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 …

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 …

Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of
macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner …

Protein–protein interactions (PPIs) drive cellular processes and responses to environmental
cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning …

The complexity of the functional proteome extends considerably beyond the coding genome,
resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is …

Nuclear pore complexes (NPCs) are huge protein assemblies within the nuclear envelope
(NE) that serve as selective gates for macromolecular transport between nucleus and …

Proteomics has revealed that the~ 20,000 human genes engender a far greater number of
proteins, or proteoforms, that are diversified in large part by post-translational modifications …

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 …

We present CFdb, a harmonized resource of interaction proteomics data from 411 co-
fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis …

Despite the availability of methods for analyzing protein complexes, systematic analysis of
complexes under multiple conditions remains challenging. Approaches based on …