To a large extent functional diversity in cells is achieved by the expansion of molecular
complexity beyond that of the coding genome. Various processes create multiple distinct but …

The ability of living systems to adapt to changing conditions originates from their capacity to
change their molecular constitution. This is achieved by multiple mechanisms that modulate …

Reproducibility in research can be compromised by both biological and technical variation,
but most of the focus is on removing the latter. Here we investigate the effects of biological …

Data-independent acquisition modes isolate and concurrently fragment populations of different
precursors by cycling through segments of a predefined precursor m/z range. Although …

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

Integrating experimental information across proteomic datasets with the wealth of publicly
available sequence annotations is a crucial part in many proteomic studies that currently lacks …

Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention time…

Single‐cell proteomics aims to characterize biological function and heterogeneity at the
level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, …

Proteins are major effectors and regulators of biological processes that can elicit multiple
functions depending on their interaction with other proteins. The organization of proteins into …

Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies
employing antibodies targeting ubiquitin-derived diGly remnants combined with mass …