Unbiased spatial proteomics with single-cell resolution in tissues

A Mund, AD Brunner, M Mann - Molecular Cell, 2022 - cell.com
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify
the entire complement of proteins in cells or tissues. Here, we review challenges and recent …

Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

L Krasny, PH Huang - Molecular omics, 2021 - pubs.rsc.org
Data-independent acquisition mass spectrometry (DIA-MS) is a next generation proteomic
methodology that generates permanent digital proteome maps offering highly reproducible …

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

F Yu, GC Teo, AT Kong, K Fröhlich, GX Li… - Nature …, 2023 - nature.com
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

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

V Demichev, L Szyrwiel, F Yu, GC Teo… - Nature …, 2022 - nature.com
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 …

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

AD Brunner, M Thielert, C Vasilopoulou… - Molecular systems …, 2022 - embopress.org
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging
and deep sequencing. However, proteins are the main drivers of cellular function and in …

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

UH Guzman, A Martinez-Val, Z Ye, E Damoc… - Nature …, 2024 - nature.com
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes
in a fast and reproducible manner. Here we present the narrow-window data-independent …

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

C Ctortecka, NM Clark, BW Boyle, A Seth… - Nature …, 2024 - nature.com
The recent technological and computational advances in mass spectrometry-based single-
cell proteomics have pushed the boundaries of sensitivity and throughput. However …

Deep Visual Proteomics defines single-cell identity and heterogeneity

A Mund, F Coscia, A Kriston, R Hollandi… - Nature …, 2022 - nature.com
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial
proteomics, a key challenge remains connecting images with single-cell-resolution protein …

Evaluating the performance of the astral mass analyzer for quantitative proteomics using data-independent acquisition

LR Heil, E Damoc, TN Arrey, A Pashkova… - Journal of proteome …, 2023 - ACS Publications
We evaluate the quantitative performance of the newly released Asymmetric Track Lossless
(Astral) analyzer. Using data-independent acquisition, the Thermo Scientific Orbitrap Astral …

Design principles for cyclin K molecular glue degraders

Z Kozicka, DJ Suchyta, V Focht, G Kempf… - Nature chemical …, 2024 - nature.com
Molecular glue degraders are an effective therapeutic modality, but their design principles
are not well understood. Recently, several unexpectedly diverse compounds were reported …