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

HM Bennett, W Stephenson, CM Rose, S Darmanis - Nature Methods, 2023 - nature.com
In the last decade, single-cell RNA sequencing routinely performed on large numbers of
single cells has greatly advanced our understanding of the underlying heterogeneity of …

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

L Gatto, R Aebersold, J Cox, V Demichev, J Derks… - Nature …, 2023 - nature.com
Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently
become technically feasible. While such analysis has the potential to accurately quantify …

Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition

V Petrosius, P Aragon-Fernandez, N Üresin… - Nature …, 2023 - nature.com
Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-
state heterogeneity and distinct cellular signaling patterns that remain obscured with …

Top-down proteomics

DS Roberts, JA Loo, YO Tsybin, X Liu, S Wu… - Nature Reviews …, 2024 - nature.com
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and
RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is …

scPROTEIN: a versatile deep graph contrastive learning framework for single-cell proteomics embedding

W Li, F Yang, F Wang, Y Rong, L Liu, B Wu, H Zhang… - Nature …, 2024 - nature.com
Single-cell proteomics sequencing technology sheds light on protein–protein interactions,
posttranslational modifications and proteoform dynamics in the cell. However, the …

[HTML][HTML] An automated nanowell-array workflow for quantitative multiplexed single-cell proteomics sample preparation at high sensitivity

C Ctortecka, D Hartlmayr, A Seth, S Mendjan… - Molecular & Cellular …, 2023 - Elsevier
Multiplexed and label-free mass spectrometry–based approaches with single-cell resolution
have attributed surprising heterogeneity to presumed homogenous cell populations. Even …

Exploring functional protein covariation across single cells using nPOP

A Leduc, RG Huffman, J Cantlon, S Khan, N Slavov - Genome Biology, 2022 - Springer
Background Many biological processes, such as cell division cycle and drug resistance, are
reflected in protein covariation across single cells. This covariation can be quantified and …

Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell

Y Wang, ZY Guan, SW Shi, YR Jiang, J Zhang… - Nature …, 2024 - nature.com
The shotgun proteomic analysis is currently the most promising single-cell protein
sequencing technology, however its identification level of~ 1000 proteins per cell is still …

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

R Ahmad, B Budnik - Analytical and Bioanalytical Chemistry, 2023 - Springer
Single-cell methodologies and technologies have started a revolution in biology which until
recently has primarily been limited to deep sequencing and imaging modalities. With the …

[HTML][HTML] Recent advances in the field of single-cell proteomics

V Petrosius, EM Schoof - Translational oncology, 2023 - Elsevier
The field of single-cell omics is rapidly progressing. Although DNA and RNA sequencing-
based methods have dominated the field to date, global proteome profiling has also entered …