Phase 5: DDA data analysis support via DIA-NN (v2.3.2+)

[ypriverol]

Overview

DIA-NN v2.3+ adds beta-stage DDA/DDA-PASEF data analysis via the --dda flag.

Confirmed by Vadim Demichev (Feb 2026):

"2.3.1 and 2.3.2, better just require 2.3.2"

Capabilities & Limitations

Use cases: Legacy DDA reanalysis, offline-fractionation library creation, immunopeptidomics, metaproteomics

Limitations (from DIA-NN docs):

• Only trust: q-values, PEP values, RT/IM values, Ms1.Apex.Area quantity, Normalisation.Factor
• PTM localization probabilities unreliable with DDA data
• MBR requires MS2-level evidence
• No isobaric labeling or reporter-tag quantification

Tasks

New params:

Parameter	Type	Default	Description
diann_dda	boolean	false	Enable DDA analysis mode

• Pass --dda to all DIA-NN steps when enabled
• Version guard: require DIA-NN >= 2.3.2
• Add --dda to blocked list for ALL DIA-NN modules
• Decide integration strategy: new workflow (workflows/dda_diann.nf) or dda_engine parameter in existing DDA workflow

Open Questions

• Should DIA-NN DDA be a separate workflow or integrated into the existing DDA branch?
• Are there additional flags beyond --dda for DDA-PASEF data?

Test Plan

• Run PXD039580 (DDA SILAC HeLa) with --diann_dda true and DIA-NN v2.3.2
• Verify --dda flag passed to all DIA-NN steps
• Version guard blocks DDA with DIA-NN < 2.3.2

Test Datasets:

Dataset	Description	Instrument
PXD039580	DDA + plexDIA SILAC HeLa	Q Exactive HF (has SDRF)
PXD024809	Immunopeptidomics DDA component	Orbitrap Fusion Lumos