{
  "experiment_id": "PXD000001",
  "pride_accession": "22134",
  "title": "TMT 6-plex Erwinia carotovora Spike-in Experiment",
  "description": "Quantitative proteomics experiment using TMT 6-plex with spike-in proteins at known ratios to validate quantification accuracy",
  "organism": {
    "name": "Erwinia carotovora",
    "ncbi_taxon": "554"
  },
  "quantification_method": "TMT 6-plex (Tandem Mass Tags)",
  "mass_spec_file": "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML",
  "reference_database": "erwinia_carotovora.fasta",
  "tmt_channels": {
    "126": {
      "sample_id": "sub1",
      "species": "Erwinia carotovora",
      "description": "Erwinia background with spike-ins at ratio position 1"
    },
    "127": {
      "sample_id": "sub2",
      "species": "Erwinia carotovora",
      "description": "Erwinia background with spike-ins at ratio position 2"
    },
    "128": {
      "sample_id": "sub3",
      "species": "Erwinia carotovora",
      "description": "Erwinia background with spike-ins at ratio position 3"
    },
    "129": {
      "sample_id": "sub4",
      "species": "Erwinia carotovora",
      "description": "Erwinia background with spike-ins at ratio position 4"
    },
    "130": {
      "sample_id": "sub5",
      "species": "Erwinia carotovora",
      "description": "Erwinia background with spike-ins at ratio position 5"
    },
    "131": {
      "sample_id": "sub6",
      "species": "Erwinia carotovora",
      "description": "Erwinia background with spike-ins at ratio position 6"
    }
  },
  "spike_in_proteins": {
    "erwinia_background": {
      "description": "Background Erwinia peptides",
      "expected_ratios": [1, 1, 1, 1, 1, 1],
      "channels": ["126", "127", "128", "129", "130", "131"]
    },
    "enolase": {
      "uniprot_id": "P00924",
      "name": "ENO1_YEAST",
      "species": "Saccharomyces cerevisiae (Yeast)",
      "expected_ratios": [10, 5, 2.5, 1, 2.5, 10],
      "channels": ["126", "127", "128", "129", "130", "131"]
    },
    "bsa": {
      "uniprot_id": "P02769",
      "name": "ALBU_BOVIN",
      "species": "Bos taurus (Bovine)",
      "expected_ratios": [1, 2.5, 5, 10, 5, 1],
      "channels": ["126", "127", "128", "129", "130", "131"]
    },
    "phosb": {
      "uniprot_id": "P00489",
      "name": "PYGM_RABIT",
      "species": "Oryctolagus cuniculus (Rabbit)",
      "expected_ratios": [2, 2, 2, 2, 1, 1],
      "channels": ["126", "127", "128", "129", "130", "131"]
    },
    "cytochrome_c": {
      "uniprot_id": "P62894",
      "name": "CYC_BOVIN",
      "species": "Bos taurus (Bovine)",
      "expected_ratios": [1, 1, 1, 1, 1, 2],
      "channels": ["126", "127", "128", "129", "130", "131"]
    }
  },
  "contacts": [
    {
      "name": "Laurent Gatto",
      "email": "lg390@cam.ac.uk",
      "affiliation": "Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge"
    },
    {
      "name": "Andy Christoforou",
      "email": "ac587@cam.ac.uk",
      "affiliation": "Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge"
    },
    {
      "name": "Kathryn S. Lilley",
      "email": "ksl23@cam.ac.uk",
      "affiliation": "Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge"
    }
  ],
  "notes": [
    "This is a spike-in validation experiment, not a biological comparison (e.g., Control vs. Fibrosis)",
    "All 6 TMT channels contain Erwinia carotovora background proteome",
    "Four spike-in proteins with known concentration ratios are mixed to validate quantification accuracy",
    "Expected ratios are relative abundances across the 6 TMT channels for each spike-in protein"
  ],
  "data_source": "PRIDE Archive - https://www.ebi.ac.uk/pride/archive/projects/PXD000001",
  "creation_date": "2025-12-13"
}