Single-Cell Mass Spectrometry of Metabolites and Proteins for Systems and Functional Biology

Portero, Erika P.; Pade, Leena R.; Li, Jie; Choi, Sam B.; Nemes, Péter

doi:10.1007/978-1-0716-2525-5_5

Cited by 3 publications

(2 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These differences are crucial in areas such as cancer research, 218 immunology, 219 and developmental biology. 220 Single-cell proteomics aims to reveal the complex protein composition of individual cells, providing a more refined view of cellular processes and cell-tocell heterogeneity within cell populations.…”

Section: Single-cell Proteomicsmentioning

confidence: 99%

“…Traditional proteomic methods usually rely on large numbers of cell samples, resulting in average protein expression profiles that can mask subtle differences between individual cells. These differences are crucial in areas such as cancer research, immunology, and developmental biology . Single-cell proteomics aims to reveal the complex protein composition of individual cells, providing a more refined view of cellular processes and cell-to-cell heterogeneity within cell populations.…”

Section: Applications Of Labeling Strategies In Quantitative Proteomicsmentioning

confidence: 99%

See 1 more Smart Citation

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

Wang,

Liu,

2024

ACS Meas. Sci. Au

View full text Add to dashboard Cite

Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.

show abstract

Section: Single-cell Proteomicsmentioning

confidence: 99%

Section: Applications Of Labeling Strategies In Quantitative Proteomicsmentioning

confidence: 99%

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

Wang,

Liu,

2024

ACS Meas. Sci. Au

View full text Add to dashboard Cite

show abstract

Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry

Shen,

Pade,

Nemes

2024

J. Proteome Res.

View full text Add to dashboard Cite

Electrophoresis-Correlative Ion Mobility Deepens Single-cell Proteomics in Capillary Electrophoresis Mass Spectrometry

Shen,

Zhou,

Nemes

2024

Preprint

View full text Add to dashboard Cite

Detection of trace-sensitive signals is a current challenge is single-cell mass spectrometry (MS) proteomics. Separation prior to detection improves the fidelity and depth of proteome identification and quantification. We recently recognized capillary electrophoresis (CE) electrospray ionization (ESI) for ordering peptides into mass-to-charge (m/z)-dependent series, introducing electrophoresis-correlative (Eco) data-independent acquisition. Here, we demonstrate that these correlations based on electrophoretic mobility in the liquid phase are transferred into the gas phase, essentially temporally ordering the peptide ions into charge-dependent ion mobility (IM, 1/K0) trends (> 0.97). Rather than sampling the entire IM region broadly, we pursued these predictable correlations to schedule narrower frames. Compared to classical ddaPASEF, Eco-framing significantly enhanced the resolution of IM on a trapped ion mobility mass spectrometer (timsTOF PRO). This approach returned ~50% more proteins from HeLa proteome digests approximating to one-to-two cells, identifying ~962 proteins from ~200 pg in <20 min of effective electrophoresis, without match-between-runs. As a proof of principle, we deployed Eco-ddaPASEF on 1,157 proteins by analyzing <4% of the total proteome in single, yolk-laden embryonic stem cells (~80-micron) that were isolated from the animal cap of the South African clawed frog (Xenopus laevis). Quantitative profiling of 9 different blastomeres revealed detectable differences among these cells, which are normally fated to form the ectoderm but retain pluripotentiality. Eco-framing effectively deepens the proteome sensitivity in IMS using ddaPASEF, raising the possibility of a proteome-driven classification of embryonic cell differentiation.

show abstract

Single-Cell Mass Spectrometry of Metabolites and Proteins for Systems and Functional Biology

Cited by 3 publications

References 83 publications

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry

Electrophoresis-Correlative Ion Mobility Deepens Single-cell Proteomics in Capillary Electrophoresis Mass Spectrometry

Contact Info

Product

Resources

About