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 …

Data‐independent acquisition mass spectrometry‐based proteomics and software tools: a glimpse in 2020

F Zhang, W Ge, G Ruan, X Cai, T Guo - Proteomics, 2020 - Wiley Online Library
This review provides a brief overview of the development of data‐independent acquisition
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

F Meier, AD Brunner, M Frank, A Ha, I Bludau… - Nature …, 2020 - nature.com
Data-independent acquisition modes isolate and concurrently fragment populations of
different precursors by cycling through segments of a predefined precursor m/z range …

The autoimmune signature of hyperinflammatory multisystem inflammatory syndrome in children

RA Porritt, A Binek, L Paschold… - The Journal of …, 2021 - Am Soc Clin Investig
Multisystem inflammatory syndrome in children (MIS-C) manifests as a severe and
uncontrolled inflammatory response with multiorgan involvement, occurring weeks after …

[HTML][HTML] Longitudinal multi-omics of host–microbe dynamics in prediabetes

W Zhou, MR Sailani, K Contrepois, Y Zhou, S Ahadi… - Nature, 2019 - nature.com
Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early
disease stages, its effects on biological processes or the transition to clinical T2D. To …

Molecular choreography of acute exercise

K Contrepois, S Wu, KJ Moneghetti, D Hornburg… - Cell, 2020 - cell.com
Acute physical activity leads to several changes in metabolic, cardiovascular, and immune
pathways. Although studies have examined selected changes in these pathways, the system …

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

BC Searle, LK Pino, JD Egertson, YS Ting… - Nature …, 2018 - nature.com
Data independent acquisition (DIA) mass spectrometry is a powerful technique that is
improving the reproducibility and throughput of proteomics studies. Here, we introduce an …

Advances in data‐independent acquisition mass spectrometry towards comprehensive digital proteome landscape

RB Kitata, JC Yang, YJ Chen - Mass spectrometry reviews, 2023 - Wiley Online Library
The data‐independent acquisition mass spectrometry (DIA‐MS) has rapidly evolved as a
powerful alternative for highly reproducible proteome profiling with a unique strength of …

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Y Liu, Y Mi, T Mueller, S Kreibich, EG Williams… - Nature …, 2019 - nature.com
Reproducibility in research can be compromised by both biological and technical variation,
but most of the focus is on removing the latter. Here we investigate the effects of biological …

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

BC Collins, CL Hunter, Y Liu, B Schilling… - Nature …, 2017 - nature.com
Quantitative proteomics employing mass spectrometry is an indispensable tool in life
science research. Targeted proteomics has emerged as a powerful approach for …