{
  "schema": "https://aptatlas.org/data/v4.6/scoring.schema.json",
  "name": "scoring",
  "title": "Scores",
  "version": "4.6",
  "last_updated": "2026-11-04",
  "licence": "CC-BY-4.0",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "citation": "Whelan CD, Smith-Byrne K. Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms. bioRxiv 2026. https://doi.org/10.64898/2026.09.10.750723",
  "archive_doi": "10.5281/zenodo.22697191",
  "third_party": [],
  "provenance": "Claude drafted the first scores, and the authors scored the platforms before opening that draft, then compared the two sets and adjudicated. Every score change, before and since release, was decided by Whelan and Smith-Byrne; Claude made edits only on their instruction. The prompt file generated in the same session as the draft also told the build to adjust scores so that platform totals fell between 28 and 33; the authors did not set this range or use platform totals when scoring or adjudicating.",
  "class_balance_provenance": "class_balance, a Help Me Combine axis, is not one of the ten scored dimensions. It is computed, not assigned: the normalised Shannon entropy of the target classes among the drug targets a pair covers, using nine ChEMBL/UniProt classes with Unclassified excluded, divided by ln(9). It is therefore derived from the ChEMBL drug-target list. The per-protein list is not published here, so the values can be checked but not regenerated from these files alone.",
  "lower_confidence": {
    "rule": "A platform with an evidence-depth score of 2 or lower has its other scores flagged as provisional. The flag never changes a score, ranking or recommendation.",
    "platforms": [
      "nomic-omni"
    ]
  },
  "data": {
    "dimensions": [
      {
        "id": "proteome_coverage",
        "label": "Proteome Coverage",
        "description": "Breadth of proteins measured",
        "shortLabel": "Coverage"
      },
      {
        "id": "precision",
        "label": "Precision",
        "description": "Reproducibility / CV",
        "shortLabel": "Precision"
      },
      {
        "id": "specificity",
        "label": "Specificity",
        "description": "Target confidence, cis-pQTL support, epitope risk",
        "shortLabel": "Specificity"
      },
      {
        "id": "sensitivity",
        "label": "Sensitivity",
        "description": "Ability to detect low-abundance proteins",
        "shortLabel": "Sensitivity"
      },
      {
        "id": "cost_efficiency",
        "label": "Cost per sample",
        "description": "Lower cost per sample = higher score",
        "shortLabel": "Cost"
      },
      {
        "id": "throughput",
        "label": "Throughput",
        "description": "Samples per day/week",
        "shortLabel": "Throughput"
      },
      {
        "id": "quantification_type",
        "label": "Quantification Type",
        "description": "Type of quantification: 4 = physical concentration (pg/mL); 3 = proteome-wide comparable label-free MS; 2 = within-assay relative units",
        "shortLabel": "Quant Type"
      },
      {
        "id": "sample_flexibility",
        "label": "Multi-Matrix Validation",
        "description": "Breadth of sample matrices with published validation (plasma, serum, CSF, tissue, cell lysate)",
        "shortLabel": "Multi-Matrix"
      },
      {
        "id": "evidence_depth",
        "label": "Evidence Depth",
        "description": "Published head-to-head data available",
        "shortLabel": "Evidence"
      },
      {
        "id": "pqtl_accuracy",
        "label": "pQTL Accuracy",
        "description": "Reliability for pQTL studies; lower epitope-binding artifact risk",
        "shortLabel": "pQTL"
      }
    ],
    "scores": {
      "olink-explore-ht": {
        "proteome_coverage": 4,
        "precision": 2,
        "specificity": 4,
        "sensitivity": 4,
        "cost_efficiency": 3,
        "throughput": 5,
        "quantification_type": 2,
        "sample_flexibility": 3,
        "evidence_depth": 5,
        "pqtl_accuracy": 3
      },
      "illumina-protein-prep": {
        "proteome_coverage": 5,
        "precision": 5,
        "specificity": 2,
        "sensitivity": 4,
        "cost_efficiency": 3,
        "throughput": 4,
        "quantification_type": 2,
        "sample_flexibility": 3,
        "evidence_depth": 5,
        "pqtl_accuracy": 2
      },
      "nulisa": {
        "proteome_coverage": 1,
        "precision": 5,
        "specificity": 4,
        "sensitivity": 5,
        "cost_efficiency": 4,
        "throughput": 3,
        "quantification_type": 2,
        "sample_flexibility": 3,
        "evidence_depth": 3,
        "pqtl_accuracy": 3
      },
      "nomic-omni": {
        "proteome_coverage": 2,
        "precision": 4,
        "specificity": 4,
        "sensitivity": 3,
        "cost_efficiency": 5,
        "throughput": 5,
        "quantification_type": 4,
        "sample_flexibility": 2,
        "evidence_depth": 1,
        "pqtl_accuracy": 3
      },
      "seer-proteograph": {
        "proteome_coverage": 5,
        "precision": 3,
        "specificity": 4,
        "sensitivity": 3,
        "cost_efficiency": 3,
        "throughput": 3,
        "quantification_type": 3,
        "sample_flexibility": 3,
        "evidence_depth": 4,
        "pqtl_accuracy": 5
      },
      "biognosys-truediscovery": {
        "proteome_coverage": 4,
        "precision": 3,
        "specificity": 4,
        "sensitivity": 3,
        "cost_efficiency": 3,
        "throughput": 3,
        "quantification_type": 3,
        "sample_flexibility": 5,
        "evidence_depth": 3,
        "pqtl_accuracy": 3
      }
    },
    "defaultWeights": {
      "proteome_coverage": 1,
      "precision": 1,
      "specificity": 1,
      "sensitivity": 1,
      "cost_efficiency": 1,
      "throughput": 1,
      "quantification_type": 1,
      "sample_flexibility": 1,
      "evidence_depth": 1,
      "pqtl_accuracy": 1
    }
  }
}