2024
DOI: 10.1101/2024.01.20.576369
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Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications

Claudia Ctortecka,
Natalie M. Clark,
Brian Boyle
et al.

Abstract: Mass spectrometry (MS)-based single-cell proteomics (SCP) has gained massive attention as a viable complement to other single cell approaches. The rapid technological and computational advances in the field have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell at reasonable proteome depth to characterize biological phenomena remains a challenge. To address some of those limitations we present a combination of fully automated… Show more

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Cited by 10 publications
(10 citation statements)
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“…The modification resulted in a remarkable 19-fold increase in sensitivity at the single-cell-equivalent level, allowing the identification of 3888 proteins with 1 ng of HeLa peptides. The detection sensitivity can be further improved using the newly released timsTOF Ultra instrument …”
Section: Discussionmentioning
confidence: 99%
“…The modification resulted in a remarkable 19-fold increase in sensitivity at the single-cell-equivalent level, allowing the identification of 3888 proteins with 1 ng of HeLa peptides. The detection sensitivity can be further improved using the newly released timsTOF Ultra instrument …”
Section: Discussionmentioning
confidence: 99%
“…Since more ions can be stored and manipulated in the v.4 TIMS cartridge, a wider dynamic range of 1 × 10 5 is seen in the HT and Flex relative to 5 × 10 4 in the SCP. The Flex is compatible with both ESI and matrix-assisted laser desorption/ionization (MALDI) ion sources, , and real-time data analysis through the parallel search engine in real-time (PaSER) is available on the timsTOF Pro 2 and other newer models. , The recently released timsTOF Ultra enables scan speeds approaching 300 Hz by integrating the sensitivity of the timsTOF SCP with the dynamic range performance of the timsTOF HT, all while creating superior front-end ion transfer efficiency compatible with high scan speeds Although not commercialized, UVPD and ECD have been coupled to timsTOF instruments with varying degrees of in-house modifications …”
Section: Ms-centric Technology Used In Modern Proteomicsmentioning
confidence: 99%
“…The combination of these two analytical tools on the analysis of peptides from cells or tissues has become the state-of-the art workflow in proteomics. New mass spectrometry configurations 8, 9 combined with robust nanoLC 10, 11 has led to considerable increase in proteome coverage and throughput. Nevertheless, deep and comprehensive proteome characterization by single-shot LC-MS still represents a challenge.…”
Section: Introductionmentioning
confidence: 99%