Proteomic analysis articles from across Nature Portfolio

The origin and dispersal of the chicken across Eurasia is unclear. Here, the authors examine eggshell fragments from southern Central Asia with paleoproteomics to identify chicken eggshells, suggesting that chickens may have been an important dietary component as early as 400BCE.

Imaging mass cytometry (IMC) is a powerful single-cell resolution platform for targeted spatial proteomics, but it can be constrained by imaging noise and resolution. Here, the authors propose SpiDe-Sr, a super-resolution network embedded with a denoising module for IMC spatial resolution enhancement.

Deep interactome profiling by mass spectrometry (DIP-MS) combines affinity purification with native BN-PAGE fractionation and mass spectrometry to resolve protein complexes sharing the same target protein. The paper also presents PPIprophet, a data-driven neural network-based protein complex deconvolution approach.

In this issue of Nature Metabolism, it is shown that the abundance of Caenorhabditis elegans branched-chain aminotransferase-1 (BCAT-1) — which catalyses the first step of branched-chain amino acid (BCAA) catabolism — declines sharply in aged wild-type nematodes but not in slowly ageing mutants, and that stimulating BCAA catabolism extends reproductive longevity.

In a group interview, early-career researchers in proteomics share how they plan for the future and navigate divides over methods.

Interactions between RNA and RNA-binding proteins (RBPs) define the fate and function of every RNA molecule. We present TREX, or targeted RNase H-mediated extraction of crosslinked RBPs, an efficient and accurate method to unbiasedly reveal the protein interactors of specific regions of RNAs isolated from living cells.

We developed Tapioca, an integrative ensemble machine learning-based framework, to accurately predict global protein–protein interaction network dynamics. Tapioca enabled the characterization of host regulation during reactivation from latency of an oncogenic virus. Introducing an interactome homology analysis method, we identified a proviral host factor with broad relevance for herpesviruses.

A new mass analyzer enables protein identification at high speed and depth.