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 …

Multi-omics approaches to disease

Y Hasin, M Seldin, A Lusis - Genome biology, 2017 - Springer
High-throughput technologies have revolutionized medical research. The advent of
genoty** arrays enabled large-scale genome-wide association studies and methods for …

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 …

On the dependency of cellular protein levels on mRNA abundance

Y Liu, A Beyer, R Aebersold - Cell, 2016 - cell.com
The question of how genomic information is expressed to determine phenotypes is of central
importance for basic and translational life science research and has been studied by …

[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 - Elsevier
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 …

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 …

Recent advances in metabolic engineering of Saccharomyces cerevisiae: new tools and their applications

J Lian, S Mishra, H Zhao - Metabolic engineering, 2018 - Elsevier
Metabolic engineering aims to develop efficient cell factories by rewiring cellular
metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae …

MSstats version 4.0: statistical analyses of quantitative mass spectrometry-based proteomic experiments with chromatography-based quantification at scale

D Kohler, M Staniak, TH Tsai, T Huang… - Journal of Proteome …, 2023 - ACS Publications
The MSstats R-Bioconductor family of packages is widely used for statistical analyses of
quantitative bottom-up mass spectrometry-based proteomic experiments to detect …

Quantitative proteomics: challenges and opportunities in basic and applied research

OT Schubert, HL Röst, BC Collins, G Rosenberger… - Nature protocols, 2017 - nature.com
In this Perspective, we discuss developments in mass-spectrometry-based proteomic
technology over the past decade from the viewpoint of our laboratory. We also reflect on …

Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing

LC Gillet, A Leitner, R Aebersold - Annual review of analytical …, 2016 - annualreviews.org
Proteins constitute a key class of molecular components that perform essential biochemical
reactions in living cells. Whether the aim is to extensively characterize a given protein or to …