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"stages": [
{
"sheet": "1. Raw Material",
"title": "STAGE 1 \u2014 Raw-material candidate characterization",
"nFields": 23,
"nMinimum": 10,
"nIdeal": 13,
"fields": [
{
"id": "RM-01",
"name": "raw_material_id",
"subsection": "Identity & sourcing",
"description": "Unique identifier for the raw-material sample; primary key linking to downstream tables.",
"tier": "Minimum",
"example": "RM_001"
},
{
"id": "RM-02",
"name": "organism_species",
"subsection": "Identity & sourcing",
"description": "Source organism (scientific name) the material is derived from.",
"tier": "Minimum",
"example": "<genus species>"
},
{
"id": "RM-03",
"name": "organism_ncbi_taxid",
"subsection": "Identity & sourcing",
"description": "NCBI Taxonomy identifier for the source organism (machine-readable).",
"tier": "Ideal",
"example": "7370"
},
{
"id": "RM-04",
"name": "tissue_or_fraction",
"subsection": "Identity & sourcing",
"description": "Specific tissue / anatomical fraction of the organism extracted.",
"tier": "Minimum",
"example": "whole body"
},
{
"id": "RM-05",
"name": "supplier",
"subsection": "Identity & sourcing",
"description": "Supplier / vendor of the raw material.",
"tier": "Minimum",
"example": "<supplier>"
},
{
"id": "RM-06",
"name": "batch_lot_id",
"subsection": "Identity & sourcing",
"description": "Supplier batch / lot number for traceability across process batches.",
"tier": "Minimum",
"example": "LOT-2024-08"
},
{
"id": "RM-07",
"name": "material_form",
"subsection": "Pretreatment",
"description": "Form of the input material (governs baseline protein concentration).",
"tier": "Minimum",
"example": "isolate"
},
{
"id": "RM-08",
"name": "defatting_method",
"subsection": "Pretreatment",
"description": "Defatting / lipid-removal method and conditions, if applied.",
"tier": "Ideal",
"example": "hexane extraction"
},
{
"id": "RM-09",
"name": "thermal_pretreatment",
"subsection": "Pretreatment",
"description": "Thermal denaturation / cooking step and conditions, if applied.",
"tier": "Ideal",
"example": "90 \u00b0C, 10 min"
},
{
"id": "RM-10",
"name": "other_pretreatment",
"subsection": "Pretreatment",
"description": "Any additional upstream pretreatment steps (e.g. pH shift, milling).",
"tier": "Ideal",
"example": "pH shift"
},
{
"id": "RM-11",
"name": "total_protein_content",
"subsection": "Composition & abundance",
"description": "Total protein content; reference value for the sample.",
"tier": "Minimum",
"example": "62.4"
},
{
"id": "RM-12",
"name": "total_protein_method",
"subsection": "Composition & abundance",
"description": "Method used for total-protein quantification (AA analysis is the reference method).",
"tier": "Minimum",
"example": "AA analysis"
},
{
"id": "RM-13",
"name": "aa_composition",
"subsection": "Composition & abundance",
"description": "Amino-acid composition profile of the raw material.",
"tier": "Minimum",
"example": "per-AA table"
},
{
"id": "RM-14",
"name": "reference_proteome_available",
"subsection": "Composition & abundance",
"description": "Whether a well-annotated reference proteome exists for the species (gates value of LC-MS/MS abundance data).",
"tier": "Minimum",
"example": "TRUE"
},
{
"id": "RM-15",
"name": "reference_proteome_source",
"subsection": "Composition & abundance",
"description": "Source and version of the reference proteome used.",
"tier": "Ideal",
"example": "UP0000XXXXX, 2024_03"
},
{
"id": "RM-16",
"name": "protein_abundance_profile",
"subsection": "Composition & abundance",
"description": "Relative protein abundance prior to hydrolysis (quantitative bottom-up proteomics).",
"tier": "Ideal",
"example": "per-protein table"
},
{
"id": "RM-17",
"name": "abundance_weighted_aa",
"subsection": "Composition & abundance",
"description": "Abundance-weighted AA composition derived from the proteomics profile; cross-check against AA analysis.",
"tier": "Ideal",
"example": "derived"
},
{
"id": "RM-18",
"name": "abundance_deposit_id",
"subsection": "Composition & abundance",
"description": "Identifier of the deposited abundance dataset in a tissue/organism abundance meta-resource (e.g. PaxDB).",
"tier": "Ideal",
"example": "see Reference Resources"
},
{
"id": "RM-19",
"name": "proxy_quant_method",
"subsection": "Composition & abundance",
"description": "Cheaper proxy protein-quant method, correlated to AA analysis, for routine QA/QC.",
"tier": "Ideal",
"example": "Dumas"
},
{
"id": "RM-20",
"name": "proxy_quant_value",
"subsection": "Composition & abundance",
"description": "Value returned by the proxy quantification method.",
"tier": "Ideal",
"example": "60.1"
},
{
"id": "RM-21",
"name": "nir_spectrum",
"subsection": "Composition & abundance",
"description": "NIR spectrum for rapid/affordable QA/QC; can be matched to AA composition via PLS modelling.",
"tier": "Ideal",
"example": "spectrum file"
},
{
"id": "RM-22",
"name": "expected_contaminants",
"subsection": "Contaminants",
"description": "Contaminant proteins/compounds expected for this material and planned for filtering.",
"tier": "Ideal",
"example": "keratin; trypsin"
},
{
"id": "RM-23",
"name": "contaminant_library_ref",
"subsection": "Contaminants",
"description": "Reference contaminant library used in the proteomics workflow.",
"tier": "Ideal",
"example": "cRAP (see References)"
}
]
},
{
"sheet": "2. Hydrolysis Process",
"title": "STAGE 2 \u2014 Hydrolysis process characterization",
"nFields": 41,
"nMinimum": 17,
"nIdeal": 24,
"fields": [
{
"id": "HP-01",
"name": "hydrolysate_id",
"subsection": "Identity & linkage",
"description": "Unique identifier for the hydrolysate batch; primary key for this stage.",
"tier": "Minimum",
"example": "PH_001"
},
{
"id": "HP-02",
"name": "source_raw_material_id",
"subsection": "Identity & linkage",
"description": "Foreign key to the raw-material sample used as substrate.",
"tier": "Minimum",
"example": "RM_001"
},
{
"id": "HP-03",
"name": "enzyme_name",
"subsection": "Enzymes",
"description": "Common / commercial name of each enzyme used.",
"tier": "Minimum",
"example": "Alcalase 2.4L"
},
{
"id": "HP-04",
"name": "enzyme_sequence",
"subsection": "Enzymes",
"description": "Amino-acid sequence of the enzyme (enables cleavage modelling).",
"tier": "Ideal",
"example": "MK..."
},
{
"id": "HP-05",
"name": "enzyme_uniprot",
"subsection": "Enzymes",
"description": "UniProt accession of the enzyme, if applicable.",
"tier": "Ideal",
"example": "P00780"
},
{
"id": "HP-06",
"name": "enzyme_grade",
"subsection": "Enzymes",
"description": "Whether the enzyme is purified or technical grade.",
"tier": "Minimum",
"example": "technical"
},
{
"id": "HP-07",
"name": "enzyme_primary_activity",
"subsection": "Enzymes",
"description": "Primary catalytic activity and associated cleavage tendencies, if known.",
"tier": "Ideal",
"example": "endopeptidase, broad specificity"
},
{
"id": "HP-08",
"name": "enzyme_secondary_activity",
"subsection": "Enzymes",
"description": "Known secondary activities (important for mixtures / technical grades).",
"tier": "Ideal",
"example": "high exopeptidase activity"
},
{
"id": "HP-09",
"name": "enzyme_application_mode",
"subsection": "Enzymes",
"description": "For multiple enzymes, whether they were applied sequentially or simultaneously.",
"tier": "Minimum",
"example": "sequential"
},
{
"id": "HP-10",
"name": "buffer_composition",
"subsection": "Reaction conditions",
"description": "Aqueous buffer composition.",
"tier": "Minimum",
"example": "50 mM Tris-HCl"
},
{
"id": "HP-11",
"name": "substrate_concentration",
"subsection": "Reaction conditions",
"description": "Concentration of substrate dissolved in the buffer.",
"tier": "Minimum",
"example": "5"
},
{
"id": "HP-12",
"name": "es_ratio_mass",
"subsection": "Reaction conditions",
"description": "Enzyme-to-substrate ratio on a protein basis.",
"tier": "Minimum",
"example": "2"
},
{
"id": "HP-13",
"name": "es_ratio_activity",
"subsection": "Reaction conditions",
"description": "Enzyme-to-substrate ratio on an activity:mass basis.",
"tier": "Ideal",
"example": "50"
},
{
"id": "HP-14",
"name": "activity_assay",
"subsection": "Reaction conditions",
"description": "Activity assay basis used to express the activity:mass ratio.",
"tier": "Ideal",
"example": "AU/g (Anson)"
},
{
"id": "HP-15",
"name": "temperature",
"subsection": "Reaction conditions",
"description": "Reaction temperature.",
"tier": "Minimum",
"example": "55"
},
{
"id": "HP-16",
"name": "pH",
"subsection": "Reaction conditions",
"description": "Reaction pH.",
"tier": "Minimum",
"example": "8.0"
},
{
"id": "HP-17",
"name": "pH_controlled",
"subsection": "Reaction conditions",
"description": "Whether pH was actively controlled during hydrolysis.",
"tier": "Minimum",
"example": "TRUE"
},
{
"id": "HP-18",
"name": "agitation",
"subsection": "Reaction conditions",
"description": "Agitation rate, or static.",
"tier": "Ideal",
"example": "150 rpm"
},
{
"id": "HP-19",
"name": "duration",
"subsection": "Reaction conditions",
"description": "Total hydrolysis duration.",
"tier": "Minimum",
"example": "120"
},
{
"id": "HP-20",
"name": "sampling_timepoint",
"subsection": "Reaction conditions",
"description": "Time point(s) at which sample(s) were extracted from the reaction.",
"tier": "Ideal",
"example": "120"
},
{
"id": "HP-21",
"name": "termination_method",
"subsection": "Termination",
"description": "Method used to terminate the reaction.",
"tier": "Minimum",
"example": "heat inactivation, 100 \u00b0C / 15 min"
},
{
"id": "HP-22",
"name": "degree_of_hydrolysis",
"subsection": "Degree of hydrolysis",
"description": "Degree of hydrolysis (DH%): fraction of peptide bonds cleaved.",
"tier": "Minimum",
"example": "18.5"
},
{
"id": "HP-23",
"name": "dh_assay",
"subsection": "Degree of hydrolysis",
"description": "Assay used for DH; choice is substrate/enzyme-specific and should be justified.",
"tier": "Minimum",
"example": "OPA"
},
{
"id": "HP-24",
"name": "centrifugation_gforce",
"subsection": "Post-hydrolysis processing",
"description": "Centrifugation g-force used to clarify the hydrolysate.",
"tier": "Ideal",
"example": "10000"
},
{
"id": "HP-25",
"name": "centrifugation_duration",
"subsection": "Post-hydrolysis processing",
"description": "Centrifugation duration.",
"tier": "Ideal",
"example": "20"
},
{
"id": "HP-26",
"name": "centrifugation_temperature",
"subsection": "Post-hydrolysis processing",
"description": "Centrifugation temperature.",
"tier": "Ideal",
"example": "4"
},
{
"id": "HP-27",
"name": "soluble_protein_yield",
"subsection": "Post-hydrolysis processing",
"description": "Soluble protein yield: how much sample ends up usable in the final product; governs how representative LC-MS/MS data are.",
"tier": "Minimum",
"example": "72"
},
{
"id": "HP-28",
"name": "soluble_protein_yield_method",
"subsection": "Post-hydrolysis processing",
"description": "Method used to determine soluble protein yield.",
"tier": "Minimum",
"example": "Lowry on supernatant"
},
{
"id": "HP-29",
"name": "filtration_fractionation",
"subsection": "Post-hydrolysis processing",
"description": "Filtration / fractionation step (e.g. membrane MWCO ultrafiltration) and parameters.",
"tier": "Ideal",
"example": "10 kDa UF"
},
{
"id": "HP-30",
"name": "drying_method",
"subsection": "Post-hydrolysis processing",
"description": "Drying method applied to the final product.",
"tier": "Ideal",
"example": "lyophilization"
},
{
"id": "HP-31",
"name": "mwd",
"subsection": "Final product characterization",
"description": "Molecular-weight distribution of the product peptidome; reference set to contrast detected peptides against.",
"tier": "Ideal",
"example": "distribution"
},
{
"id": "HP-32",
"name": "mwd_method",
"subsection": "Final product characterization",
"description": "Method and parameters for MWD measurement.",
"tier": "Ideal",
"example": "SEC; column details"
},
{
"id": "HP-33",
"name": "faa_content",
"subsection": "Final product characterization",
"description": "Free amino-acid content; constrains the set of truly undetected peptides (mass below LC-MS/MS cutoff).",
"tier": "Ideal",
"example": "8.2"
},
{
"id": "HP-34",
"name": "product_aa_analysis",
"subsection": "Final product characterization",
"description": "AA analysis (or a highly correlated proxy) of the final product.",
"tier": "Ideal",
"example": "per-AA table"
},
{
"id": "HP-35",
"name": "amino_nitrogen",
"subsection": "Final product characterization",
"description": "Amino nitrogen (AN).",
"tier": "Ideal",
"example": "\u2014"
},
{
"id": "HP-36",
"name": "total_nitrogen",
"subsection": "Final product characterization",
"description": "Total nitrogen (TN).",
"tier": "Ideal",
"example": "\u2014"
},
{
"id": "HP-37",
"name": "an_tn_ratio",
"subsection": "Final product characterization",
"description": "AN/TN ratio (derived from AN and TN).",
"tier": "Ideal",
"example": "\u2014"
},
{
"id": "HP-38",
"name": "ash_content",
"subsection": "Final product characterization",
"description": "Ash content.",
"tier": "Ideal",
"example": "\u2014"
},
{
"id": "HP-39",
"name": "moisture_content",
"subsection": "Final product characterization",
"description": "Moisture content.",
"tier": "Ideal",
"example": "\u2014"
},
{
"id": "HP-40",
"name": "product_pH",
"subsection": "Final product characterization",
"description": "pH of the final product.",
"tier": "Ideal",
"example": "6.8"
},
{
"id": "HP-41",
"name": "mineral_profile",
"subsection": "Final product characterization",
"description": "Mineral content: calcium, iron, magnesium, phosphorus, potassium, sodium.",
"tier": "Ideal",
"example": "per-mineral table"
}
]
},
{
"sheet": "3. LC-MS-MS",
"title": "STAGE 3 \u2014 LC-MS/MS process characterization",
"nFields": 43,
"nMinimum": 13,
"nIdeal": 30,
"fields": [
{
"id": "MS-01",
"name": "run_id",
"subsection": "Identity & linkage",
"description": "Unique identifier for the LC-MS/MS run; primary key for this stage.",
"tier": "Minimum",
"example": "RUN_001"
},
{
"id": "MS-02",
"name": "source_hydrolysate_id",
"subsection": "Identity & linkage",
"description": "Foreign key to the hydrolysate analyzed.",
"tier": "Minimum",
"example": "PH_001"
},
{
"id": "MS-03",
"name": "sample_prep_filtering",
"subsection": "Sample prep & LC",
"description": "Filtering / clean-up steps (e.g. desalting); can remove non-peptidomic content but also drop some peptides.",
"tier": "Minimum",
"example": "C18 desalting"
},
{
"id": "MS-04",
"name": "sample_prep_equipment",
"subsection": "Sample prep & LC",
"description": "Equipment / sorbent used for clean-up.",
"tier": "Ideal",
"example": "C18 StageTip"
},
{
"id": "MS-05",
"name": "sample_prep_conditions",
"subsection": "Sample prep & LC",
"description": "Conditions of the clean-up step.",
"tier": "Ideal",
"example": "30 min"
},
{
"id": "MS-06",
"name": "lc_column_chemistry",
"subsection": "Sample prep & LC",
"description": "LC column stationary-phase chemistry.",
"tier": "Minimum",
"example": "C18"
},
{
"id": "MS-07",
"name": "lc_column_dimensions",
"subsection": "Sample prep & LC",
"description": "Column dimensions and particle size.",
"tier": "Ideal",
"example": "75 \u00b5m \u00d7 25 cm; 1.7 \u00b5m"
},
{
"id": "MS-08",
"name": "lc_load_amount",
"subsection": "Sample prep & LC",
"description": "Amount loaded per column; influences expected input quantity of each peptide.",
"tier": "Ideal",
"example": "1"
},
{
"id": "MS-09",
"name": "lc_flow_regime",
"subsection": "Sample prep & LC",
"description": "Flow regime.",
"tier": "Ideal",
"example": "nano"
},
{
"id": "MS-10",
"name": "lc_flow_rate",
"subsection": "Sample prep & LC",
"description": "Flow rate.",
"tier": "Ideal",
"example": "300"
},
{
"id": "MS-11",
"name": "lc_gradient_length",
"subsection": "Sample prep & LC",
"description": "Gradient length.",
"tier": "Ideal",
"example": "90"
},
{
"id": "MS-12",
"name": "lc_resolution_metrics",
"subsection": "Sample prep & LC",
"description": "Reported LC resolution / selectivity / co-elution metrics (retention, selectivity, efficiency; separation factor).",
"tier": "Ideal",
"example": "separation factor"
},
{
"id": "MS-13",
"name": "ms_instrument",
"subsection": "MS acquisition (MS1)",
"description": "MS instrument model/type; sets transmission and detection efficiency.",
"tier": "Minimum",
"example": "Orbitrap"
},
{
"id": "MS-14",
"name": "acquisition_mode",
"subsection": "MS acquisition (MS1)",
"description": "Acquisition mode.",
"tier": "Minimum",
"example": "DDA"
},
{
"id": "MS-15",
"name": "ms1_scan_range",
"subsection": "MS acquisition (MS1)",
"description": "MS1 scan range; precursors outside this m/z window are never transmitted.",
"tier": "Ideal",
"example": "350\u20131500"
},
{
"id": "MS-16",
"name": "ms1_agc_target",
"subsection": "MS acquisition (MS1)",
"description": "MS1 Automatic Gain Control target (drives detection efficiency).",
"tier": "Ideal",
"example": "1e6"
},
{
"id": "MS-17",
"name": "ms1_max_injection_time",
"subsection": "MS acquisition (MS1)",
"description": "MS1 maximum injection time.",
"tier": "Ideal",
"example": "50"
},
{
"id": "MS-18",
"name": "ms1_resolution",
"subsection": "MS acquisition (MS1)",
"description": "MS1 resolution.",
"tier": "Ideal",
"example": "60000"
},
{
"id": "MS-19",
"name": "min_intensity_threshold",
"subsection": "Precursor gating",
"description": "Minimum MS1 intensity threshold required to trigger fragmentation.",
"tier": "Ideal",
"example": "1e4"
},
{
"id": "MS-20",
"name": "cycle_time_peak_width",
"subsection": "Precursor gating",
"description": "Cycle-time vs peak-width relationship (number of sampling points across a peak).",
"tier": "Ideal",
"example": "12 s / 1.5 s"
},
{
"id": "MS-21",
"name": "topN",
"subsection": "Precursor gating",
"description": "Number of precursors fragmented per cycle (TopN).",
"tier": "Ideal",
"example": "12"
},
{
"id": "MS-22",
"name": "charge_state_range",
"subsection": "Precursor gating",
"description": "Allowed precursor charge states.",
"tier": "Ideal",
"example": "2+ to 6+"
},
{
"id": "MS-23",
"name": "isolation_window",
"subsection": "Precursor gating",
"description": "Isolation window width.",
"tier": "Ideal",
"example": "1.0"
},
{
"id": "MS-24",
"name": "ms2_fragmentation_method",
"subsection": "MS2 fragmentation",
"description": "Fragmentation method.",
"tier": "Ideal",
"example": "HCD"
},
{
"id": "MS-25",
"name": "normalized_collision_energy",
"subsection": "MS2 fragmentation",
"description": "Normalized collision energy (only for collision-based methods).",
"tier": "Ideal",
"example": "28"
},
{
"id": "MS-26",
"name": "ms2_resolution",
"subsection": "MS2 fragmentation",
"description": "MS2 resolution.",
"tier": "Ideal",
"example": "15000"
},
{
"id": "MS-27",
"name": "precursor_mass_tolerance",
"subsection": "MS2 fragmentation",
"description": "Mass accuracy / precursor tolerance.",
"tier": "Ideal",
"example": "5"
},
{
"id": "MS-28",
"name": "fragment_ion_coverage",
"subsection": "MS2 fragmentation",
"description": "Fragment ion coverage: matched vs theoretically possible fragment ions for the sequence.",
"tier": "Ideal",
"example": "8 / 10"
},
{
"id": "MS-29",
"name": "search_engine",
"subsection": "Computational identification",
"description": "Search engine identity and version.",
"tier": "Minimum",
"example": "MaxQuant 2.4"
},
{
"id": "MS-30",
"name": "fdr_threshold",
"subsection": "Computational identification",
"description": "FDR threshold and the level at which it is applied.",
"tier": "Minimum",
"example": "1% at PSM level"
},
{
"id": "MS-31",
"name": "decoy_strategy",
"subsection": "Computational identification",
"description": "Decoy strategy used for FDR control.",
"tier": "Ideal",
"example": "target-decoy (reversed)"
},
{
"id": "MS-32",
"name": "search_database",
"subsection": "Computational identification",
"description": "Search database (FASTA) source and version.",
"tier": "Minimum",
"example": "UniProt <organism>, 2024_03"
},
{
"id": "MS-33",
"name": "enzyme_specificity_setting",
"subsection": "Computational identification",
"description": "Enzyme-specificity setting used in the search.",
"tier": "Ideal",
"example": "semi-tryptic"
},
{
"id": "MS-34",
"name": "missed_cleavages",
"subsection": "Computational identification",
"description": "Allowed missed cleavages.",
"tier": "Ideal",
"example": "2"
},
{
"id": "MS-35",
"name": "modifications",
"subsection": "Computational identification",
"description": "Fixed/variable sequence modifications considered.",
"tier": "Ideal",
"example": "Met oxidation; deamidation"
},
{
"id": "MS-36",
"name": "peptide_length_range",
"subsection": "Computational identification",
"description": "Minimum/maximum peptide length searched.",
"tier": "Ideal",
"example": "2\u201350"
},
{
"id": "MS-37",
"name": "detection_call_aggregation",
"subsection": "Computational identification",
"description": "Rule for calling a peptide detected across replicate runs.",
"tier": "Minimum",
"example": "\u22652 of 3 replicates"
},
{
"id": "MS-38",
"name": "pride_deposit_id",
"subsection": "Data deposition",
"description": "Public repository accession for raw + processed data (e.g. PRIDE).",
"tier": "Minimum",
"example": "PXD0XXXXXX"
},
{
"id": "MS-39",
"name": "workflow_repository",
"subsection": "Data deposition",
"description": "Link to the reproducible end-to-end computational workflow (raw data \u2192 final peptide list).",
"tier": "Ideal",
"example": "repository URL"
},
{
"id": "MS-40",
"name": "peptide_sequence",
"subsection": "Peptide-level output",
"description": "Identified peptide sequence.",
"tier": "Minimum",
"example": "LVNELTEFAK"
},
{
"id": "MS-41",
"name": "parent_protein",
"subsection": "Peptide-level output",
"description": "Parent protein accession(s) for the peptide.",
"tier": "Ideal",
"example": "P00XXX"
},
{
"id": "MS-42",
"name": "ms1_intensity",
"subsection": "Peptide-level output",
"description": "MS1 intensity / flyability signal (abundance \u00d7 ionization \u00d7 transmission \u00d7 detection).",
"tier": "Ideal",
"example": "1.2e7"
},
{
"id": "MS-43",
"name": "detected_flag",
"subsection": "Peptide-level output",
"description": "Whether the peptide was classified as detected (the prediction target).",
"tier": "Minimum",
"example": "TRUE"
}
]
},
{
"sheet": "4. Bioactivity & CCM",
"title": "STAGE 4 \u2014 Peptide bioactivity & cell-culture performance",
"nFields": 14,
"nMinimum": 9,
"nIdeal": 5,
"fields": [
{
"id": "BA-01",
"name": "peptide_id",
"subsection": "Peptide bioactivity",
"description": "Foreign key to the identified peptide (sequence + run).",
"tier": "Minimum",
"example": "RUN_001:LVNELTEFAK"
},
{
"id": "BA-02",
"name": "known_bioactivity",
"subsection": "Peptide bioactivity",
"description": "Known bioactivity annotation(s) for the observed peptide.",
"tier": "Minimum",
"example": "ACE-inhibitory"
},
{
"id": "BA-03",
"name": "bioactivity_source_db",
"subsection": "Peptide bioactivity",
"description": "Source database for the known bioactivity annotation.",
"tier": "Ideal",
"example": "curated bioactive-peptide DB"
},
{
"id": "BA-04",
"name": "predicted_bioactivity",
"subsection": "Peptide bioactivity",
"description": "Predicted bioactivity (only from adequately validated tools, given current tool limitations).",
"tier": "Ideal",
"example": "\u2014"
},
{
"id": "BA-05",
"name": "prediction_tool",
"subsection": "Peptide bioactivity",
"description": "Tool and version used for bioactivity prediction.",
"tier": "Ideal",
"example": "tool + version"
},
{
"id": "BA-06",
"name": "ccm_formulation_id",
"subsection": "CCM context",
"description": "Unique identifier for the cell-culture-media (CCM) formulation tested.",
"tier": "Minimum",
"example": "CCM_001"
},
{
"id": "BA-07",
"name": "hydrolysate_id",
"subsection": "CCM context",
"description": "Foreign key to the hydrolysate incorporated into the media.",
"tier": "Minimum",
"example": "PH_001"
},
{
"id": "BA-08",
"name": "hydrolysate_inclusion",
"subsection": "CCM context",
"description": "Hydrolysate inclusion concentration in the media.",
"tier": "Minimum",
"example": "2"
},
{
"id": "BA-09",
"name": "media_components",
"subsection": "CCM context",
"description": "Full list of every media component and its concentration (mixtures behave differently from isolated peptides).",
"tier": "Minimum",
"example": "component table"
},
{
"id": "BA-10",
"name": "cell_line",
"subsection": "CCM context",
"description": "Cell line used in the evaluation.",
"tier": "Minimum",
"example": "<cell line>"
},
{
"id": "BA-11",
"name": "cell_line_context_data",
"subsection": "CCM context",
"description": "Generalizable cell-line-specific context data (e.g. RNA-seq profile).",
"tier": "Ideal",
"example": "dataset / accession"
},
{
"id": "BA-12",
"name": "performance_metric_type",
"subsection": "Performance outcome",
"description": "Type of quantitative performance metric measured (comparable across contexts).",
"tier": "Minimum",
"example": "proliferation"
},
{
"id": "BA-13",
"name": "performance_value",
"subsection": "Performance outcome",
"description": "Measured value of the performance metric.",
"tier": "Minimum",
"example": "1.8e6 cells/mL"
},
{
"id": "BA-14",
"name": "cost_per_litre",
"subsection": "Performance outcome",
"description": "Media cost per litre (cross-context economic performance metric).",
"tier": "Ideal",
"example": "12.5"
}
]
}
]
} |