pediatric onset life-long, multisystemic, associated with poor prognosis.

Language: Английский

Citations

0
Mass spectrometry-based mapping of plasma protein QTLs in children and adolescents DOI
Yansheng Liu

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

Language: Английский

Citations

0
Proteomics and metabolomics in cancer biomarker discovery DOI

Rinki Basoya,

N Bhasin,

Preeti Jain

et al.

Methods in cell biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0