Auto Proteomics

Author: Guo Xuan 郭轩

Contact: xguo608@connect.hkust-gz.edu.cn

auto-proteomics is a public v0.x skill for processed proteomics downstream work.

The current public promise is intentionally narrow:

• one shipped runnable workflow: dda-lfq-processed
• one public input family: processed DDA LFQ protein-level tables
• one public comparison model: group-a vs group-b

Everything else in this repository should be read as routing context, internal prototype, or future scaffold unless a document explicitly marks it as part of the public promise.

Presence of a script, schema, or branch document does not mean the route is publicly supported.

In particular, dia-quant is intentionally exposed as an internal prototype route for correct routing and contract validation, not as a shipped public workflow.

Use this skill when

• the user already has processed protein-level quantification output
• the main table is MaxQuant-like proteinGroups.txt
• the goal is QC, normalized matrix generation, and two-group differential protein analysis
• the user wants a low-token, file-driven workflow instead of a long chat-only protocol

Do not use this skill when

• the user starts from raw spectra and needs search/identification
• the request is primarily DIA, phosphoproteomics, enrichment, or multi-omics execution
• the task requires more than one comparison design in the current release
• the user only wants generic statistics with no proteomics context

Public promise in v0.x

Shipped and supported now:

• route processed DDA LFQ downstream requests into dda-lfq-processed
• validate the expected processed-input shape
• generate matrix, QC, differential tables, report, and manifest outputs

Not promised yet:

• raw-spectrum search pipelines
• DIA public execution support
• phosphoproteomics execution
• enrichment execution
• multi-omics execution
• generalized study-design handling beyond the current two-group path

Internal prototype route available for routing only:

• dia-quant may be selected only when the request is explicitly about processed DIA quant tables that fit the checked-in DIA contract
• selecting dia-quant means internal prototype triage, never a public v0.x execution recommendation

Important boundary:

• non-shipped branches may contain scaffold or prototype execution files for internal framework development
• smaller models must not treat those files as public runnable recommendations unless a route is explicitly marked shipped

Minimal workflow

1. Read references/WORKFLOW_INDEX.yaml
2. If the route is unclear, run scripts/decision/route_proteomics.py
3. Check that the request fits the public v0.x boundary
4. Run scripts/workflows/dda_lfq_processed.sh
5. Use references/ for runtime, onboarding, and development rules

Public runnable entrypoint

bash scripts/workflows/dda_lfq_processed.sh \
  --input-dir <run_dir> \
  --protein-groups <proteinGroups.txt> \
  --summary <summary.txt> \
  --parameters <parameters.txt> \
  --output-dir <output_dir> \
  --group-a <condition_a> \
  --group-b <condition_b>

Input contract

Required:

• proteinGroups.txt with LFQ intensity or Intensity columns
• summary.txt with Raw file and Experiment columns

Optional:

• parameters.txt

Output contract

The shipped workflow produces:

• normalized protein matrix files under matrix/
• QC outputs under qc/
• differential protein tables under stats/
• REPORT.md
• summary.json
• run_manifest.json

Repository layers

• SKILL.md: public entry and release boundary
• references/WORKFLOW_INDEX.yaml: machine-readable routing and shipped-vs-non-shipped map
• references/BRANCH_FRAMEWORK.md: standard branch contract for future routes
• references/branches/: per-branch specs for scaffold and prototype workflows
• references/DIA_INPUT_SCHEMA.md: first narrow schema for DIA prototype intake
• scripts/workflows/dda_lfq_processed.sh: shipped workflow entrypoint
• shipped public guidance lives in documents that explicitly describe the processed DDA v0.x path
• non-shipped reference docs exist for internal framework development and must not be surfaced as public support

Read next

• references/WORKFLOW_INDEX.yaml
• references/RUNTIME_REQUIREMENTS.md
• references/BRANCH_FRAMEWORK.md
• references/DEMO_INPUT_GUIDE.md
• references/DEVELOPMENT_GUIDE.md