MIAO: data and analysis resources accompanying the manuscript

The dataset includes the Human intORF Atlas catalogue and catalogue-level Benjamini–Yekutieli analysis; 105 sample-level Dirichlet–multinomial result tables from six GEO series; the nine-method spike-in benchmark and H1 replicate reproducibility analyses; GSE131650 iPSC–cardiomyocyte RNA-seq counts, DESeq2 scripts and results; pancreatic HLA-I immunopeptidomics reanalysis; exact random-library generation materials and core native results for the Atlas and 100 matched random libraries; figure Source Data; and Fig. 6 integration and confidence-interval scripts.The 9,921 exact-candidate search union is distinct from the supported catalogue of 1,762 isoforms and 1,684 families.

The core 101-search archive contains 1,515 matched sample-level PSM and peptide table pairs, with selected large or regenerable intermediates intentionally excluded. Supplementary Tables 3–8 are designated for submission with the manuscript and are not duplicated here. The archive comprises 21 data/provenance packages plus README.md, MANIFEST.json and SHA256SUMS.txt (24 files; approximately 24.681 GB).