Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new
disease biomarkers. However, certain critical steps of study design such as cohort selection …
disease biomarkers. However, certain critical steps of study design such as cohort selection …
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …
biology depend on obtaining consistent and quantitatively accurate proteomics data from …
Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation
Dietary fibres can exert beneficial anti-inflammatory effects through microbially fermented
short-chain fatty acid metabolites,, although the immunoregulatory roles of most fibre diets …
short-chain fatty acid metabolites,, although the immunoregulatory roles of most fibre diets …
Missing value imputation approach for mass spectrometry-based metabolomics data
Missing values exist widely in mass-spectrometry (MS) based metabolomics data. Various
methods have been applied for handling missing values, but the selection can significantly …
methods have been applied for handling missing values, but the selection can significantly …
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Quantitative proteomics employing mass spectrometry is an indispensable tool in life
science research. Targeted proteomics has emerged as a powerful approach for …
science research. Targeted proteomics has emerged as a powerful approach for …
Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver …
The data-independent acquisition (DIA) approach has recently been introduced as a novel
mass spectrometric method that promises to combine the high content aspect of shotgun …
mass spectrometric method that promises to combine the high content aspect of shotgun …
[HTML][HTML] A multi-network approach identifies protein-specific co-expression in asymptomatic and symptomatic Alzheimer's disease
Here, we report proteomic analyses of 129 human cortical tissues to define changes
associated with the asymptomatic and symptomatic stages of Alzheimer's disease (AD) …
associated with the asymptomatic and symptomatic stages of Alzheimer's disease (AD) …
Accounting for the multiple natures of missing values in label-free quantitative proteomics data sets to compare imputation strategies
Missing values are a genuine issue in label-free quantitative proteomics. Recent works have
surveyed the different statistical methods to conduct imputation and have compared them on …
surveyed the different statistical methods to conduct imputation and have compared them on …
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial
Advancements in mass spectrometry‐based proteomics have enabled experiments
encompassing hundreds of samples. While these large sample sets deliver much‐needed …
encompassing hundreds of samples. While these large sample sets deliver much‐needed …
A systematic evaluation of normalization methods in quantitative label-free proteomics
To date, mass spectrometry (MS) data remain inherently biased as a result of reasons
ranging from sample handling to differences caused by the instrumentation. Normalization is …
ranging from sample handling to differences caused by the instrumentation. Normalization is …