A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

Madern, Moritz; Reiter, Wolfgang; Stanek, Florian; Hartl, Natascha; Mechtler, Karl; Hartl, Markus

doi:10.1016/j.mcpro.2023.100694

Molecular & Cellular Proteomics

2024

DOI: 10.1016/j.mcpro.2023.100694

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A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

Moritz Madern,

Wolfgang Reiter,

Florian Stanek

et al.

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2024

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Cited by 2 publications

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Data acquisition approaches for single cell proteomics

Ghosh,

Shannon,

Searle

2024

Proteomics

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Single‐cell proteomics (SCP) aims to characterize the proteome of individual cells, providing insights into complex biological systems. It reveals subtle differences in distinct cellular populations that bulk proteome analysis may overlook, which is essential for understanding disease mechanisms and developing targeted therapies. Mass spectrometry (MS) methods in SCP allow the identification and quantification of thousands of proteins from individual cells. Two major challenges in SCP are the limited material in single‐cell samples necessitating highly sensitive analytical techniques and the efficient processing of samples, as each biological sample requires thousands of single cell measurements. This review discusses MS advancements to mitigate these challenges using data‐dependent acquisition (DDA) and data‐independent acquisition (DIA). Additionally, we examine the use of short liquid chromatography gradients and sample multiplexing methods that increase the sample throughput and scalability of SCP experiments. We believe these methods will pave the way for improving our understanding of cellular heterogeneity and its implications for systems biology.

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Data acquisition approaches for single cell proteomics

Ghosh,

Shannon,

Searle

2024

Proteomics

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Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications

Ctortecka,

Clark,

Boyle

et al. 2024

Nat Commun

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The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell remains challenging. To address some of those limitations, we present a dedicated sample preparation chip, the proteoCHIP EVO 96 that directly interfaces with the Evosep One. This, in combination with the Bruker timsTOF demonstrates double the identifications without manual sample handling and the newest generation timsTOF Ultra identifies up to 4000 with an average of 3500 protein groups per single HEK-293T without a carrier or match-between runs. Our workflow spans 4 orders of magnitude, identifies over 50 E3 ubiquitin-protein ligases, and profiles key regulatory proteins upon small molecule stimulation. This study demonstrates that the proteoCHIP EVO 96-based sample preparation with the timsTOF Ultra provides sufficient proteome depth to study complex biology beyond cell-type classifications.

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A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

Cited by 2 publications

References 63 publications

Data acquisition approaches for single cell proteomics

Data acquisition approaches for single cell proteomics

Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications

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