website/src/data/ms_protocols.json

{
  "_note": "MS acquisition protocol per source paper (hcode), PDF-verified 2026-07-12. Used for condition-aware model ranking (species -> enzyme -> protocol). Vocabulary: nano-LC-MS/MS, UPLC-MS/MS, LC-MS/MS, HPLC-MS/MS, MALDI-TOF/TOF, other.",
  "protocol_vocabulary": ["nano-LC-MS/MS", "UPLC-MS/MS", "LC-MS/MS", "HPLC-MS/MS", "MALDI-TOF/TOF", "other"],
  "by_hcode": {
    "H2":  {"protocol": "UPLC-MS/MS",     "instrument": "Q Exactive Plus (Orbitrap)",  "mode": "DDA"},
    "H3":  {"protocol": "nano-LC-MS/MS",  "instrument": "Orbitrap Elite",               "mode": "DDA"},
    "H4":  {"protocol": "nano-LC-MS/MS",  "instrument": "Q Exactive HF",                "mode": "DDA"},
    "H5":  {"protocol": "nano-LC-MS/MS",  "instrument": "Q Exactive HF",                "mode": "DDA"},
    "H6":  {"protocol": "LC-MS/MS",       "instrument": "Q Exactive (analytical UHPLC)","mode": "not stated"},
    "H7":  {"protocol": "nano-LC-MS/MS",  "instrument": "Orbitrap Fusion Lumos",        "mode": "DDA"},
    "H8":  {"protocol": "nano-LC-MS/MS",  "instrument": "Orbitrap Elite",               "mode": "DDA"},
    "H9":  {"protocol": "nano-LC-MS/MS",  "instrument": "Orbitrap Fusion",              "mode": "not stated"},
    "H11": {"protocol": "UPLC-MS/MS",     "instrument": "Q Exactive",                   "mode": "DDA"}
  }
}