Journal of Proteome Research, Год журнала: 2024, Номер unknown
Опубликована: Ноя. 12, 2024
Tandem mass spectrometry (MS/MS) is the gold standard for intact glycopeptide identification, enabling peptide sequence elucidation and site-specific localization of glycan compositions. Beam-type collisional activation generally sufficient
Язык: Английский
Molecular & Cellular Proteomics, Год журнала: 2024, Номер 23(5), С. 100760 - 100760
Опубликована: Апрель 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.
Язык: Английский
Процитировано
20
Environmental Science & Technology, Год журнала: 2024, Номер 58(29), С. 12784 - 12822
Опубликована: Июль 10, 2024
In the modern "omics" era, measurement of human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics metabolomics, has emerged as leading technology to broadly profile chemical exposure agents related biomolecules for accurate measurement, high sensitivity, rapid data acquisition, increased resolution space. Non-targeted approaches are increasingly accessible, supporting shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical computational infrastructures needed expand analysis coverage through streamlined, scalable, harmonized workflows pipelines that permit longitudinal tracking, retrospective validation, multi-omics integration meaningful health-oriented inferences. this article, we survey literature on state-of-the-art technologies, review current informatic pipelines, provide an up-to-date reference exposomic chemists, toxicologists, epidemiologists, care providers, stakeholders health sciences medicine. We propose efforts benchmark fit-for-purpose platforms expanding space, including gas/liquid chromatography-HRMS (GC-HRMS LC-HRMS), discuss opportunities, challenges, strategies advance burgeoning field exposome.
Язык: Английский
Процитировано
20
Medicinal Research Reviews, Год журнала: 2025, Номер unknown
Опубликована: Янв. 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.
Язык: Английский
Процитировано
2
Nature Chemistry, Год журнала: 2025, Номер unknown
Опубликована: Янв. 13, 2025
Abstract Understanding the dynamics of membrane protein–ligand interactions within a native lipid bilayer is major goal for drug discovery. Typically, cell-based assays are used, however, they often blind to effects protein modifications. In this study, using archetypal G protein-coupled receptor rhodopsin, we found that and its effectors can be released directly from retina rod disc membranes infrared irradiation in mass spectrometer. Subsequent isolation dissociation by multiphoton enabled sequencing individual proteoforms. Specifically, categorized distinct proteoforms localized labile palmitoylations, discovered Gβγ proteoform abolishes association defined modifications on proteins influence their assembly. Given reports undesirable side-effects involving vision, characterized off-target binding two phosphodiesterase 5 inhibitors, vardenafil sildenafil, 6 (PDE6). The results demonstrate differential reactivity with PDE6 an interaction preference lipidated proteins. summary, study highlights opportunities probing proteoform–ligand natural environments.
Язык: Английский
Процитировано
2
Nature Protocols, Год журнала: 2025, Номер unknown
Опубликована: Янв. 17, 2025
Язык: Английский
Процитировано
0
Molecular & Cellular Proteomics, Год журнала: 2025, Номер unknown, С. 100968 - 100968
Опубликована: Апрель 1, 2025
Ongoing advancements in instrumentation has established mass spectrometry (MS) as an essential tool proteomics research and drug discovery. The newly released Asymmetric Track Lossless (Astral) analyzer represents a major step forward MS instrumentation. Here, we evaluate the Orbitrap Astral spectrometer context of tandem tag-based multiplexed activity-based proteome profiling, highlighting its sensitivity boost relative to Tribrid platform-50% at peptide 20% protein level. We compare TMT DDA label-free DIA on same instrument, both which quantify over 10,000 human proteins per sample within one hour. offers higher quantitative precision data completeness, while is free ratio compression thereby more accurate. Our results suggest that prevalent with high-resolution MS2-based quantification Astral, real-time search-based MS3 platform effectively restores accuracy. Additionally, benchmark TMT-based profiling by interrogating cysteine ligandability. measures 30,000 cysteines single-shot experiment, 54% increase Eclipse. further leverage this remarkable profile target engagement landscape FDA-approved covalent drugs, including Sotorasib Adagrasib. herein provide reference for optimal use advanced platform.
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июнь 18, 2024
The physiological response of a cell to stimulation depends on its proteome configuration. Therefore, the abundance variation regulatory proteins across unstimulated single cells can be associatively linked with their stimulation. Here we developed an approach that leverages this association individual and nuclei systematically identify potential regulators biological processes, followed by targeted validation. Specifically, applied nucleocytoplasmic protein transport in macrophages stimulated lipopolysaccharide (LPS). To end, quantified proteomes 3,412 nuclei, sampling dynamic LPS treatment, linking functional variability proteomic variability. Minutes after stimulation, correlated strongly known regulators, thus revealing impact natural cellular response. We found simple biophysical constraints, such as quantity nuclear pores, partially explain LPS-induced transport. Among many newly identified associated response, selected 16 for validation knockdown. knockdown phenotypes confirmed inferences derived from demonstrating (sub-)single-cell proteomics infer regulation. expect generalize broad applications enhance interpretability single-cell omics data.
Язык: Английский
Процитировано
4
Journal of Proteome Research, Год журнала: 2025, Номер unknown
Опубликована: Фев. 13, 2025
Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies enable large-scale cohort proteogenomic analyses. As such, the data infrastructure search engines required to process must also scale. This challenge is amplified that rely on library-free match between runs (MBR) search, which enhanced depth-per-sample completeness. However, date, no MBR-based could scale cohorts thousands or more individuals. Here, we present a strategy deploy distributed cloud environment without source code modification, thereby enhancing resource scalability throughput. Additionally, an algorithm, Scalable MBR, replicates MBR procedure popular DIA-NN software for samples. We demonstrate can MS raw files few hours compared days original results are almost indistinguishable those native MBR. additionally show empirical spectra generated by better approximates semiempirical alternatives such as ID-RT-IM preserving user choice use libraries large analysis. The method has been tested over 15,000 injections available Proteograph Analysis Suite.
Язык: Английский
Процитировано
0
Journal of Proteome Research, Год журнала: 2025, Номер unknown
Опубликована: Фев. 21, 2025
The exponential increase in proteomics data presents critical challenges for conventional processing workflows. These pipelines often consist of fragmented software packages, glued together using complex in-house scripts or error-prone manual workflows running on local hardware, which are costly to maintain and scale. MSAID Platform offers a fully automated, managed pipeline, consolidating formerly disjointed functions into unified, API-driven services that cover the entire process from raw biological insights. Backed by cloud-native search algorithm CHIMERYS, as well scalable cloud compute instances lakes, platform facilitates efficient large sets, automation via command line, systematic result storage, analysis, visualization. lake supports elastically growing storage unified query capabilities, facilitating large-scale analyses reuse previously processed data, such aggregating longitudinally acquired studies. Users interact with web interface, CLI client, API, providing flexible, automated access. Readily available tools accessing include browser-based interrogation one-click visualizations statistical analysis. streamlines research processes, making advanced proteomic accessible broader range scientists. is globally https://platform.msaid.io.
Язык: Английский
Процитировано
0
Analytical Chemistry, Год журнала: 2025, Номер unknown
Опубликована: Март 4, 2025
The ability to identify isomers of human milk oligosaccharides (HMOs) remains a challenge. Typically, HMOs are analyzed using combination liquid chromatography and tandem mass spectrometry (LC-MS/MS). Yet, separation methods have been unable resolve several HMO isomers, necessitating the need for fragmentation that can differentiate these structures within mixtures. Common methods, such as collision-induced dissociation (CID), often fail form fragments linkage branching isomers. Previously, we determined electron transfer (ETD) yields distinct products when certain metal-charge carriers, Co2+. Here, compare including CID, higher-energy collisional (HCD), ETD, transfer, (EThcD) Co2+- Na+-adducted formation only ETD EThcD, but not CID HCD, indicates from dissociation. EThcD enabled differentiation Co2+-adducted tri-, tetra-, pentasaccharide while were incapable differentiating all examined Co2+, Na+, 2Na2+ adducts. We also show Co2+ adduction combined with generates related core structure fucose location, allowing further validation structures. This work establishes general method be used HMOs, which should enable improved identification structural various carbohydrate
Язык: Английский
Процитировано
0