Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

C Ludwig, L Gillet, G Rosenberger, S Amon… - Molecular systems …, 2018 - embopress.org
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

Protein phosphorylation: a major switch mechanism for metabolic regulation

SJ Humphrey, DE James, M Mann - Trends in Endocrinology & Metabolism, 2015 - cell.com
Metabolism research is undergoing a renaissance because many diseases are increasingly
recognized as being characterized by perturbations in intracellular metabolic regulation …

[HTML][HTML] 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 …

[HTML][HTML] Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results

R Bruderer, OM Bernhardt, T Gandhi, Y Xuan… - Molecular & Cellular …, 2017 - ASBMB
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key
objectives of quantitative proteomics. Here, we present an implementation of data …

Illuminating the dark phosphoproteome

EJ Needham, BL Parker, T Burykin, DE James… - Science …, 2019 - science.org
Protein phosphorylation is a major regulator of protein function and biological outcomes.
This was first recognized through functional biochemical experiments, and in the past …

[HTML][HTML] Phosphoproteomics in the age of rapid and deep proteome profiling

NM Riley, JJ Coon - Analytical chemistry, 2016 - ACS Publications
Protein phosphorylation is a post-translational modification (PTM) that orchestrates a diverse
array of cellular processes. Because this modification serves as a rapid and reversible …

mTORC1 directly inhibits AMPK to promote cell proliferation under nutrient stress

NXY Ling, A Kaczmarek, A Hoque, E Davie… - Nature …, 2020 - nature.com
Highly conserved signalling pathways controlled by mammalian target of rapamycin (mTOR)
and AMP-activated protein kinase (AMPK) are central to cellular metabolism and cell …

Cytochrome c phosphorylation: Control of mitochondrial electron transport chain flux and apoptosis

HA Kalpage, J Wan, PT Morse, MP Zurek… - The international journal …, 2020 - Elsevier
Cytochrome c (Cytc) 1 is a cellular life and death decision molecule that regulates cellular
energy supply and apoptosis through tissue specific post-translational modifications. Cytc is …

[HTML][HTML] 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 …

[HTML][HTML] A multipathway phosphopeptide standard for rapid phosphoproteomics assay development

BC Searle, A Chien, A Koller, D Hawke… - Molecular & Cellular …, 2023 - ASBMB
Recent advances in methodology have made phosphopeptide analysis a tractable problem
for many proteomics researchers. There are now a wide variety of robust and accessible …