We present a concise workflow to enhance the mass spectrometric detection of crosslinked peptides by introducing sequential digestion and the crosslink identification software xiSEARCH. Sequential digestion enhances peptide detection by selective shortening of long tryptic peptides. We demonstrate our simple 12‐fraction protocol for crosslinked multi‐protein complexes and cell lysates, quantitative analysis, and high‐density crosslinking, without requiring specific crosslinker features. This overall approach reveals dynamic protein–protein interaction sites, which are accessible, have fundamental functional relevance and are therefore ideally suited for the development of small molecule inhibitors.

This paper summarises the state-of-the-art in multiple tree visualisations. It discusses the spectrum of current representation techniques used on single trees, pairs of trees and finally multiple trees, in order to identify which representations are best suited to particular tasks and to find gaps in the representation space where opportunities for future multiple tree visualisation research may exist. The application areas from where multiple tree data are derived are enumerated, and the distinct structures that multiple trees make in combination with each other and the effect on subsequent approaches to their visualisation are discussed, along with the basic high-level goals of existing multiple tree visualisations.

xiView provides a common platform for the downstream analysis and visualisation of Crosslinking Mass Spectrometry data. It is independent of the search software used and its input is compliant with the relevant mass spectrometry data standards. It uses established visualisation techniques, notably Multiple Coordinated Views, to help the user explore the data and is designed to facilitate comparisons between different datasets.