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Creating a New Lab Protocol for Review and Approval

User Story​

As a lab scientist I want to create a new experimental protocol and get it reviewed and approved by my PI So that everyone on the team follows the same validated procedure

Scenario​

You've developed a new DNA extraction protocol that improves yield and purity. You need to document it, get feedback from your colleagues, and obtain formal approval from your Principal Investigator before the team adopts it.

Prerequisites​

  • You have a user account in AtomicQMS
  • You're a member of your lab's organization
  • You have write permissions to the lab's protocols repository

Workflow Steps​

Step 1: Create a New Protocol Document​

  1. Navigate to your lab's Protocols repository
  2. Click the New File button
  3. Name your file following your lab's convention (e.g., DNA-extraction-v2.md)
  4. Write your protocol using Markdown formatting:
# High-Yield DNA Extraction Protocol v2.0

## Purpose
Extract high-quality genomic DNA from whole blood samples with >90% yield.

## Materials
- QIAamp DNA Blood Mini Kit
- Ethanol (96-100%)
- Proteinase K
- Buffer AL, AW1, AW2, AE (included in kit)

## Procedure

### Sample Preparation
1. Collect 200 μL whole blood in EDTA tube
2. Store at 4°C if processing within 24 hours
3. For longer storage, freeze at -20°C

### DNA Extraction
1. Add 20 μL Proteinase K to microcentrifuge tube
2. Add 200 μL blood sample
3. Add 200 μL Buffer AL, mix by vortexing (10 sec)
4. Incubate at 56°C for 10 minutes
5. Add 200 μL ethanol (96-100%), mix thoroughly
6. Transfer to QIAamp Mini spin column
7. Centrifuge at 8,000 rpm for 1 minute
8. Discard flow-through

### Washing Steps
1. Add 500 μL Buffer AW1
2. Centrifuge at 8,000 rpm for 1 minute
3. Discard flow-through
4. Add 500 μL Buffer AW2
5. Centrifuge at 14,000 rpm for 3 minutes
6. Discard flow-through

### Elution
1. Transfer column to clean microcentrifuge tube
2. Add 200 μL Buffer AE
3. Incubate at room temperature for 1 minute
4. Centrifuge at 8,000 rpm for 1 minute
5. Store DNA at -20°C

## Quality Control
- Measure concentration using NanoDrop (expect 50-200 ng/μL)
- Verify purity: A260/A280 ratio should be 1.7-1.9
- Run 1% agarose gel to check for degradation

## Expected Results
- Yield: 4-10 μg genomic DNA from 200 μL blood
- Purity: A260/A280 = 1.8 ± 0.1
- Integrity: High molecular weight band on gel

## References
- QIAamp DNA Blood Mini Kit Handbook (Qiagen, Cat. No. 51104)
- Lab notebook: ERP-2024-11-15

## Revision History
- v2.0 (2024-11-23): Optimized incubation times, added QC specs
- v1.0 (2024-09-01): Initial protocol
  1. Add a commit message: "Add new high-yield DNA extraction protocol"
  2. Select Create a new branch and name it dna-extraction-protocol
  3. Check Create Change Request
  4. Click Commit Changes

Step 2: Create Change Request for Review​

AtomicQMS will automatically create a Change Request. Now you'll configure it for review:

  1. In the Change Request page, add a clear title:

    New Protocol: High-Yield DNA Extraction v2.0

  2. Write a description explaining the changes:

    ## Summary
    This new DNA extraction protocol improves yield from ~60% to >90%
    compared to our current method (v1.0).

    ## Key Changes
    - Extended proteinase K incubation from 5 to 10 minutes
    - Increased final centrifuge speed to 14,000 rpm
    - Added specific QC acceptance criteria

    ## Testing
    - Validated with 15 blood samples
    - Average yield: 7.2 μg (up from 4.1 μg with v1.0)
    - All samples met purity criteria (A260/A280 = 1.79 ± 0.06)

    ## Request for Review
    @lab-colleagues: Please review the procedure for clarity
    @PI: Please approve for lab-wide adoption

  3. Add Reviewers:

    • Add your PI as a required reviewer
    • Add experienced lab members as optional reviewers

  4. Add Labels:

    • protocol
    • needs-approval
    • high-priority

  5. Click Create Change Request

Step 3: Respond to Review Comments​

Your colleagues and PI will review the protocol:

Example feedback from colleague:

In Step 2.4, you specify "10 minutes" but our incubator timer only goes to 5-minute intervals. Should we round to 10 or be precise with a separate timer?

Your response:

  1. Click Reply on the comment

  2. Answer the question:

    Good catch! Let's round to 10 minutes using the incubator timer.
    I'll update the protocol to note this.

  3. Make the edit directly in the PR:

    • Click the Files changed tab
    • Click the ... menu on the file
    • Select Edit file
    • Update line: 4. Incubate at 56°C for 10 minutes (use incubator timer)
    • Commit: "Clarify timer instructions"

  4. Mark the conversation as Resolved

Step 4: Address All Comments​

Continue responding to feedback:

  • Answer questions
  • Make requested changes
  • Update procedures for clarity
  • Add missing safety warnings
  • Clarify QC criteria

PI's comment:

Looks good overall. Please add a troubleshooting section for common issues and note the cost per sample for budget tracking.

Your updates:

## Troubleshooting

| Problem | Cause | Solution |
|---------|-------|----------|
| Low yield | Insufficient lysis | Extend proteinase K incubation to 15 min |
| Poor purity | Ethanol carryover | Ensure complete drying after AW2 wash |
| Degraded DNA | Old samples | Process blood within 24h or freeze immediately |

## Cost per Sample
- Kit consumables: $4.50
- Reagents: $0.75
- **Total: ~$5.25 per sample**

Step 5: Get Final Approval​

Once all reviewers are satisfied:

  1. PI approves the Change Request:

    • They click Approve in the review
    • They may add: "Approved for lab-wide use. Effective date: 2024-12-01"

  2. Merge the protocol:

    • You (or the PI) click Merge Change Request
    • Select merge method: Squash and merge (cleaner history)
    • Confirm the merge

  3. The protocol is now official:

    • It appears in the main branch
    • All team members can access it
    • Full version history is preserved
    • Your name is recorded as the author

Step 6: Communicate to the Team​

After merging:

  1. Announce to the team:

    • Post in your team chat: "New DNA extraction protocol (v2.0) is now available in AtomicQMS"
    • Link to the file: https://atomicqms.com/lab/protocols/DNA-extraction-v2.md

  2. Schedule training (if needed):

    • Add a calendar event for protocol demonstration
    • Share the direct link in the meeting invite

  3. Update related documents:

    • If you have an SOP index, add this protocol
    • Update any related workflows that reference DNA extraction

Tips for Success​

Writing Clear Protocols​

  • Use numbered steps for sequential procedures
  • Include times, temperatures, and quantities for all steps
  • Add warnings for safety-critical steps
  • Specify equipment (model numbers help)
  • Document expected results so users know if something went wrong

Getting Quick Approvals​

  • Tag reviewers in your initial Change Request description
  • Set a deadline (e.g., "Requesting review by Nov 30")
  • Be responsive to comments within 24 hours
  • Make it easy - provide context, not just raw protocol text

Version Control Best Practices​

  • Use semantic versioning (v1.0, v1.1, v2.0)
  • Document changes in revision history section
  • Keep old versions accessible (AtomicQMS does this automatically)
  • Cross-reference related protocols and SOPs

What You've Accomplished​

✅ Created a new protocol with complete documentation ✅ Obtained peer review from experienced colleagues ✅ Received formal PI approval ✅ Published the official version for team use ✅ Maintained full audit trail of all changes and approvals

Your new protocol is now the single source of truth for your lab's DNA extraction procedure. Everyone follows the same validated method, and all changes are tracked forever.

Next Steps​