bigbio · ypriverol · Mar 9, 2026 · Feb 23, 2026 · Feb 26, 2026 · Feb 26, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -44,6 +44,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - **Version bump to v1.1.0**.
+- **BREAKING: `comment[technical replicate]`** changed from RECOMMENDED to REQUIRED in base template. All inheriting templates now require a technical replicate column. Existing SDRF files without this column will fail validation -- add the column with value `1` for single-run samples.
+- **BREAKING: Immunopeptidomics field renames**: `characteristics[MHC class]` → `characteristics[MHC protein complex]` (GO:0042611), `characteristics[MHC allele]`/`characteristics[HLA typing]` → `characteristics[MHC typing]` (PRIDE:0000893), `characteristics[HLA typing method]` → `characteristics[MHC typing method]` (PRIDE:0000894). Values updated to use MRO/GO ontology terms. Existing datasets must update column names and values.
+- **Organism templates**: `developmental stage` and `strain/breed` changed to REQUIRED in invertebrates, vertebrates, and plants. `sex` changed to RECOMMENDED in vertebrates. `growth conditions` and `treatment` changed to RECOMMENDED in plants.
+- **Human template**: `age` and `sex` changed to REQUIRED. Age pattern now allows standalone month/week/day values (e.g. `6M`, `3W`, `14D`).
+- **BioSample accession**: regex fixed from `^SAM[NED]A?\d+$` to `^SAM(N|EA|D)\d+$` to reject invalid prefixes.
+- **Affinity proteomics**: version set to 1.0.0. `comment[instrument]` renamed to `comment[platform]` (REQUIRED); new `comment[instrument]` added as OPTIONAL for actual sequencer/reader. Sample type values normalized to use spaces (`sample control`, `negative control`, etc.).
+- **Cell-lines**: added PATO ontology to disease field for `normal` (PATO:0000461). Added `characteristics[culture medium]` (RECOMMENDED) and `characteristics[storage temperature]` (RECOMMENDED).
+- **MS-proteomics/DDA**: mass tolerance patterns updated to accept `not available`/`not applicable` when those flags are set. DDA mass tolerance kept as RECOMMENDED.
 - **Specification restructured** with clearer organization: Quick Start → Validation → Specification Structure → Notational Conventions → Sample Metadata → Data File Metadata → Templates → Factor Values.
 - **Column naming**: `fileformat` changed to `file_format` for consistency with underscore convention.
 - **Ontology recommendations**: added NCIT and PRIDE to general purpose; added PATO for healthy samples (`normal` = PATO:0000461).

diff --git a/llms.txt b/llms.txt
@@ -24,10 +24,9 @@
 - sdrf-proteomics/templates/invertebrates/README.adoc - Invertebrates: Drosophila, C. elegans
 - sdrf-proteomics/templates/plants/README.adoc - Plants: Arabidopsis, crops
 - sdrf-proteomics/templates/cell-lines/README.adoc - Cell Lines: Cellosaurus integration
-- sdrf-proteomics/templates/dda-acquisition/README.adoc - DDA Acquisition: dissociation method, collision energy
 - sdrf-proteomics/templates/dia-acquisition/README.adoc - DIA Acquisition: scan windows, isolation width
 - sdrf-proteomics/templates/single-cell/README.adoc - Single-Cell Proteomics: cell isolation, carrier proteome
-- sdrf-proteomics/templates/immunopeptidomics/README.adoc - Immunopeptidomics: MHC class, HLA typing
+- sdrf-proteomics/templates/immunopeptidomics/README.adoc - Immunopeptidomics: MHC protein complex, MHC typing
 - sdrf-proteomics/templates/crosslinking/README.adoc - Crosslinking MS: crosslinker reagents
 - sdrf-proteomics/templates/metaproteomics/README.adoc - Metaproteomics: environmental and microbiome samples
 - sdrf-proteomics/templates/olink/README.adoc - Olink: proximity extension assays
@@ -54,15 +53,13 @@ Machine-readable YAML definitions used by sdrf-pipelines for validation. Each te
   - sdrf-proteomics/sdrf-templates/plants/1.1.0/plants.sdrf.tsv - Plants example
 - sdrf-proteomics/sdrf-templates/cell-lines/1.1.0/cell-lines.yaml - Cell Lines (experiment layer): Cellosaurus integration
   - sdrf-proteomics/sdrf-templates/cell-lines/1.1.0/cell-lines.sdrf.tsv - Cell Lines example
-- sdrf-proteomics/sdrf-templates/dda-acquisition/1.1.0/dda-acquisition.yaml - DDA Acquisition (experiment layer): dissociation method, collision energy
-  - sdrf-proteomics/sdrf-templates/dda-acquisition/1.1.0/dda-acquisition.sdrf.tsv - DDA example
 - sdrf-proteomics/sdrf-templates/dia-acquisition/1.1.0/dia-acquisition.yaml - DIA Acquisition (experiment layer): scan windows, isolation width
   - sdrf-proteomics/sdrf-templates/dia-acquisition/1.1.0/dia-acquisition.sdrf.tsv - DIA example
 - sdrf-proteomics/sdrf-templates/crosslinking/1.1.0/crosslinking.yaml - Crosslinking MS (experiment layer): crosslinker reagents
   - sdrf-proteomics/sdrf-templates/crosslinking/1.1.0/crosslinking.sdrf.tsv - Crosslinking example
 - sdrf-proteomics/sdrf-templates/single-cell/1.0.0/single-cell.yaml - Single-Cell (experiment layer): cell isolation, carrier proteome
   - sdrf-proteomics/sdrf-templates/single-cell/1.0.0/single-cell.sdrf.tsv - Single-Cell example
-- sdrf-proteomics/sdrf-templates/immunopeptidomics/1.0.0-dev/immunopeptidomics.yaml - Immunopeptidomics (experiment layer): MHC class, HLA typing
+- sdrf-proteomics/sdrf-templates/immunopeptidomics/1.0.0-dev/immunopeptidomics.yaml - Immunopeptidomics (experiment layer): MHC protein complex, MHC typing
 - sdrf-proteomics/sdrf-templates/metaproteomics/1.0.0-dev/metaproteomics.yaml - Metaproteomics (experiment layer): environmental and microbiome samples
   - sdrf-proteomics/sdrf-templates/metaproteomics/1.0.0-dev/metaproteomics.sdrf.tsv - Metaproteomics example
 - sdrf-proteomics/sdrf-templates/olink/1.0.0/olink.yaml - Olink (experiment layer): proximity extension assays

diff --git a/psi-document/sdrf-proteomics-specification-v1.1.0-dev.pdf b/psi-document/sdrf-proteomics-specification-v1.1.0-dev.pdf
diff --git a/psi-document/v1.1.0-dev/supplementary-files/quickstart-v1.1.0-dev.adoc b/psi-document/v1.1.0-dev/supplementary-files/quickstart-v1.1.0-dev.adoc
@@ -79,7 +79,7 @@ Add extra columns for specific experimental workflows:
 |DIA-specific parameters. link:templates/dia-acquisition/README.adoc[View template]
 
 |**immunopeptidomics**
-|HLA typing and related metadata. link:templates/immunopeptidomics/README.adoc[View template]
+|MHC typing and related metadata. link:templates/immunopeptidomics/README.adoc[View template]
 
 |**crosslinking**
 |XL-MS specific columns. link:templates/crosslinking/README.adoc[View template]

diff --git a/psi-document/v1.1.0-dev/supplementary-files/template-definitions-v1.1.0-dev.adoc b/psi-document/v1.1.0-dev/supplementary-files/template-definitions-v1.1.0-dev.adoc
@@ -29,7 +29,6 @@ base (construction artifact - not user-facing)
 ├── TECHNOLOGY LAYER (mutually exclusive)
 │   ├── ms-proteomics              # Mass spectrometry proteomics
 │   │   └── EXPERIMENT LAYER
-│   │       ├── dda-acquisition    # Data-dependent acquisition
 │   │       ├── dia-acquisition    # Data-independent acquisition
 │   │       ├── single-cell        # Single-cell proteomics
 │   │       ├── immunopeptidomics  # MHC peptide analysis
@@ -70,7 +69,7 @@ cell-lines (EXPERIMENT layer - requires technology + sample)
 
 | `experiment`
 | Defines methodology-specific columns. Multiple can be combined if not mutually exclusive.
-| dda-acquisition, single-cell, olink, cell-lines
+| dia-acquisition, single-cell, olink, cell-lines
 |===
 
 === Mutual Exclusivity
@@ -82,7 +81,6 @@ Some templates cannot be combined because they represent mutually exclusive conc
 | Template A | Template B | Reason
 
 | ms-proteomics | affinity-proteomics | Different technologies
-| dda-acquisition | dia-acquisition | Different acquisition methods
 | somascan | olink | Different affinity platforms
 | human | vertebrates | Different organism types
 | human | invertebrates | Different organism types
@@ -476,7 +474,7 @@ When multiple templates are combined:
 **Example valid combination:**
 [source]
 ----
-ms-proteomics + human + dda-acquisition + cell-lines
+ms-proteomics + human + dia-acquisition + cell-lines
      ↓             ↓           ↓              ↓
  technology    sample    experiment     experiment
 ----
@@ -576,10 +574,10 @@ parse_sdrf validate-sdrf --sdrf_file file.sdrf.tsv --template ms-proteomics
 parse_sdrf validate-sdrf --sdrf_file file.sdrf.tsv \
   --template ms-proteomics \
   --template human \
-  --template dda-acquisition
+  --template dia-acquisition
 
 # Check template compatibility
-parse_sdrf check-templates --templates ms-proteomics,human,dda-acquisition
+parse_sdrf check-templates --templates ms-proteomics,human,dia-acquisition
 ----
 
 == References

diff --git a/sdrf-proteomics/README.adoc b/sdrf-proteomics/README.adoc
@@ -117,7 +117,7 @@ For the complete versioning strategy — including template versioning, ontology
 [[reserved-words]]
 === Reserved words
 
-There are general scenarios where cell values cannot be provided with actual data. The following reserved words MUST be used in these cases:
+There are general scenarios where cell values cannot be provided with actual data. The following reserved words MUST be used in these cases. Reserved words MUST be all lowercase (e.g., `not available`, NOT `Not Available` or `Not available`):
 
 - **not available**: In some cases, the column is mandatory in the format, but for some samples the corresponding value is unknown or could not be determined. In those cases, users SHOULD use *not available*.
 - **not applicable**: In some cases, the column is mandatory, but for some samples the corresponding value or concept does not apply. In those cases, users SHOULD use *not applicable*.
@@ -258,9 +258,9 @@ The value for each property, (e.g. characteristics, comment, factor value) corre
 
 - **Ontology url (Computer readable)**: Users can provide the corresponding URI (Uniform Resource Identifier) of the ontology/CV term as a value. This is recommended for enriched files where the user does not want to use intermediate tools to map from free text to ontology/CV terms.
 
-- **Key=value representation (Human and Computer readable)**: The current representation aims to provide a mechanism to represent the complete information of the ontology/CV term including Accession, Name and other additional properties. In the key=value pair representation, the Value of the property is represented as an Object with multiple properties, where the key is one of the properties of the object and the value is the corresponding value for the particular key. An example of key value pairs is post-translational modification (see link:templates/ms-proteomics.html#_protein_modifications[Protein Modifications]):
+- **Key=value representation (Human and Computer readable)**: The current representation aims to provide a mechanism to represent the complete information of the ontology/CV term including Accession, Name and other additional properties. In the key=value pair representation, the Value of the property is represented as an Object with multiple properties, where the key is one of the properties of the object and the value is the corresponding value for the particular key. The key order MUST be `NT` (name) first, followed by `AC` (accession), then any additional keys. An example of key value pairs is post-translational modification (see link:templates/ms-proteomics.html#_protein_modifications[Protein Modifications]):
 
-  NT=Glu->pyro-Glu;MT=fixed;PP=Anywhere;AC=Unimod:27;TA=E
+  NT=Glu->pyro-Glu;AC=Unimod:27;MT=fixed;PP=Anywhere;TA=E
 
 [[validation]]
 == Validating SDRF Files
@@ -420,6 +420,8 @@ For detailed documentation of sample preparation and MS/MS fragmentation propert
 - **Fractionation**: fractionation method (used with `comment[fraction identifier]`)
 - **Fragmentation**: collision energy, dissociation method
 
+NOTE: For HCD (Higher-energy C-trap Dissociation), the canonical accession is https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000422[MS:1000422 - beam-type collision-induced dissociation]. Use `NT=beam-type collision-induced dissociation;AC=MS:1000422` or the short label `HCD`. Do not use PRIDE:0000590 or MS:1002481.
+
 [[data-acquisition-method]]
 === Proteomics data acquisition method
 
@@ -495,12 +497,41 @@ Templates follow a layered hierarchy:
 |Organism-specific metadata
 
 |**EXPERIMENT** (optional)
-|link:templates/cell-lines/README.adoc[cell-lines], link:templates/crosslinking/README.adoc[crosslinking], link:templates/dda-acquisition/README.adoc[dda-acquisition], link:templates/dia-acquisition/README.adoc[dia-acquisition], link:templates/single-cell/README.adoc[single-cell], link:templates/immunopeptidomics/README.adoc[immunopeptidomics]
+|link:templates/cell-lines/README.adoc[cell-lines], link:templates/crosslinking/README.adoc[crosslinking], link:templates/dia-acquisition/README.adoc[dia-acquisition], link:templates/single-cell/README.adoc[single-cell], link:templates/immunopeptidomics/README.adoc[immunopeptidomics]
 |Methodology-specific columns
 |===
 
 Child templates inherit all columns from parents and may add new columns or strengthen requirements (e.g., `optional` → `required`).
 
+=== Template Combination Rules
+
+Templates within the same layer are **mutually exclusive** - you MUST choose exactly one from each applicable layer:
+
+|===
+|Layer |Mutually Exclusive Templates |Rule
+
+|TECHNOLOGY
+|`ms-proteomics` vs `affinity-proteomics`
+|Choose one (REQUIRED)
+
+|SAMPLE
+|`human` vs `vertebrates` vs `invertebrates` vs `plants`
+|Choose one based on organism (RECOMMENDED)
+
+|EXPERIMENT (affinity platform)
+|`olink` vs `somascan`
+|Choose one if using affinity-proteomics (OPTIONAL)
+|===
+
+Templates from different layers can be freely combined. Common valid combinations:
+
+- `ms-proteomics` + `human` (human DDA proteomics)
+- `ms-proteomics` + `human` + `dia-acquisition` (human DIA proteomics)
+- `ms-proteomics` + `human` + `immunopeptidomics` (human immunopeptidomics)
+- `ms-proteomics` + `vertebrates` + `cell-lines` (mouse cell line proteomics)
+- `ms-proteomics` + `human` + `crosslinking` (human crosslinking MS)
+- `affinity-proteomics` + `human` + `olink` (human Olink)
+
 === Specifying Templates in SDRF Files
 
 Declare templates using `comment[sdrf template]` columns. Only list leaf templates (parents are implied). When using multiple templates, add multiple columns with the same name. Two formats are supported:
@@ -540,11 +571,10 @@ sample_1	...	human v1.1.0	crosslinking v1.0.0
 
 **Experiment-type templates**:
 
-- link:templates/dda-acquisition/README.adoc[DDA Acquisition] - dissociation method, collision energy, modifications
 - link:templates/dia-acquisition/README.adoc[DIA Acquisition] - scan windows, isolation width, spectral library
 - link:templates/cell-lines/README.adoc[Cell Lines] - Cellosaurus integration
 - link:templates/single-cell/README.adoc[Single-Cell] - cell isolation, carrier proteome
-- link:templates/immunopeptidomics/README.adoc[Immunopeptidomics] - MHC class, HLA typing
+- link:templates/immunopeptidomics/README.adoc[Immunopeptidomics] - MHC protein complex, MHC typing
 - link:templates/crosslinking/README.adoc[Crosslinking MS] - crosslinker reagents
 - link:templates/metaproteomics/README.adoc[Metaproteomics] - environmental sample type
 

diff --git a/sdrf-proteomics/metadata-guidelines/sample-metadata.adoc b/sdrf-proteomics/metadata-guidelines/sample-metadata.adoc
@@ -163,17 +163,12 @@ For model organisms, use specific stages when applicable: `embryonic day 14` (mo
 
 For samples without disease, the terminology matters for standardization:
 
-**`normal`** (PATO:0000461) - **Recommended**
+**`normal`** (PATO:0000461) - **REQUIRED term for healthy samples**
 
 - Standard term in pathology ("normal tissue" vs "tumor tissue")
-- Well-defined ontology mapping to PATO:0000461
+- Well-defined ontology mapping to https://www.ebi.ac.uk/ols4/ontologies/pato/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPATO_0000461[PATO:0000461]
 - Widely used in existing proteomics datasets
-
-**`healthy`** (SIO:001012) - **Accepted alternative**
-
-- More intuitive for clinical/human samples
-- Has valid ontology support (Semanticscience Integrated Ontology)
-- Validators should accept both `normal` and `healthy`
+- This is the single canonical term for healthy/control samples
 
 [[WARNING]]
 ====
@@ -252,7 +247,6 @@ Both `healthy_1` and `adjacent_1` have `normal` as their disease state (no tumor
 |Disease |SDRF Value |Ontology Link
 
 |Healthy/no disease |normal |https://www.ebi.ac.uk/ols4/ontologies/pato/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPATO_0000461[PATO:0000461]
-|Healthy (alternative) |healthy |https://www.ebi.ac.uk/ols4/ontologies/sio/classes/http%253A%252F%252Fsemanticscience.org%252Fresource%252FSIO_001012[SIO:001012]
 |Breast cancer |breast carcinoma |https://www.ebi.ac.uk/ols4/ontologies/mondo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0004989[MONDO:0004989]
 |===