The technological landscape and applications of single-cell multi-omics

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(10), P. 695 - 713

Published: June 6, 2023

Language: Английский

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Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

Molecular Systems Biology, Journal Year: 2022, Volume and Issue: 18(3)

Published: Feb. 28, 2022

Language: Английский

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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: July 8, 2022

The dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity in proteomic experiments. Here we present a two-dimensional peak-picking algorithm generation of optimized spectral libraries, as well take advantage neural network-based processing data. Our computational platform boosts depth by up 83% compared previous work, is specifically beneficial for fast experiments those with low sample amounts. It quantifies over 5300 proteins single injections recorded at 200 samples per day throughput using Evosep One chromatography system on timsTOF Pro mass spectrometer almost 9000 93-min nanoflow gradient 2, from ng HeLa peptides. A user-friendly implementation provided through the incorporation algorithms DIA-NN software FragPipe workflow library generation.

Language: Английский

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Spatial profiling technologies illuminate the tumor microenvironment

Cancer Cell, Journal Year: 2023, Volume and Issue: 41(3), P. 404 - 420

Published: Feb. 16, 2023

Language: Английский

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Primary cilia as dynamic and diverse signalling hubs in development and disease

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(7), P. 421 - 441

Published: April 18, 2023

Language: Английский

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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

Nature Methods, Journal Year: 2023, Volume and Issue: 20(3), P. 363 - 374

Published: March 1, 2023

Language: Английский

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Unbiased spatial proteomics with single-cell resolution in tissues

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(12), P. 2335 - 2349

Published: June 1, 2022

Language: Английский

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Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics

Molecular & Cellular Proteomics, Journal Year: 2021, Volume and Issue: 20, P. 100138 - 100138

Published: Jan. 1, 2021

Recent advances in efficiency and ease of implementation have rekindled interest ion mobility spectrometry, a technique that separates gas phase ions by their size shape can be hybridized with conventional LC MS. Here, we review the recent development trapped spectrometry (TIMS) coupled to TOF mass analysis. In particular, parallel accumulation–serial fragmentation (PASEF) operation mode offers unique advantages terms sequencing speed sensitivity. Its defining feature is it synchronizes release from TIMS device downstream selection precursors for quadrupole configuration. As are compressed into narrow peaks, number peptide fragment spectra obtained data-dependent or targeted analyses increased an order magnitude without compromising Taking advantage correlation between mass, PASEF principle also multiplies data-independent acquisition. This makes technology well suited rapid proteome profiling, increasingly important attribute clinical proteomics, as ultrasensitive measurements down single cells. The accuracy enable precise collisional cross section values at scale more than million data points neural networks capable predicting them based only on sequences. Peptide differ isobaric sequences positional isomers post-translational modifications. additional information may leveraged real time direct acquisition postprocessing increase confidence identifications. These developments make powerful expandable platform proteomics beyond.

Language: Английский

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Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF

Molecular & Cellular Proteomics, Journal Year: 2022, Volume and Issue: 21(9), P. 100279 - 100279

Published: Aug. 6, 2022

Language: Английский

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Protein profile of fiber types in human skeletal muscle: a single-fiber proteomics study

Skeletal Muscle, Journal Year: 2021, Volume and Issue: 11(1)

Published: Nov. 2, 2021

Abstract Background Human skeletal muscle is composed of three major fiber types, referred to as type 1, 2A, and 2X fibers. This heterogeneous cellular composition complicates the interpretation studies based on whole lysate. A single-fiber proteomics approach required obtain a fiber-type resolved quantitative information pathophysiology. Methods Single fibers were dissected from vastus lateralis biopsies young adult males processed for mass spectrometry-based proteomics. We provide analyze resource dataset relatively pure fibers, containing at least 80% either MYH7 (marker slow 1 fibers), MYH2 fast 2A or MYH1 fibers). Results In more than 3800 proteins detected by proteomics, we selected 404 showing statistically significant difference among types. identified numerous type–specific protein markers, defined present 3-fold higher levels in these compared other contrast, could detect only two 2A-specific markers addition MYH2. observed patterns: differential distribution according sequence > 2–specific expressed 3 times greater precisely quantifying known patterns, our study revealed several novel features specificity, including selective enrichment components dystrophin integrin complexes, well microtubular proteins, The some was validated immunofluorescence analyses with specific antibodies. Conclusion here show that whose function unknown, are selectively enriched pointing potential implications reinforces notion together recently developed approaches single-cell will be instrumental explore quantify cell heterogeneity.

Language: Английский

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