Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Фев. 1, 2024

Abstract Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) ~200 Hz using 2-Th isolation windows, dissolving differences between data-dependent -independent methods. This is achieved by pairing quadrupole Orbitrap mass spectrometer asymmetric track lossless (Astral) analyzer which provides >200-Hz MS/MS scanning speed, high resolving power sensitivity, low-ppm accuracy. The nDIA enables profiling >100 full yeast per day, or 48 human day at depth ~10,000 protein groups half-an-hour ~7,000 proteins 5 min, representing 3× higher coverage compared current state-of-the-art MS. Multi-shot offline fractionated samples ~3 h. High quantitative precision accuracy are demonstrated three-species proteome mixture, quantifying 14,000+ single run.

Язык: Английский

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The status of the human gene catalogue

Nature, Год журнала: 2023, Номер 622(7981), С. 41 - 47

Опубликована: Окт. 4, 2023

Язык: Английский

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Artificial Intelligence in Molecular Medicine

New England Journal of Medicine, Год журнала: 2023, Номер 388(26), С. 2456 - 2465

Опубликована: Июнь 28, 2023

Machine-learning methods for analyzing genomic, transcriptomic, epigenomic, proteomic, and metabolomic data sets have yielded clinically directive information, mostly rare genetic diseases.

Язык: Английский

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What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

Molecular & Cellular Proteomics, Год журнала: 2023, Номер 22(9), С. 100631 - 100631

Опубликована: Авг. 11, 2023

Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands noncanonical sites ribosome translation outside currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 ORFs are translated, which, first glance, potential to expand number protein CDSs 30%, from ∼19,500 over 26,000 CDSs. Yet, additional scrutiny these raised numerous questions about what fraction them truly produce a product those can be understood as proteins according conventional term. Adding further complication is fact published estimates vary widely around 30-fold, several thousand hundred thousand. The summation this research left genomics proteomics communities both excited prospect new regions in but searching guidance on how proceed. Here, we discuss current state ORF research, databases, interpretation, focusing assess whether given said "protein coding."

Язык: Английский

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Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

ACS Measurement Science Au, Год журнала: 2024, Номер 4(4), С. 338 - 417

Опубликована: Июнь 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.

Язык: Английский

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Instrumentation at the Leading Edge of Proteomics

Analytical Chemistry, Год журнала: 2024, Номер 96(20), С. 7976 - 8010

Опубликована: Май 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

Язык: Английский

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The One Hour Human Proteome

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

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Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Май 10, 2024

Abstract Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs be considered during sequence database searching. This leads an inflation search space results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring a powerful enhancement standard searching that boosts performance. We analyze 302,105 unique synthesized non-tryptic peptides ProteomeTools project on timsTOF-Pro generate ground-truth dataset containing 93,227 MS/MS spectra 74,847 peptides, used fine-tune deep learning-based fragment ion intensity prediction model Prosit. demonstrate up 3-fold improvement identification immunopeptides, as well increased detection low input samples.

Язык: Английский

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Mass-spectrometry-based proteomics: from single cells to clinical applications

Nature, Год журнала: 2025, Номер 638(8052), С. 901 - 911

Опубликована: Фев. 26, 2025

Язык: Английский

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Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit

PROTEOMICS, Год журнала: 2023, Номер 24(8)

Опубликована: Сен. 6, 2023

Abstract Machine learning (ML) and deep (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used various applications, ranging from data‐independent acquisition (DIA) data analysis to data‐driven rescoring search engine results. Here, we present Oktoberfest, an open source Python package our spectral library generation pipeline originally only available online via ProteomicsDB. Oktoberfest is largely agnostic provides access predictions, promoting adoption state‐of‐the‐art ML/DL proteomics pipelines. We demonstrate its ability reproduce even improve results previously published analyses on two distinct use cases. freely GitHub ( https://github.com/wilhelm‐lab/oktoberfest ) can easily be installed locally through cross‐platform PyPI package.

Язык: Английский

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