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 (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 …

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 …

A pragmatic guide to enrichment strategies for mass spectrometry–based glycoproteomics

NM Riley, CR Bertozzi, SJ Pitteri - Molecular & Cellular Proteomics, 2021 - ASBMB
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of
implications in molecular biology. This heterogeneity precludes enrichment strategies that …

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

CC Tsou, D Avtonomov, B Larsen, M Tucholska… - Nature …, 2015 - nature.com
As a result of recent improvements in mass spectrometry (MS), there is increased interest in
data-independent acquisition (DIA) strategies in which all peptides are systematically …

Quantitative variability of 342 plasma proteins in a human twin population

Y Liu, A Buil, BC Collins, LCJ Gillet… - Molecular systems …, 2015 - embopress.org
The degree and the origins of quantitative variability of most human plasma proteins are
largely unknown. Because the twin study design provides a natural opportunity to estimate …

Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics

MEH White, LR Sinn, DM Jones, J de Folter… - Nature Biomedical …, 2024 - nature.com
Protein glycosylation, a complex and heterogeneous post-translational modification that is
frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a …

Chemical glycoproteomics

KK Palaniappan, CR Bertozzi - Chemical reviews, 2016 - ACS Publications
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers
to studying protein glycosylation, the most widespread and complex form of posttranslational …

Advances in mass spectrometry-based clinical biomarker discovery

CA Crutchfield, SN Thomas, LJ Sokoll, DW Chan - Clinical proteomics, 2016 - Springer
The greatest unmet needs in biomarker discovery are those discoveries that lead to the
development of clinical diagnostic tests. These clinical diagnostic tests can provide early …

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 …