Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

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 …

We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural
networks and new quantification and signal correction strategies for the processing of data …

Quantitative proteomics employing mass spectrometry is an indispensable tool in life
science research. Targeted proteomics has emerged as a powerful approach for …

Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS
spectra from screening small molecules in fields such as environmental analysis, drug …

Numerous software tools exist for data-independent acquisition (DIA) analysis of clinical
samples, necessitating their comprehensive benchmarking. We present a benchmark …

Reproducible research is the bedrock of experimental science. To enable the deployment of
large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time …

Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the main
method for high-throughput identification and quantification of peptides and inferred …

Targeted proteomics technique has emerged as a powerful protein quantification tool in
systems biology, biomedical research, and increasing for clinical applications. The most …

Currently data-dependent acquisition (DDA) is the method of choice for mass spectrometry-
based proteomics discovery experiments, but data-independent acquisition (DIA) is steadily …