Paleoproteomics

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(16), P. 13401 - 13446

Published: July 15, 2022

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at intersection molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages longevity diversity proteins to explore fundamental questions about past. While its origins predate characterization DNA, it was only with advent soft ionization mass spectrometry that became truly feasible. Technological gains over past 20 years have allowed increasing opportunities better understand preservation, degradation, recovery rich bioarchive found in archaeological paleontological records. Growing from handful studies 1990s on individual highly abundant paleoproteomics today an expanding diverse applications ranging taxonomic identification fragmented bones shells phylogenetic resolution extinct species exploration cuisines dental calculus pottery food crusts diseases. More broadly, these opened new doors understanding human–animal interactions, reconstruction environments environmental changes, expansion hominin fossil record through large scale screening nondiagnostic bone fragments, vertebrate record. Even advances, much proteomic still remains unexplored. Here we provide overview history field, summary major methods currently use, critical evaluation current challenges. We conclude by looking future, for which innovative solutions emerging technology will play important role enabling us access unexplored “dark” proteome, allowing fuller can interpretation

Language: Английский

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Instrumentation at the Leading Edge of Proteomics

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

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Top-down proteomics

Nature Reviews Methods Primers, Journal Year: 2024, Volume and Issue: 4(1)

Published: June 13, 2024

Language: Английский

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Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation

Journal of Proteome Research, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field more challenging than its bottom-up counterpart because species are much bigger have a larger number possible combinations sequences modifications; thus, there great need for technological development. With improvements in instrumentation multiplicity fragmentation modes available, top-down quickly gaining popularity renewed attention on increasing confidence identification quantification. Here, we systematically evaluated Sciex ZenoTOF 7600 system proteomics, applying standards to validate platform further experimenting capabilities electron-activated dissociation modification site localization. The instrument demonstrated robustness standard QC, as aided by zeno trapping. We were also able apply histone modifications, achieving high sequence coverage that allowed PTM's localization across protein optimized EAD fragmentation. ability analyze spanning range included analysis glycosylated proteins. This reference point future experiments be conducted system.

Language: Английский

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Proteomes Are of Proteoforms: Embracing the Complexity

Proteomes, Journal Year: 2021, Volume and Issue: 9(3), P. 38 - 38

Published: Aug. 31, 2021

Proteomes are complex—much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. of proteoforms, canonical proteins. While having a catalogue amino acid sequences provides invaluable information, this is Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess myriad proteoforms that arise at any point before, after, between translation transcription (e.g., isoforms, splice variants, post-translational modifications [PTM]), as well newly defined species. There numerous analytical methods currently used to address proteome depth here critically evaluate these in terms current ‘state-of-the-field’. We thus discuss both pros cons available approaches where improvements refinements needed quantitatively characterize proteomes. enable next-generation approach, suggest advances lie transdisciplinarity via integration proteomic yield unified discipline capitalizes on strongest qualities each. Such necessary (if revolutionary) shift cannot be accomplished by continued primary focus proteo-genomics/-transcriptomics. embrace complexity. Yes, hard questions, will easy…but fun easy?

Language: Английский

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Recent advances in proteomics and metabolomics in plants

Molecular Horticulture, Journal Year: 2022, Volume and Issue: 2(1)

Published: July 23, 2022

Over the past decade, systems biology and plant-omics have increasingly become main stream in plant research. New developments mass spectrometry bioinformatics tools, methodological schema to integrate multi-omics data leveraged recent advances proteomics metabolomics. These progresses are driving a rapid evolution field of research, greatly facilitating our understanding mechanistic aspects metabolisms interactions plants with their external environment. Here, we review MS-based metabolomics tools workflows special focus on applications research using several case studies related stress response, gene/protein function characterization, metabolic signaling pathways exploration, natural product discovery. We also present projection concerning future perspectives development including challenges for system biology. This is intended provide readers an overview how advanced MS technology, integrated application can be used advance

Language: Английский

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Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Top-Down Mass Spectrometry

Journal of the American Chemical Society, Journal Year: 2021, Volume and Issue: 143(31), P. 12014 - 12024

Published: July 30, 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry, and the S glycosylation plays key roles in altering viral binding/function infectivity. However, molecular structures glycan heterogeneity of new O-glycans found on regional-binding domain (S-RBD) remain cryptic because challenges intact glycoform analysis by conventional bottom-up glycoproteomic approaches. Here, we report complete structural elucidation O-glycan proteoforms through a hybrid native denaturing top-down mass spectrometry (MS) approach employing both trapped ion mobility (TIMS) quadrupole time-of-flight ultrahigh-resolution Fourier transform cyclotron resonance (FTICR)-MS. Native TIMS-MS/MS separates conformers S-RBD reveal their gas-phase heterogeneity, FTICR-MS/MS provides in-depth for unambiguous identification glycosites. A total eight O-glycoforms relative abundance are structurally elucidated first time. These findings demonstrate that this MS can provide high-resolution proteoform-resolved mapping diverse glycoprotein, which lays strong foundation uncover functional O-glycans. This be applied O-glycoform emergent SARS-CoV-2 variants as well other O-glycoproteins general.

Language: Английский

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

Journal of Proteome Research, Journal Year: 2022, Volume and Issue: 21(12), P. 2846 - 2892

Published: Nov. 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.

Language: Английский

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Improved Identification of Proteoforms in Top-Down Proteomics Using FAIMS with Internal CV Stepping

Analytical Chemistry, Journal Year: 2022, Volume and Issue: 94(8), P. 3600 - 3607

Published: Feb. 17, 2022

In top-down (TD) proteomics, prefractionation prior to mass spectrometric (MS) analysis is a crucial step for both the high confidence identification of proteoforms and increased proteome coverage. addition liquid-phase separations, gas-phase fractionation strategies such as field asymmetric ion mobility spectrometry (FAIMS) have been shown be highly beneficial in TD proteomics. However, so far, only external compensation voltage (CV) stepping has demonstrated i.e., single CVs were applied each run. Here, we investigated use internal CV (multiple per acquisition) single-shot analysis, which huge advantages terms measurement time amount sample required. addition, MS parameters optimized individual since different target certain ranges. For example, small identified mainly with more negative can lower resolution number microscans than larger proteins primarily via less CVs. We optimal combination gradient lengths validated settings low-molecular-weight CaCo-2 cells obtained using range preparation techniques. Compared measurements without FAIMS, protein groups (+60–94%) (+46–127%) their significantly increased, while remained identical. total, 684 2675 from 24 h multi-CV method.

Language: Английский

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High sensitivity top–down proteomics captures single muscle cell heterogeneity in large proteoforms

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(19)

Published: May 1, 2023

Single-cell proteomics has emerged as a powerful method to characterize cellular phenotypic heterogeneity and the cell-specific functional networks underlying biological processes. However, significant challenges remain in single-cell for analysis of proteoforms arising from genetic mutations, alternative splicing, post-translational modifications. Herein, we have developed highly sensitive functionally integrated top–down comprehensive single cells. We applied this muscle fibers (SMFs) resolve their heterogeneous proteomic properties at level. Notably, detected large (>200 kDa) SMFs. Using SMFs obtained three distinct muscles, found fiber-to-fiber among sarcomeric which can be related heterogeneity. Importantly, multiple isoforms myosin heavy chain (~223 kDa), motor protein that drives contraction, with high reproducibility enable classification individual fiber types. This study reveals cell establishes direct relationship between types, highlighting potential uncovering molecular underpinnings cell-to-cell variation complex systems.

Language: Английский

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