Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics DOI Open Access
Gergő Kalló, Khadiza Zaman,

László Potor

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(24), С. 13665 - 13665

Опубликована: Дек. 20, 2024

Vulnerable atherosclerotic plaques, especially hemorrhaged lesions, are the major cause of mortalities related to vascular pathologies. The early identification vulnerable plaques helps stratify patients at risk developing acute events. In this study, proteomics analyses human carotid artery samples collected from with atheromatous and complicated respectively, as well healthy controls were performed. proteins isolated analyzed by a bottom-up shotgun approach that relied on nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) using both data-dependent (DDA) data-independent (DIA) acquisitions. data obtained high-resolution DIA displayed stronger distinction among groups compared DDA analyses. Differentially expressed further examined Ingenuity Pathway Analysis® focus pathological molecular processes driving atherosclerosis. From more than 150 significantly regulated canonical pathways, atherosclerosis signaling neutrophil extracellular trap verified protein-targeted extraction. results our study expected facilitate better understanding disease progression's drivers provide inspiration for multiomics hypothesis-driven studies.

Язык: Английский

Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity DOI Creative Commons
Julia A. Bubis,

Tabiwang N. Arrey,

Eugen Damoc

и другие.

Nature Methods, Год журнала: 2025, Номер unknown

Опубликована: Янв. 16, 2025

Язык: Английский

Процитировано

5
Aggregate-selective removal of pathological tau by clustering-activated degraders DOI
Jonathan Benn, Shi Cheng, Sophie Keeling

и другие.

Science, Год журнала: 2024, Номер 385(6712), С. 1009 - 1016

Опубликована: Авг. 29, 2024

Selective degradation of pathological protein aggregates while sparing monomeric forms is major therapeutic interest. The E3 ligase tripartite motif–containing 21 (TRIM21) degrades antibody-bound proteins in an assembly state–specific manner due to the requirement TRIM21 RING domain clustering for activation, yet effective targeting intracellular assemblies remains challenging. Here, we fused a target-specific nanobody create intracellularly expressed constructs capable selectively degrading assembled proteins. We evaluated this approach against green fluorescent protein–tagged histone 2B (H2B-GFP) and tau, that undergoes aggregation Alzheimer’s other neurodegenerative diseases. RING-nanobody degraders prevented or reversed tau culture vivo, with minimal impact on tau. This may have potential many disorders driven by aggregation.

Язык: Английский

Процитировано

17
Co-opting templated aggregation to degrade pathogenic tau assemblies and improve motor function DOI Creative Commons
Lauren V. C. Miller, Guido Papa, Marina Vaysburd

и другие.

Cell, Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Язык: Английский

Процитировано

14
Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics DOI Creative Commons
Erin M. Humphries, Peter G. Hains, Phillip J. Robinson

и другие.

ACS Omega, Год журнала: 2025, Номер 10(7), С. 6891 - 6900

Опубликована: Фев. 16, 2025

Many liquid chromatography–mass spectrometry (LC–MS) studies have compared formalin-fixed paraffin-embedded (FFPE) tissues with matched fresh-frozen (FF) to examine the effect of preservation techniques on proteome; however, few included phosphoproteome. A high degree overlap and correlation between two would demonstrate importance FFPE as a valuable biomedical resource. Our aim was quantitatively compare proteome phosphoproteome FF using data-independent acquisition LC–MS. Four organs from three rats were cut in half produce tissue pairs. Excellent overlaps 85–97% for 82–98% observed, depending organ type, techniques. Most unique identifications found less than 0.3% being tissues. Strong agreement pairs observed Pearson coefficients 0.93–0.97 0.79–0.87 phosphoproteome, respectively. Digestion efficiency slightly higher (92–94%) (86–89%), search data subset formaldehyde induced chemical modifications revealed that only 0.05% precursors This suggests quality sample preparation methods it is not necessary include when analyzing We attribute lower number inaccurate peptide quantitation, which resulted MS load tryptic enrichment load. results both proteomic phosphoproteomic analyses are highly comparable highlight suitability analysis.

Язык: Английский

Процитировано

1
Unifying the analysis of bottom-up proteomics data with CHIMERYS DOI Creative Commons
Martin Frejno, Michelle T. Berger, Johanna Tüshaus

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 27, 2024

Abstract Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), creating thousands of spectra, most which chimeric and contain fragment ions from more than one peptide. Because differences in data acquisition strategies such as data-dependent (DDA), data-independent (DIA) or parallel reaction monitoring (PRM), separate software packages employing different analysis concepts used for identification quantification, even though the underlying information is principally same. Here, we introduce CHIMERYS, a novel, spectrum-centric search algorithm designed deconvolution spectra unifies proteomic analysis. Using accurate predictions retention time, ion intensities applying regularized linear regression, it explains much intensity possible with few peptides possible. Together rigorous false discovery rate control, CHIMERYS accurately identifies quantifies multiple per tandem spectrum DDA, DIA PRM experiments.

Язык: Английский

Процитировано

6
Unifying the analysis of bottom-up proteomics data with CHIMERYS DOI Creative Commons
Martin Frejno, Michelle T. Berger, Johanna Tüshaus

и другие.

Nature Methods, Год журнала: 2025, Номер unknown

Опубликована: Апрель 22, 2025

Abstract Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography–tandem mass spectrometry, creating thousands of spectra, most which chimeric and contain fragment ions from more than one peptide. Because differences in data acquisition strategies such as data-dependent, data-independent or parallel reaction monitoring, separate software packages employing different analysis concepts used for identification quantification, even though the underlying information is principally same. Here, we introduce CHIMERYS, a spectrum-centric search algorithm designed deconvolution spectra unifies proteomic analysis. Using accurate predictions retention time, ion intensities applying regularized linear regression, it explains much intensity possible with few peptides possible. Together rigorous false discovery rate control, CHIMERYS accurately identifies quantifies multiple per tandem spectrum monitoring experiments.

Язык: Английский

Процитировано

0
Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics DOI
Erin M. Humphries, Clare Loudon, George E. Craft

и другие.

Analytical Chemistry, Год журнала: 2024, Номер 96(33), С. 13358 - 13370

Опубликована: Авг. 5, 2024

Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences number, intensity, reproducibility identifications. By comparing four deparaffinization rehydration methods, including heptane, histolene, SubX, xylene, we found that heptane methanol produced lowest coefficients variation (CVs). Using this, five extraction methods from literature were modified evaluated their performance using kidney, leg muscle, lung, testicular rat organs. All performed well, except SP3 due to insufficient tissue lysis. Heat n' Beat was fastest most reproducible with highest digestion efficiency CVs. S-Trap peptide yield, while TFE best phosphopeptide enrichment efficiency. quantitation FFPE-derived peptides remains an ongoing challenge bias in UV fluorescence assays across notably SPEED. Functional analysis demonstrated each favored extracting some gene ontology cellular components over others chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, nucleoplasm protein groups. outcome is a set recommendations choosing appropriate different settings.

Язык: Английский

Процитировано

2
Challenges of MS‐based small extracellular vesicles proteomics DOI Creative Commons
Daniel Fochtman, Łukasz Marczak, Monika Pietrowska

и другие.

Journal of Extracellular Vesicles, Год журнала: 2024, Номер 13(12)

Опубликована: Дек. 1, 2024

Abstract Proteomic profiling of small extracellular vesicles (sEV) is a powerful tool for discovering biomarkers various diseases. This process most often assisted by mass spectrometry (MS) usually lacks standardization and recognition challenges which may lead to unreliable results. General recommendations sEV MS analyses have been briefly given in the MISEV2023 guidelines. The present work goes into detail every step protein with an overview factors influencing such analyses. includes reporting defining source vesicle isolation, solubilization digestion, ‘offline’ ‘online’ sample complexity reduction, analysis type itself, subsequent data analysis. Every stage this affects others, could result different outcomes. Although characterization comparisons isolation methods are known accessible MS‐based details provided cell or tissue samples, no consensus has ever published describe whole proteomic Reliable results can be obtained from that well planned, prepared for, backed pilot studies appropriate research.

Язык: Английский

Процитировано

0
Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics DOI Open Access
Gergő Kalló, Khadiza Zaman,

László Potor

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(24), С. 13665 - 13665

Опубликована: Дек. 20, 2024

Vulnerable atherosclerotic plaques, especially hemorrhaged lesions, are the major cause of mortalities related to vascular pathologies. The early identification vulnerable plaques helps stratify patients at risk developing acute events. In this study, proteomics analyses human carotid artery samples collected from with atheromatous and complicated respectively, as well healthy controls were performed. proteins isolated analyzed by a bottom-up shotgun approach that relied on nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) using both data-dependent (DDA) data-independent (DIA) acquisitions. data obtained high-resolution DIA displayed stronger distinction among groups compared DDA analyses. Differentially expressed further examined Ingenuity Pathway Analysis® focus pathological molecular processes driving atherosclerosis. From more than 150 significantly regulated canonical pathways, atherosclerosis signaling neutrophil extracellular trap verified protein-targeted extraction. results our study expected facilitate better understanding disease progression's drivers provide inspiration for multiomics hypothesis-driven studies.

Язык: Английский

Процитировано

0