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Running
| { | |
| "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" | |
| } | |
| ] | |
| } | |
| ] | |
| } |