Opentrons Shotgun Proteomics Sample Preparation Protocol v.0.1.1

This repository houses the scripts to be used in the protocol to automate experimental steps in proteomics sample preparation with the Opentrons OT-2 automated liquid handling systems.

Three digestion scripts are provided in the digestion_scripts folder:

• NoSP3_digestion.py: Digestion without SP3 detergent removal
• SP3_digestion.py: Digestion with SP3 detergent removal
• SP3_peptide_cleanup.py: Post-digestion SP3 peptide cleanup

In addition, one helper script is provided in the misc_scripts folder:

• BCA_protocol.py: Total protein quantification using BCA assay

Getting Started

Hardware requirements

This protocol requires an Opentrons OT-2 automated liquid handling system along with suitable accessories:

• OT-2 pipettes (P20/P50 and P300)
• Pipette tips
• 4-in-1 tube rack set
• Aluminum block set
• Magnetic module
• Temperature module
• 96-well 2mL deep well plates

Software requirements

• Python v.3.5+
• Opentrons API v2

The Opentrons API v2 can be acquired in pip via:

pip install opentrons

Authors

• Erin Yu Han, PhD - Code/design - EYH
• Cody Thomas, BSc - Code/design - CodyT21
• Sara Wennersten, BSc - Code/design - sara-wennersten

Additional Information

See also the Opentrons API v2 documentation.

Contributing

Please contact us if you wish to contribute, and submit pull requests to us.

License

This project is licensed under the MIT License - see the LICENSE file for details.