Multi-omics profiling with untargeted proteomics for blood-based early detection of lung cancer DOI Open Access
Brian D. Koh, Manway Liu,

Rebecca Almonte

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 4, 2024

Abstract Blood-based approaches to detect early-stage cancer provide an opportunity improve survival rates for lung cancer, the most lethal world-wide. Multiple blood-based detection using molecular analytes derived from individual ‘omics (cell-free DNA, RNA transcripts, proteins, metabolites) have been developed and tested, generally showing significantly lower sensitivity versus late-stage cancer. We hypothesized that approach multiple types of analytes, including broad untargeted coverage could identify biomarkers more directly reveal changes in gene expression phenotype response carcinogenesis potentially To end, we designed conducted one largest multi-omics, observational studies date, enrolling 2513 case control subjects. Multi-omics profiling detected 113,671 peptides corresponding 8385 protein groups, 219,729 71,756 introns, 1801 metabolites across all subject samples. then a machine learning-based classifier comprising 682 these multi-omics analytes. This demonstrated 89%, 80%, 98-100% all-stage, stage I, III-IV respectively, at 89% specificity validation set. The application platform discovery disease biomarkers, proteins complementary enables noninvasive with potential downstaging initial diagnosis improvement clinical outcomes.

Language: Английский

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition DOI Creative Commons
Lilian R. Heil, Eugen Damoc,

Tabiwang N. Arrey

et al.

Journal of Proteome Research, Journal Year: 2023, Volume and Issue: 22(10), P. 3290 - 3300

Published: Sept. 8, 2023

We evaluate the quantitative performance of newly released Asymmetric Track Lossless (Astral) analyzer. Using data-independent acquisition, Thermo Scientific Orbitrap Astral mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art spectrometers, which have long been gold standard for high-resolution proteomics. Our results demonstrate that can produce high-quality measurements across a wide dynamic range. also use developed extracellular vesicle enrichment protocol to reach new depths coverage in plasma proteome, quantifying over 5000 proteins 60 min gradient with spectrometer.

Language: Английский

Citations

118
Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome DOI Creative Commons
Florian A. Rosenberger, Marvin Thielert, Maximilian T. Strauss

et al.

Nature Methods, Journal Year: 2023, Volume and Issue: 20(10), P. 1530 - 1536

Published: Oct. 1, 2023

Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion complex tissues would greatly enhance insights. Here we describe single-cell Deep Visual Proteomics (scDVP), technology that integrates high-content imaging, laser microdissection multiplexed spectrometry. scDVP resolves context-dependent, spatial proteome murine hepatocytes at current depth 1,700 proteins from cell slice. Half was differentially regulated in manner, with protein levels changing dramatically proximity central vein. We applied machine learning classes images, which subsequently inferred imaging data alone. applicable healthy diseased complements other omics technologies.

Language: Английский

Citations

79
Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics DOI Creative Commons
Ronghui Lou, Ye Cao, Shanshan Li

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Jan. 6, 2023

A plethora of software suites and multiple classes spectral libraries have been developed to enhance the depth robustness data-independent acquisition (DIA) data processing. However, how combination a DIA tool library impacts outcome proteomics phosphoproteomics analysis has rarely investigated using benchmark that mimics biological complexity. In this study, we create sets simulating regulation thousands proteins in complex background, which are collected on both an Orbitrap timsTOF instruments. We evaluate four commonly used (DIA-NN, Spectronaut, MaxDIA Skyline) combined with seven different global proteome analysis. Moreover, assess their performances analyzing phosphopeptide standards TNF-α-induced phosphoproteome regulation. Our study provides practical guidance construct robust pipeline for studies implementing technique.

Language: Английский

Citations

69
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel DOI Creative Commons
Marvin Thielert, Corazon Ericka Mae M. Itang, Constantin Ammar

et al.

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(9)

Published: Aug. 21, 2023

Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited proteomic depth, throughput, robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated complete dimethyl labeling bulk or single-cell samples, without losing depth. Lys-N digestion enables five-plex quantification MS1 MS2 level. Because channels are quantitatively isolated from each other, mDIA accommodates reference channel that does not interfere with target channels. Our algorithm RefQuant takes advantage this confidently quantifies twice as many per single cell compared our previous work (Brunner et al, PMID 35226415), while allows routine analysis 80 cells day. Finally, combined spatial increase throughput Deep Visual Proteomics seven-fold for microdissection four-fold MS analysis. Applying primary cutaneous melanoma, discovered signatures within distinct tumor microenvironments, showcasing its potential precision oncology.

Language: Английский

Citations

58
Immobility-associated thromboprotection is conserved across mammalian species from bear to human DOI
Manuela Thienel, Johannes B. Mueller‐Reif, Zhe Zhang

et al.

Science, Journal Year: 2023, Volume and Issue: 380(6641), P. 178 - 187

Published: April 13, 2023

Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a major cause of morbidity mortality. Short-term immobility-related conditions are risk factor for the development VTE. Paradoxically, long-term immobilized free-ranging hibernating brown bears paralyzed spinal cord injury (SCI) patients protected from We aimed to identify mechanisms immobility-associated VTE protection in cross-species approach. Mass spectrometry-based proteomics revealed an antithrombotic signature platelets with heat shock protein 47 (HSP47) as most substantially reduced protein. HSP47 down-regulation or ablation attenuated immune cell activation neutrophil extracellular trap formation, contributing thromboprotection bears, SCI patients, mice. This conserved platelet may give rise therapeutics prognostic markers beyond

Language: Английский

Citations

42
Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023 DOI Creative Commons
Ronghui Lou, Wenqing Shui

Molecular & Cellular Proteomics, Journal Year: 2024, Volume and Issue: 23(2), P. 100712 - 100712

Published: Jan. 4, 2024

Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate and reproducible quantitative proteomics. This review provides comprehensive overview of recent advances in both the experimental computational methods DIA proteomics, from data schemes to analysis strategies software tools. are categorized based on design precursor isolation windows, highlighting wide-window, overlapping-window, narrow-window, scanning quadrupole-based, parallel accumulation-serial fragmentation (PASEF)-enhanced methods. For analysis, major classified into spectrum reconstruction, sequence-based search, library-based de novo sequencing sequencing-independent approaches. A wide array tools implementing these reviewed, with details their overall workflows scoring approaches at different steps. The generation optimization spectral libraries, which critical resources also discussed. Publicly available benchmark datasets covering global proteomics phosphoproteomics summarized facilitate performance evaluation various workflows. Continued synergistic developments versatile components expected further enhance power DIA-based

Language: Английский

Citations

39
Instrumentation at the Leading Edge of Proteomics DOI
Trenton M. Peters-Clarke, Joshua J. Coon, Nicholas M. Riley

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(20), P. 7976 - 8010

Published: May 13, 2024

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTInstrumentation at the Leading Edge of ProteomicsTrenton M. Peters-ClarkeTrenton Peters-ClarkeDepartment Chemistry, University Wisconsin─Madison, Madison, Wisconsin 53706, United StatesDepartment Biomolecular StatesMore by Trenton Peters-ClarkeView Biographyhttps://orcid.org/0000-0002-9153-2525, Joshua J. CoonJoshua CoonDepartment StatesMorgridge Institute for Research, 53715, CoonView Biographyhttps://orcid.org/0000-0002-0004-8253, and Nicholas Riley*Nicholas RileyDepartment Washington, Seattle, Washington 98195, States*Email: [email protected]More RileyView Biographyhttps://orcid.org/0000-0002-1536-2966Cite this: Anal. Chem. 2024, 96, 20, 7976–8010Publication Date (Web):May 13, 2024Publication History Received6 October 2023Accepted19 April 2024Revised17 2024Published online13 May inissue 21 2024https://pubs.acs.org/doi/10.1021/acs.analchem.3c04497https://doi.org/10.1021/acs.analchem.3c04497review-articleACS PublicationsCopyright © 2024 American Chemical SocietyRequest reuse permissionsArticle Views2104Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are COUNTER-compliant sum full text article downloads since November 2008 (both PDF HTML) across all institutions individuals. These metrics regularly updated to reflect usage leading up last few days.Citations number other articles citing this article, calculated Crossref daily. Find more information about citation counts.The Altmetric Attention Score is a quantitative measure attention that research has received online. Clicking on donut icon will load page altmetric.com with additional details score social media presence given article. how calculated. Share Add toView InAdd Full Text ReferenceAdd Description ExportRISCitationCitation abstractCitation referencesMore Options onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Dissociation,Ions,Mass spectrometry,Peptides proteins,Proteomics Get e-Alerts

Language: Английский

Citations

21
The One Hour Human Proteome DOI Creative Commons
Lia R. Serrano, Trenton M. Peters-Clarke,

Tabiwang N. Arrey

et al.

Molecular & Cellular Proteomics, Journal Year: 2024, Volume and Issue: 23(5), P. 100760 - 100760

Published: April 3, 2024

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

Language: Английский

Citations

20
C-terminal amides mark proteins for degradation via SCF–FBXO31 DOI Creative Commons
Matthias Muhar, Jakob Farnung, Martina Cernakova

et al.

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

Published: Jan. 29, 2025

During normal cellular homeostasis, unfolded and mislocalized proteins are recognized removed, preventing the build-up of toxic byproducts1. When protein homeostasis is perturbed during ageing, neurodegeneration or stress, can accumulate several forms chemical damage through reactive metabolites2,3. Such modifications have been proposed to trigger selective removal chemically marked proteins3-6; however, identifying that sufficient induce degradation has remained challenging. Here, using a semi-synthetic biology approach coupled assays, we found C-terminal amide-bearing (CTAPs) rapidly cleared from human cells. A CRISPR screen identified FBXO31 as reader amides. substrate receptor for SKP1-CUL1-F-box (SCF) ubiquitin ligase SCF-FBXO31, which ubiquitylates CTAPs subsequent proteasomal degradation. conserved binding pocket enables bind almost any peptide bearing an amide while retaining exquisite selectivity over non-modified clients. This mechanism facilitates turnover endogenous formed after oxidative stress. dominant mutation in neurodevelopmental disorders reverses CTAP recognition, such non-amidated neosubstrates now degraded becomes markedly toxic. We propose may represent vanguard largely unexplored class modified amino acid degrons could provide general strategy yet broad surveillance damaged proteins.

Language: Английский

Citations

3
Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics DOI Creative Commons
George S. Biggs, Emma E. Cawood, Aini Vuorinen

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 2, 2025

Abstract Identifying pharmacological probes for human proteins represents a key opportunity to accelerate the discovery of new therapeutics. High-content screening approaches expand ligandable proteome offer potential expedite novel chemical study protein function. Screening libraries reactive fragments by chemoproteomics offers compelling approach ligand discovery, however, optimising sample throughput, proteomic depth, and data reproducibility remains challenge. We report versatile, label-free quantification proteomics platform competitive profiling cysteine-reactive against native proteome. This high-throughput combines SP4 plate-based preparation with rapid chromatographic gradients. Data-independent acquisition performed on Bruker timsTOF Pro 2 consistently identified ~23,000 cysteine sites per run, total ~32,000 profiled in HEK293T Jurkat lysate. Crucially, this depth cysteinome coverage is met high completeness, enabling robust identification liganded proteins. In study, 80 were screened two cell lines identifying >400 ligand-protein interactions. Hits validated through concentration-response experiments was utilised hit expansion live experiments. significant step forward evaluate ligandability cysteines across

Language: Английский

Citations

2