Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

A Martínez-Val, K Fort, C Koenig… - Nature …, 2023 - nature.com
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-
based phosphoproteomics for signaling pathway reconstitution is challenging, especially …

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

DB Bekker-Jensen, OM Bernhardt, A Hogrebe… - Nature …, 2020 - nature.com
Quantitative phosphoproteomics has transformed investigations of cell signaling, but it
remains challenging to scale the technology for high-throughput analyses. Here we report a …

A data-independent acquisition-based global phosphoproteomics system enables deep profiling

RB Kitata, WK Choong, CF Tsai, PY Lin… - Nature …, 2021 - nature.com
Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep
and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here …

Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry

RT Lawrence, BC Searle, A Llovet, J Villén - Nature methods, 2016 - nature.com
Systematic approaches to studying cellular signaling require phosphoproteomic techniques
that reproducibly measure the same phosphopeptides across multiple replicates, conditions …

Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced …

JG Abelin, J Patel, X Lu, CM Feeney, L Fagbami… - Molecular & Cellular …, 2016 - ASBMB
Profiling post-translational modifications represents an alternative dimension to gene
expression data in characterizing cellular processes. Many cellular responses to drugs are …

Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics

P Bortel, I Piga, C Koenig, C Gerner… - Molecular & Cellular …, 2024 - ASBMB
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics
analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from …

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

CF Tsai, YT Wang, CC Hsu, RB Kitata, RK Chu… - Communications …, 2023 - nature.com
Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily
due to significant sample loss associated with non-specific surface adsorption during …

Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal …

EL de Graaf, P Giansanti, AFM Altelaar… - Molecular & Cellular …, 2014 - ASBMB
Quantitative phosphoproteomics workflows traditionally involve additional sample labeling
and fractionation steps for accurate and in-depth analysis. Here we report a high-throughput …

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

SJ Humphrey, O Karayel, DE James, M Mann - Nature protocols, 2018 - nature.com
Mass spectrometry has transformed the field of cell signaling by enabling global studies of
dynamic protein phosphorylation ('phosphoproteomics'). Recent developments are enabling …

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 …