Protein analysis articles from across Nature Portfolio

Data-independent acquisition mass spectrometry (DIA-MS) has emerged as a key technology in quantitative proteomics. Here, the authors introduce DIA-BERT, a transformer model pre-trained on existing DIA datasets to enhance peptide identification and quantification.

Microbes within the gut vary in how they encode genes, both in terms of the genetic codes and gene structures, which are often unexplored in metagenomic analysis. Here, the authors develop a lineage-specific gene approach that optimizes prediction of small proteins and apply it to 9,634 metagenomes and 3,594 genomes from the human gut, increasing the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups.

Using protein covariation network analysis, this study uncovers the mechanism of action for AX-53802, a new ferroptosis inducer, validating GPX4 as its direct target, and proposes combination therapies targeting FAK/Src to enhance cancer cell death.

In structural bioinformatics, predicting protein similarity and function is critical. Here, authors introduce a fast approach using protein energy profiles for efficient comparison, revealing insights into protein relationships and enabling fast predictions with reduced computational cost.

A phylogenetic approach for detecting coevolving pairs via maximum parsimony-based ancestral reconstruction followed by regression analysis of separate and concurrent changes.

In honor of the 100th birthday of Margaret Dayhoff, we spotlight her footprint in the field of bioinformatics.

This Genome Watch discusses strategies to detect small open reading frames and study microproteins encoded in microbiomes to understand their diversity and functions across microorganisms.

To handle increasingly large protein databases, a new ultrafast, highly sensitive method — Dense Homolog Retriever (DHR) — detects remote homologs using dense retrieval and protein language models. Its alignment-free nature makes it much faster than traditional approaches, and the newly found remote homologs benefit our understanding of protein evolution, structure and function.

This Genome Watch highlights how a tailor-made search through bacterial genomes revealed the widespread presence of a new class of bacterial signalling peptides that lack conventional characteristics.

This study reveals that the production of cobalamin and succinyl-CoA is increased in the anal microbiome of patients with precancerous anal lesions. Testing for these two metabolites significantly improves diagnostic accuracy over standard cytology screening, which suggests potential for enhanced screening strategies for anal cancer.