The Human Proteomic Perturbation Atlas (PPA) is an NCEMS initiative designed to transform thousands of publicly available human proteomics studies into a standardized, harmonized, and reusable resource for large-scale analysis. A initial and major component of the PPA is metadata harmonization with the Hybrid Agentic Metadata Literature Extraction and Technical (HAMLET) annotator, an NCEMS-developed tool that uses LLM-assisted extraction to recover detailed experimental and sample metadata from PRIDE records and their associated publications. Furthermore a new ontology which organizes treatments, experimental conditions, and sample characteristics into hierarchical broad, coarse-grained, and fine-grained categories was developed for public proteomics datasets. By converting heterogeneous and inconsistently reported study metadata into a common structured framework, the Human PPA makes it substantially more feasible to systematically reprocess, quantify, and compare large numbers of proteomics datasets using standardized workflows. The resulting atlas links harmonized experimental metadata with consistently processed quantitative proteomics data, enabling cross-study analyses of shared and context-specific proteome responses, integration of measurements reporting on protein abundance and conformational changes, and machine-learning applications that require aligned quantitative matrices and standardized experimental annotations.