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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Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides

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

Опубликована: Март 15, 2024

Circular RNAs (circRNAs) are covalently closed non-coding lacking the 5' cap and poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents immunopeptidomics workflow with a specific focus on generating circRNA-specific protein fasta reference. The main goal this is to streamline process identifying validating leukocyte antigen (HLA) bound peptides originating from circRNAs. We increase analytical stringency our by retaining identified independently two mass spectrometry search engines and/or applying group-specific FDR for canonical-derived circRNA-derived peptides. A subset specifically encoded region spanning back-splice junction (BSJ) validated targeted MS, direct Sanger sequencing respective transcripts. Our identifies 54 unique BSJ-spanning immunopeptidome melanoma lung cancer samples. approach enlarges catalog proteins explored immunotherapy.

Язык: Английский

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Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping

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

Опубликована: Фев. 2, 2024

Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technologies face challenges, such as uncertainty regarding identity, non-specific binding, handling of variants that affect epitope affinity binding. Mass spectrometry-based can overcome some these challenges. Here we report a pQTL study the Proteograph™ Product Suite workflow (Seer, Inc.) where quantify over 18,000 unique peptides from nearly 3000 proteins in more than 320 blood samples multi-ethnic cohort bottom-up, peptide-centric, mass approach. We identify 184 protein-altering 137 genes are significantly associated with their corresponding variant peptides, confirming specificity co-associated binders, identifying putatively causal cis-encoded providing experimental presence blood, including may be inaccessible to proteomics.

Язык: Английский

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Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst

Journal of Proteome Research, Год журнала: 2024, Номер unknown

Опубликована: Сен. 10, 2024

The FragPipe computational proteomics platform is gaining widespread popularity among the research community because of its fast processing speed and user-friendly graphical interface. Although produces well-formatted output tables that are ready for analysis, there still a need an easy-to-use downstream statistical analysis visualization tool. FragPipe-Analyst addresses this by providing R shiny web server to assist users in conducting analyses resulting quantitative data. It supports major quantification workflows, including label-free quantification, tandem mass tags, data-independent acquisition. offers range useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) using Limma, gene ontology pathway enrichment Enrichr. To support advanced customized visualizations, we also developed FragPipeAnalystR, package encompassing all functionalities extended site-specific post-translational modifications (PTMs). FragPipeAnalystR both open-source freely available.

Язык: Английский

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C-terminal amides mark proteins for degradation via SCF–FBXO31

Nature, Год журнала: 2025, Номер unknown

Опубликована: Янв. 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.

Язык: Английский

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diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 2, 2025

Abstract Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves accuracy depth achievable using acquisition. We introduce diaTracer, spectrum-centric computational tool optimized data. diaTracer performs three-dimensional (mass to charge ratio, retention time, mobility) peak tracing feature detection generate precursor-resolved “pseudo-tandem spectra”, facilitating direct (“spectral-library free”) identification from is stand-alone fully integrated FragPipe platform. demonstrate performance data triple-negative breast cancer, cerebrospinal fluid, plasma samples, phosphoproteomics human leukocyte antigens immunopeptidomics experiments, low-input spatial study. also show that enables unrestricted post-translational modifications open/mass-offset searches.

Язык: Английский

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Recent advances in the field of single-cell proteomics

Translational Oncology, Год журнала: 2022, Номер 27, С. 101556 - 101556

Опубликована: Окт. 19, 2022

The field of single-cell omics is rapidly progressing. Although DNA and RNA sequencing-based methods have dominated the to date, global proteome profiling has also entered main stage. Single-cell proteomics was facilitated by advancements in different aspects mass spectrometry (MS)-based proteomics, such as instrument design, sample preparation, chromatography ion mobility. (scp-MS) moved beyond being a mere technical development, now able deliver actual biological application been successfully applied characterize cell states. Here, we review some key developments scp-MS, provide background field, discuss various available foresee possible future directions.

Язык: Английский

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Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Окт. 31, 2022

Abstract We present Slice-PASEF, a novel mass spectrometry technology based on trapped ion mobility separation of ions. Slice-PASEF allows to achieve the theoretical maximum MS/MS sensitivity and boosts proteomics low sample amounts. Leveraging we show, for first time, that comprehensive profiling single cell-level peptide amounts is possible using ultra-fast microflow chromatography general-purpose spectrometer, allowing quantification 1417 proteins from 200 picograms HeLa cell standard an Evosep One LC system coupled timsTOF Pro 2, at samples per day throughput. implemented module in our DIA-NN data processing software, make it readily available community.

Язык: Английский

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Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition

Molecular & Cellular Proteomics, Год журнала: 2022, Номер 22(2), С. 100489 - 100489

Опубликована: Дек. 22, 2022

Язык: Английский

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Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

Journal of Proteome Research, Год журнала: 2022, Номер 21(12), С. 2846 - 2892

Опубликована: Ноя. 10, 2022

The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in spectrometry. It is thus not surprising that MS instrument attracts most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase (RPLC) remains somewhat its shadow. Consequently, wisdom fundaments slowly vanishing from some laboratories. However, full potential advanced instruments cannot be achieved without highly efficient RPLC. This impossible to attain understanding fundamental processes chromatographic system and properties peptides important their behavior. We wrote this tutorial intending give practitioners an overview critical aspects RPLC facilitate setting LC parameters so they can leverage capabilities instruments. After briefly introducing gradient peptides, we discuss affect quality chromatograms most. Next, address in-column extra-column broadening. last section devoted key methods. also extracted trends practice recent proteomics studies correlated them knowledge on separation.

Язык: Английский

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