Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently
become technically feasible. While such analysis has the potential to accurately quantify …

A typical output of a metabolomic experiment is a peak table corresponding to the intensity
of measured signals. Peak table processing, an essential procedure in metabolomics, is …

Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

Current mass spectrometry methods enable high-throughput proteomics of large sample
amounts, but proteomics of low sample amounts remains limited in depth and throughput. To …

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 …

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics
data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves …

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

Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …

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 …

Vendor-independent software tools for quantification of small molecules and metabolites are
lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source …