DIA-NN advanced features: phosphoproteomics, plexDIA, immunopeptidomics, DDA, and infrastructure improvements #663
Description
Summary
quantms currently supports label-free DIA analysis with DIA-NN v1.8.1. DIA-NN has evolved significantly through v2.3.2 with features that the community needs: QuantUMS quantification, plexDIA multiplexing, phosphoproteomics with site localization, InfinDIA for immunopeptidomics, and beta DDA support.
This epic tracks the full refactoring across 6 phases, ordered by complexity. The workflow will support all DIA-NN versions (v1.8.1 through v2.3.2) with version-aware feature gating.
Phases
| Phase | Category | Feature | Risk | Min DIA-NN | Issue |
|---|---|---|---|---|---|
| 1 | Technical fixes | Container flexibility + config parsing fix + QPX output + test fix | Low | Any | #TBD_1 |
| 2 | Small additions | QuantUMS + timsTOF + Phospho params | Low | v1.9 | #TBD_2 |
| 3 | New feature | plexDIA (Multiplexed DIA) | Medium | v1.9 | #TBD_3 |
| 4 | New feature | Immunopeptidomics / InfinDIA + Model fine-tuning | Higher | v2.0 | #TBD_4 |
| 5 | Big refactoring | DDA Support via DIA-NN | Medium | v2.3.2 | #TBD_5 |
| 6 | Big refactoring | Parameter Architecture (config gen migration) | Medium | Any | #TBD_6 |
DIA-NN Version Compatibility Matrix
| Feature | Min Version | Key Flags |
|---|---|---|
| Basic LFQ DIA | v1.8.1 | (current baseline) |
| QuantUMS | v1.9 | --quant-train-runs, --quant-sel-runs |
| plexDIA | v1.9 | --channels, --fixed-mod ... label, --lib-fixed-mod |
| Synchro-PASEF | v1.9 | --quant-tims-sum, --im-window |
| Parquet output | v1.9.1 | (automatic) |
| Phospho improvements | v1.9.2 | --monitor-mod, peptidoform scoring |
| InfinDIA | v2.0 | --pre-select, --pre-select-force |
| Model fine-tuning | v2.0 | --tune-rt, --tune-im |
| Site report | v2.0 | --site-ms1-quant |
| DDA support (beta) | v2.3.2 | --dda |
Dependencies
Phase 1 (technical fixes)
|
|--> Phase 2 (small additions — can test immediately)
|--> Phase 3 (plexDIA — needs sdrf-pipelines release from Phase 1)
|--> Phase 4 (InfinDIA — needs v2.0+ container from Phase 1)
|--> Phase 5 (DDA — needs v2.3.2 container from Phase 1)
|--> Phase 6 (param refactoring — best done after Phase 3)
Repos Involved
- quantms (Nextflow) — workflow, modules, config
- quantms-utils (Python) —
dianncfg.py,diann2mztab.py(being deprecated) - qpx (Python) — QPX output format, DIA-NN converter
- sdrf-pipelines (Python) — DIA-NN SDRF converter (plexDIA, per-file tolerances)
- quantms-containers (Docker) — DIA-NN v2.3.2 container needed
- pride-ontology (OBO) — mTRAQ/Dimethyl terms (committed, needs release)
Related Existing Issues
- DIANN parameters are generated in multiple places #659 — DIANN parameters are generated in multiple places (Phase 6)
- test_dia runs into THERMORAWFILEPARSER error #661 — test_dia THERMORAWFILEPARSER error (Phase 1)
- Passing external arguments to DIA-NN workflow #640 — Passing external arguments to DIA-NN workflow (Phase 2)
- DIANN phospho data configuration #510 — DIANN phospho data configuration
--monitor-mod(Phase 2) - Support for timsTOF data #440 — Support for timsTOF data (Phase 2)
- Support for Phosphoproteomics datasets. #334 — Support for Phosphoproteomics datasets (Phase 2)