A review of the current state of single-cell proteomics and future perspective

Analytical and Bioanalytical Chemistry, Journal Year: 2023, Volume and Issue: 415(28), P. 6889 - 6899

Published: June 7, 2023

Abstract Single-cell methodologies and technologies have started a revolution in biology which until recently has primarily been limited to deep sequencing imaging modalities. With the advent subsequent torrid development of single-cell proteomics over last 5 years, despite fact that proteins cannot be amplified like transcripts, it now become abundantly clear is worthy complement transcriptomics. In this review, we engage an assessment current state art including workflow, sample preparation techniques, instrumentation, biological applications. We investigate challenges associated with working very small volumes acute need for robust statistical methods data interpretation. delve into what believe promising future research at resolution highlight some exciting discoveries already made using proteomics, identification rare cell types, characterization cellular heterogeneity, investigation signaling pathways disease mechanisms. Finally, acknowledge there are number outstanding pressing problems scientific community vested advancing technology needs resolve. Of prime importance set standards so becomes widely accessible allowing novel easily verifiable. conclude plea solve these rapidly can part robust, high-throughput, scalable multi-omics platform ubiquitously applied elucidating insights diagnosis treatment all diseases afflict us.

Language: Английский

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Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics

Journal of Proteome Research, Journal Year: 2023, Volume and Issue: 22(9), P. 2775 - 2784

Published: Aug. 2, 2023

Missing values are a notable challenge when analyzing mass spectrometry-based proteomics data. While the field is still actively debating best practices, increased with emergence of single-cell and dramatic increase in missing values. A popular approach to deal perform imputation. Imputation has several drawbacks for which alternatives exist, but currently, imputation practical solution widely adopted data analysis. This perspective discusses advantages We also highlight 5 main challenges linked value management proteomics. Future developments should aim solve these challenges, whether it through or modeling. The concludes recommendations reporting values, methods that proper encoding

Language: Английский

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Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics

Cell stem cell, Journal Year: 2024, Volume and Issue: 31(7), P. 1072 - 1090.e8

Published: May 15, 2024

Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances sequencing technologies led to identification of gene regulatory programs that control emergence and their derivatives. However, proteome-based studies early mammalian scarce. To overcome this, we utilized gastruloids multilayered mass spectrometry-based proteomics approach investigate global dynamics (phospho) protein expression gastruloid differentiation. Our findings revealed many proteins with temporal unique profiles for each layer, also validated using single-cell technology. Additionally, profiled enhancer interaction landscapes P300 proximity labeling, numerous gastruloid-specific transcription factors chromatin remodelers. Subsequent degron-based perturbations combined RNA (scRNA-seq) identified role ZEB2 mouse human somitogenesis. Overall, this study provides rich resource developmental synthetic biology communities endeavoring understand embryogenesis.

Language: Английский

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Recent advances in microfluidics for single-cell functional proteomics

Lab on a Chip, Journal Year: 2023, Volume and Issue: 23(7), P. 1726 - 1751

Published: Jan. 1, 2023

This article covers exciting developments of recent microfluidics-based single-cell proteomics methods and their utilizations to tackle important biological questions for both basic translational research.

Language: Английский

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Characterizing the omics landscape based on 10,000+ datasets

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 25, 2025

Abstract The characteristics of data produced by omics technologies are pivotal, as they critically influence the feasibility and effectiveness computational methods applied in downstream analyses, such harmonization differential abundance analyses. Furthermore, variability these across datasets plays a crucial role, leading to diverging outcomes benchmarking studies, which essential for guiding selection appropriate analysis all fields. Additionally, tools often developed within specific communities due presumed differences attributed each technology. In this study, we investigate over ten thousand understand how proteomics, metabolomics, lipidomics, transcriptomics, microbiome vary characteristics. We were able show patterns investigated types provide tool that enables researchers assess representative given dataset is its respective discipline. Moreover, illustrate can impact analyses at example normalization presence sample-dependent proportions missing values. Given characteristics, encourage systematic inspection benchmark studies prevent suboptimal method unintended bias.

Language: Английский

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Challenges and Opportunities for Single-cell Computational Proteomics

Molecular & Cellular Proteomics, Journal Year: 2023, Volume and Issue: 22(4), P. 100518 - 100518

Published: Feb. 23, 2023

Single-cell proteomics is growing rapidly and has made several technological advancements. As most research been focused on improving instrumentation sample preparation methods, very little attention given to algorithms responsible for identifying quantifying proteins. Given the inherent difference between bulk data single-cell data, it necessary realize that current being employed were designed have underlying assumptions may not hold true data. In order develop optimize we need characterize differences assess how perform Here, present a review of peptides We will give each type algorithm works, relies on, performs possible optimizations solutions could be used address in

Language: Английский

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Instrumentation at the leading edge of proteomics

Published: April 22, 2024

The proteome, or collection of proteoforms expressed in a biological system, is dynamic and heterogeneous. As our appreciation for the complexity proteome has evolved, so have technologies we use to interrogate its composition. More than three decades ago, rapid expansion field proteomics was driven by advent soft ionization techniques focusing on capturing protein sequence information using mass spectrometry (MS). tools automate peptide sequencing with tandem MS (MS/MS) matured, recognized limits qualitatively cataloguing gene products. This realization drove multi-pronged MS-centric that seek capture various aspects proteins, including their abundance, modification states, conformation structure, spatiotemporal relationships. Here review innovations MS-based instrumentation continue expand ability survey ever increasing sensitivity, speed, flexibility. march progress been steady over better half past century, but discussion here focuses developments within five years ushered an exciting era proteomics, where poised be dominant platform exploring phenotypes basic translational sciences foreseeable future.

Language: Английский

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Instrumentation at the leading edge of proteomics

Published: Nov. 17, 2023

The proteome, or collection of proteoforms expressed in a biological system, is dynamic and heterogeneous. As our appreciation for the complexity proteome has evolved, so have technologies we use to interrogate its composition. More than three decades ago, rapid expansion field proteomics was driven by advent soft ionization techniques focusing on capturing protein sequence information using mass spectrometry (MS). tools automate peptide sequencing with tandem MS (MS/MS) matured, recognized limits qualitatively cataloguing gene products.1,2 This realization drove multi-pronged MS-centric that seek capture various aspects proteins, including their abundance, modification states, conformation structure, spatiotemporal relationships.3–7 Here review innovations MS-based instrumentation continue expand ability survey ever increasing sensitivity, speed, flexibility. march progress been steady over better half past century, but discussion here focuses developments within five years ushered an exciting era proteomics, where poised be dominant platform exploring phenotypes basic translational sciences foreseeable future.

Language: Английский

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Toward Single Bacterium Proteomics

Journal of the American Society for Mass Spectrometry, Journal Year: 2023, Volume and Issue: 34(10), P. 2098 - 2106

Published: Sept. 15, 2023

Bacteria are orders of magnitude smaller than mammalian cells, and while single cell proteomics (SCP) currently detects quantifies several thousands proteins per cell, it is not clear whether conventional SCP methods will be suitable for bacteria. Here we report on the first successful attempt to detect from individual Escherichia coli bacteria, with validation our findings by comparison two bacteria samples bulk data. Data available via ProteomeXchange identifier PXD043473.

Language: Английский

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Standardized Workflow for Mass-Spectrometry-Based Single-Cell Proteomics Data Processing and Analysis Using the scp Package

Methods in molecular biology, Journal Year: 2024, Volume and Issue: unknown, P. 177 - 220

Published: Jan. 1, 2024

Language: Английский

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