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 …

The crucial role of multiomic approach in cancer research and clinically relevant outcomes

M Lu, X Zhan - EPMA Journal, 2018 - Springer
Cancer with heavily economic and social burden is the hot point in the field of medical
research. Some remarkable achievements have been made; however, the exact …

Mll3 and Mll4 facilitate enhancer RNA synthesis and transcription from promoters independently of H3K4 monomethylation

KM Dorighi, T Swigut, T Henriques, NV Bhanu… - Molecular cell, 2017 - cell.com
Monomethylation of histone H3 at lysine 4 (H3K4me1) and acetylation of histone H3 at
lysine 27 (H3K27ac) are correlated with transcriptionally engaged enhancer elements, but …

Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment

JC Chan, CP Morgan, N Adrian Leu, A Shetty… - Nature …, 2020 - nature.com
Extracellular vesicles (EVs) are a unique mode of intercellular communication capable of
incredible specificity in transmitting signals involved in cellular function, including germ cell …

Advances in targeted proteomics and applications to biomedical research

T Shi, E Song, S Nie, KD Rodland, T Liu, WJ Qian… - …, 2016 - Wiley Online Library
Targeted proteomics technique has emerged as a powerful protein quantification tool in
systems biology, biomedical research, and increasing for clinical applications. The most …

SWATH‐MS as a tool for biomarker discovery: From basic research to clinical applications

SI Anjo, C Santa, B Manadas - Proteomics, 2017 - Wiley Online Library
In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in
particular associated with the use of data‐independent acquisition, it is time to perform an …

EpiProfile 2.0: a computational platform for processing epi-proteomics mass spectrometry data

ZF Yuan, S Sidoli, DM Marchione… - Journal of proteome …, 2018 - ACS Publications
Epigenetics has become a fundamental scientific discipline with various implications for
biology and medicine. Epigenetic marks, mostly DNA methylation and histone post …

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

JG Meyer, B Schilling - Expert review of proteomics, 2017 - Taylor & Francis
Introduction: While selected/multiple-reaction monitoring (SRM or MRM) is considered the
gold standard for quantitative protein measurement, emerging data-independent acquisition …

Enzymatic transfer of acetate on histones from lysine reservoir sites to lysine activating sites

M Mendoza, G Egervari, S Sidoli, G Donahue… - Science …, 2022 - science.org
Histone acetylation is governed by nuclear acetyl-CoA pools generated, in part, from local
acetate by metabolic enzyme acetyl-CoA synthetase 2 (ACSS2). We hypothesize that during …

Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription

G Jih, N Iglesias, MA Currie, NV Bhanu, JA Paulo… - Nature, 2017 - nature.com
Heterochromatic DNA domains have important roles in the regulation of gene expression
and maintenance of genome stability by silencing repetitive DNA elements and transposons …