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Five PAD datasets show 0 proteins on PRIDE because proteins-above-lod returned an empty list. Causes, from the deposited files: - Olink exports with both LODNPX and LOD (count-based) were compared with LOD: no NPX ever exceeded it (PAD000037). The reader now uses LODNPX. - hand-rearranged NPX files with shifted columns put text in NPX/LOD and the LOD comparison raised (PAD000024). NPX/LOD/LODNPX are coerced to numbers; broken rows become NaN. - table-only ADATs without ^HEADER/^COL_DATA markers were rejected (PAD000045 v4.0 file). They are parsed as a TABLE_BEGIN body. - SomaScan ADATs with study samples only (no buffers) have no LOD source (PAD000003, PAD000011, PAD000045 1.3k file). All measured protein reagents (Type == "Protein") are returned with a warning; Olink without any LOD still returns none. Counting also now uses the report's LOD resolver (moved to processing.lod.resolve_lod_with_source; SomaScan uses eLOD, not NCLOD on buffers) and only study samples, so controls below LOD no longer lower the per-assay share (PAD000002 1858 -> 1943, PAD000004 149 -> 186).
Fix zero protein counts on PRIDE (proteins-above-lod)
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