Carotid plaque rupture is a major cause of ischemic stroke, yet routine clinical indicators cannot accurately judge plaque rupture risk. Fibrous cap thickness is the core morphological marker for plaque vulnerability: thin-cap plaques (TnC, <200 μm) carry high rupture risk, while thick-cap plaques (TkC, ≥200 μm) remain stable. This work applied spatial proteomics to resolve subregional molecular differences between two plaque phenotypes, and identified PCSK9 as a critical local driver of plaque instability.

This work addresses three common limitations of existing de novo peptide sequencing algorithms and builds an AI model paired with a cloud computing platform to lower operation barriers for proteomics researchers.

Based on data-independent acquisition mass spectrometry analysis of more than 13,000 proteins across 2,856 samples, the work charts protein distributions across 58 major tissue types, 251 tissue subtypes and 25 carcinoma types.

Given the close interplay between microbiome, human proteome, host physiology and disease mechanisms, this comprehensive summary addresses long-standing statistical bottlenecks in microbiome cohort studies and delivers actionable guidance for large-scale omics research.