SDRF-Proteomics: Human Template

All columns from the base template are inherited (source name, organism, organism part, biological replicate, assay name, technology type, instrument, technical replicate, data file). Technology-specific columns (cleavage agent, label, fraction identifier, etc.) come from the technology template (ms-proteomics or affinity-proteomics).

Format: Alphanumeric pseudonymized identifier (e.g., patient_001, P023455, donor_1).

Enables tracking of:

Examples:

When multiple samples come from the same patient, use consistent identifier:

Use not available when ancestry is unknown, not applicable for non-human samples or cell lines where ancestry doesn’t apply.

For longitudinal studies, indicates when sample was collected relative to a reference point.

Values: baseline, week 1, day 7, post-treatment, follow-up.

Comorbidities or pre-existing medical conditions. For multiple conditions, use multiple columns (preferred) or semicolon-separated values.

Disease staging captures overall disease progression, including cancer staging, chronic disease phases, and severity classifications.

Examples:

Use not available when staging is unknown, not applicable for non-disease samples.

Free-text or structured clinical details about samples that don’t fit into other structured fields. Use this column for receptor status, treatment history, surgical details, and other clinical annotations.

Examples:

Best Practice: Consider using structured columns (e.g., separate columns for ER/PR/HER2 status) when possible. Use clinical data for additional context that doesn’t fit elsewhere.

Captures relevant medical history information for the patient.

TNM staging describes the extent of cancer spread. Format: T{0-4}N{0-3}M{0-1} where T = tumor size/extent, N = lymph node involvement, M = distant metastasis. Prefix p indicates pathological staging (post-surgery), c indicates clinical staging.

Examples:

Histological tumor grade describes how abnormal cancer cells look under a microscope. Grade correlates with tumor aggressiveness.

Examples:

Location where cancer has spread from the primary site.

Format: {value} {unit} (e.g., 2.5 cm, 15 mm, 50 g)

Specific anatomical location where biopsy was performed.

Examples: left leg, right breast, Brodmann area 46, liver segment 7

Format: {value} {unit} (e.g., 24 months, 3 years)

Used for survival analysis studies to track patient outcomes.

Format: {value} {unit} (e.g., 12 months, 2 years)

Time of last clinical follow-up for longitudinal studies.

Number of mitoses per high-power field. Used for histological grading in some cancer types.

Breast cancer subtype (characteristics[breast cancer subtype]):

Other cancer-specific staging systems:

These two columns work together to provide hierarchical anatomical information:

Use characteristics[sampling site] when you need to specify:

Pattern 1: Cancer Studies (Tumor/Normal/Adjacent)

Examples:

Pattern 2: Anatomical Sub-Regions

There are two valid approaches for anatomical annotation:

Option 1: Most specific level in organism part (preferred for simple cases)

When no additional context is needed, use the most specific anatomical term directly:

Option 2: General + sampling site (preferred for complex cases)

When you need additional context (e.g., tumor vs. normal), use both columns:

Guidelines:

In clinical proteomics, phenotype is commonly used to capture biomarker status for patient stratification:

Examples:

For pharmacoproteomics and precision medicine studies:

For human genetic variants, use genotype to capture specific mutations:

General treatment or intervention applied to samples. Use for treatment categories when more general than specific compounds.

Examples:

Use untreated for no treatment, not available when unknown.

Chemical compound, drug, or biological agent applied to samples. Use ChEBI ontology for standardized compound identification.

Examples:

Best Practice: Include ChEBI accession in format compound_name (CHEBI:XXXXX) when available.

Format: {value} {unit}

Examples:

Format: {value} {unit} where unit is hour, day, week, month (or h, d, w abbreviations)

Duration of treatment exposure.

Examples:

Values: pre-treatment, on treatment, post-treatment, treatment naive.

Describes the method or type of genetic modification applied to samples (particularly relevant for engineered cell lines and model organisms).

Examples:

For comprehensive pharmacoproteomics annotation, combine compound, dose, and treatment time:

For female patients. Values: pre-menopausal, peri-menopausal, post-menopausal.