The proteomic landscape of genome-wide genetic perturbations

Cell, Journal Year: 2023, Volume and Issue: 186(9), P. 2018 - 2034.e21

Published: April 1, 2023

Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global expression is driven complex interplay of (1) general biological properties, including translation rate, turnover, the formation complexes, growth genome architecture, followed (2) such as connectivity genetic, metabolic, physical interaction Moreover, show complements current annotation through assessment proteome profile similarity, covariation, reverse profiling. Thus, our study reveals principles govern provides genome-spanning resource annotation.

Language: Английский

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midiaPASEF maximizes information content in data-independent acquisition proteomics

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 2, 2023

Abstract Data-independent acquisition (DIA) approaches provide comprehensive records of all detectable pre-cursor and fragment ions. Here we introduce midiaPASEF, a novel DIA scan mode using mobility-specific micro-encoding overlapping quadrupole windows to optimally cover the ion population in mobility-mass charge plane. Using mobility-encoded windows, midiaPASEF maximizes information content acquisitions which enables determination precursor m/z each with precision less than 2 Th. The Snakemake-based MIDIAID pipeline integrates algorithms for multidimensional peak detection machine-learning-based classification precursor-fragment relationships. fully automated processing deconvolution midia-PASEF files exports highly specific DDA-like MSMS spectra are suitable de novo sequencing can be searched directly established tools including PEAKS, FragPipe Mascot. identifies over 40 unique peptides per second provides powerful library-free analyses phosphopeptidome immunopeptidome samples.

Language: Английский

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CTSB promotes sepsis-induced acute kidney injury through activating mitochondrial apoptosis pathway

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 13, 2023

Acute kidney injury is a common and severe complication of sepsis. Sepsis -induced acute injury(S-AKI) an independent risk factor for mortality among sepsis patients. However, the mechanisms S-AKI are complex poorly understand. Therefore, exploring underlying may lead to development therapeutic targets.A model was established in male C57BL/6 mice using cecal ligation puncture (CLP). The data-independent acquisition (DIA)-mass spectrometry-based proteomics used explore protein expression changes analyze key profile control CLP group. methodology also identify proteins pathways. vitro by treating HK-2 cells with lipopolysaccharide (LPS). Subsequently, effect mechanism Cathepsin B (CTSB) inducing apoptosis were observed verified.The renal scores, serum creatinine, blood urea nitrogen, molecule 1 higher septic than non-septic mice. proteomic analysis identified total 449 differentially expressed (DEPs). GO KEGG showed that DEPs mostly enriched lysosomal-related cell structures CTSB MAPK as S-AKI. Electron microscopy enlarged lysosomes, swelled ruptured mitochondria, cytoplasmic vacuolization TUNEL staining activity test group In model, mRNA increased LPS-treated cells. Acridine orange LPS caused lysosomal membrane permeabilization (LMP). CA074 inhibitor could effectively inhibit activity. CCK8 Annexin V/PI results indicated reversed LPS-induced JC-1 western blot inhibited mitochondrial potential activated pathway, which be CA074.LMP contribute pathogenesis treatment induced activating pathway. Inhibition might new strategy alleviate sepsis-induced injury.

Language: Английский

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Proteomics of the heart

Physiological Reviews, Journal Year: 2024, Volume and Issue: 104(3), P. 931 - 982

Published: Feb. 1, 2024

Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at molecular level. Proteomics provides biologists with snapshot of context-dependent and proteoform expression, structural conformations, dynamic turnover, protein-protein interactions. Cardiac can offer broader deeper understanding the mechanisms that underscore cardiovascular disease, it foundational to development future therapeutic interventions. This review encapsulates evolution, current technologies, perspectives proteomic-based mass spectrometry as applies study heart. Key technological advancements have allowed researchers proteomes single-cell level employ robot-assisted automation systems for enhanced sample preparation techniques, increase fidelity spectrometers has unambiguous numerous posttranslational modifications. Animal models ranging from early animal experiments heart failure preserved ejection fraction, provided tools challenging organ laboratory. Further will pave way implementation even closer within clinical setting, allowing not only scientists but also patients benefit an interplay relates cardiac disease physiology.

Language: Английский

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The Landscape and Perspectives of the Human Gut Metaproteomics

Molecular & Cellular Proteomics, Journal Year: 2024, Volume and Issue: 23(5), P. 100763 - 100763

Published: April 10, 2024

The human gut microbiome is closely associated with health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of by analyzing entire proteins present in microbial communities. Recent advancements liquid chromatography tandem mass spectrometry (LC-MS/MS) techniques have expanded detection range metaproteomics. However, overall coverage proteome metaproteomics still limited. While metagenomics studies revealed substantial diversity functional potential microbiome, few summarized studied landscape metaproteomics.In this paper, we current re-analyzing identification results from fifteen published studies. We quantified limited high proportion annotation metaproteomics-identified proteins. conducted preliminary comparison between view identifying key areas consistency divergence. Based on metaproteomics, discuss feasibility using to study functionally unknown propose whole workflow peptide-centric analysis. Additionally, suggest enhancing analysis refining taxonomic classification calculating confidence scores, well developing tools interaction taxonomy function.

Language: Английский

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From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies

Molecular Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: April 2, 2024

In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for discovery, is underpinned by big data, transformative force in current era. Omics characterized its heterogeneity enormity, ushered biological biomedical research into data domain. Acknowledging significance integrating diverse omics strata, known as multi-omics studies, researchers delve intricate interrelationships among various layers. review navigates expansive landscape, showcasing tailored assays each layer through genomes to metabolomes. The sheer volume generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging robust tools. These datasets not only refine classification but also enhance diagnostics foster development therapeutic strategies. Through integration high-throughput focuses targeting modeling multiple disease-regulated networks, validating interactions targets, enhancing potential using network pharmacology approaches. Ultimately, this exploration aims illuminate impact era, shaping future research.

Language: Английский

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Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(19)

Published: May 2, 2024

Gene expression varies between individuals and corresponds to a key step linking genotypes phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes large population 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA abundances are weakly correlated at gene level. While coexpression network recapitulates major biological functions, differential patterns reveal proteomic signatures related specific populations. Comprehensive association analyses highlight variants associated with variation in (pQTL) (eQTL) levels poorly overlap (3%). Our results demonstrate transcriptome proteome governed by distinct bases, likely explained turnover. It also highlights importance integrating these different better understand genotype–phenotype relationship.

Language: Английский

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Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid‐2018–2022)

Journal of Separation Science, Journal Year: 2023, Volume and Issue: 46(12)

Published: Feb. 26, 2023

This review gives a wide overview of recent advances and applications capillary electrophoresis microchip methods in the fields proteomics peptidomics period from mid‐2018 up to end 2022. The methodological topics covering sample preparation concentration techniques, hyphenation with mass spectrometry, multidimensional separations by on‐line or off‐line coupled different liquid chromatography techniques are described new developments both bottom‐up top‐down approaches presented. In addition, various proteomic peptidomic studies demonstrated. They include monitoring protein posttranslational modifications biological biochemical research, clinical proteomics, food analysis.

Language: Английский

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Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography

PROTEOMICS, Journal Year: 2023, Volume and Issue: 24(1-2)

Published: June 7, 2023

Abstract Increased throughput in proteomic experiments can improve accessibility of platforms, reduce costs, and facilitate new approaches systems biology biomedical research. Here we propose combination analytical flow rate chromatography with ion mobility separation peptide ions, data‐independent acquisition, data analysis the DIA‐NN software suite, to achieve high‐quality from limited sample amounts, at a up 400 samples per day. For instance, when benchmarking our workflow using 500‐μL/min 3‐min chromatographic gradients, report quantification 5211 proteins 2 μg mammalian cell‐line standard high quantitative accuracy precision. We further used this platform analyze blood plasma cohort COVID‐19 inpatients, gradient alternating column regeneration on dual pump system. The method delivered comprehensive view proteome, allowing classification patients according disease severity revealing biomarker candidates.

Language: Английский

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Proteomic approaches advancing targeted protein degradation

Trends in Pharmacological Sciences, Journal Year: 2023, Volume and Issue: 44(11), P. 786 - 801

Published: Sept. 29, 2023

Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) molecular glue (MG) degraders (MGDs) represent the most advanced approaches, with some already used in clinical settings. Despite these advances, still faces many challenges, pertaining to both development of effective, selective, tissue-penetrant understanding their mode action. In this review, we focus on progress made addressing challenges. particular, discuss utility application recent proteomic as indispensable tools enable insights into degrader development, including target engagement, selectivity, efficacy, safety,

Language: Английский

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