Application
Protein Purification
Protein purification is the process of isolating a specific protein from a complex biological mixture, such as cell lysates, fermentation broths, or culture supernatants, to obtain it in a usable, functional form. This is crucial for studying a protein’s function, structure, and interactions or for therapeutic use. For intracellular proteins, the process starts with cell lysis to release the target protein. This is followed by clarification to remove debris, and then chromatographic and concentration steps tailored to the protein’s properties and required purity.
Protein purification is widely used in biopharma, diagnostics, life science research, and the food industry, enabling teams to develop safer therapies, advanced diagnostics, and high-quality ingredients. Biopharma produces therapeutic proteins such as monoclonal antibodies, hormones, and enzymes under strict regulatory standards. In diagnostics, purified proteins are used in assay development and biomarker discovery.
In research, they enable studies on protein structure, function, and interactions. In the food industry, protein purification supports the production of functional proteins, enzymes, and nutritional additives used in food processing and quality control.
How Hamilton Supports Your Protein Purification Workflows
All Hamilton platforms can be customized to meet the specific requirements of protein purification workflows. For this, Hamilton offers a range of on-deck modules, as well as proprietary and third-party consumables, to automate the majority of the steps in the protein purification workflow. For clarification steps, Hamilton’s on-deck centrifuge can be used for precipitation, and the on-deck vacuum station or the [MPE]2 module can be used for filtration. Protein enrichment via Solid Phase Extraction (SPE) is also supported by the Hamilton [MPE]2 module and the On-Deck Vacuum Station.
A variety of functionalized tips, including validated DPX and IMCS tips, serve as reliable tools for chromatography-based purification steps or buffer exchange. Dialysis with automation-friendly dialysis plates, such as Scienova’s Xpress Dialyzer Plate, can also be used.
Explore our Protein Purification Solutions and Applications in Detail
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The Hamilton Microlab Prep is an affordable liquid handler perfect for automating workflows. This entry-level liquid handler supports automated PCR setup and serial dilution.
The Hamilton Microlab STAR is a reliable and versatile automated liquid handling platform. With advanced features like multi-probe heads, pipetting technologies, and VENUS software, this premier liquid handling system fits your laboratory needs. Revolutionize your workflows with the STAR today!
Hamilton STAR V, a cutting-edge liquid handling robot, unites Microlab STAR flexibility with Microlab VANTAGE high-performance capabilities to boost efficiency. The Microlab STAR V offers speed, precision, and technology for automated liquid handling. Upgrade your lab—explore the Microlab STAR V!
Hamilton VANTAGE 2.0 is a cutting-edge liquid handling system with automated precision. Optimize workflows with the VANTAGE robot, all while boosting performance, safeguarding samples, and maximizing walk-away time. Discover the Hamilton VANTAGE liquid handler for your current & future needs.
Lab Syringes
Gastight Syringes
The solution for dispensing both gases and heterogeneous liquids. Hamilton Gastight syringes are equipped with a precision-machined PTFE plunger tip to create a leak-free seal.
Good to Know About Protein Purification workflows
This section provides a selection of additional resources related to the application described on this page. It includes helpful articles, videos, and blogs that offer deeper insights into the topic.
Useful Links
External resources not written by Hamilton but valuable for understanding the topic, such as industry guidelines, explanatory videos, or relevant tools.
| Strategies for protein purification - Cytiva Handbook | Read Handbook |
| Protein and peptide purification - Cytiva Guide | Read Guide |
Scientific Articles
Peer-reviewed journal publications that feature Hamilton products, demonstrating their use in real-world research and application
| Schär, S., Räss, L., Malinovska, L., Savickas, S., Cavallo, F., Below, C., Tognetti, M., Shichkova, P., Gourdet, B., Robles, G., Iu, L., Vowinckel, J., Feng, Y. (2025). A flexible end-to-end automated sample preparation workflow enables standardized and scalable bottom-up proteomics. Analytical Chemistry. | Read Article |
| Mitchell, C., Moore, D. N., Kates, P. A., Stevens, J., Sly, J., & Lee, L. A. (2021, February 4). Evaluation of a novel peptide‑based affinity ligand for human IgM purification: Use of an automated liquid‑handling system for rapid assessment of binding kinetics and capacity. BioProcess International. | Read Article |
Hamilton Products in Action
A collection of videos showcasing Hamilton products in use, providing practical insights into their functionality and benefits.
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Solutions for the Top 3 Challenges for Protein Purification Workflows
Reproducibility
Challenge: Reliable protein purification depends heavily on consistent homogenization and sample preparation. Even small variations can affect the results.
Solution: Hamilton’s automated liquid handling platforms standardize critical purification steps such as cell lysis, reagent addition, and mixing. This ensures uniform sample processing across replicates and batches, leading to reproducible results.
Throughput
Challenge: Achieving high throughput in protein purification often requires compromising on consistency, speed, or flexibility.
Solution: Hamilton’s automation platforms support true high-throughput purification by integrating 96-head pipetting capabilities, allowing full microplate processing in parallel. Moreover, we partner with leading providers of in-tip chromatography and in-plate dialysis to automate and validate key steps such as binding, washing, and buffer exchange, delivering scalable performance without compromising quality.
Protein Stability
Challenge: Protein stability is sensitive to factors such as temperature, buffer composition, and handling time. These factors can vary significantly among samples when purification is performed manually.
Solution: Hamilton systems maintain tightly controlled on-deck conditions, such as precise temperature regulation and timed workflows, while minimizing manual handling. These features help preserve protein integrity throughout the purification process.
Protein Purification Techniques
The choice of techniques in a protein purification workflow varies depending on the protein’s origin (intracellular or secreted), size, solubility, stability, required purity, and downstream application. Below are some of the most common techniques
Clarification removes cells, debris, and other particles before purification:
- Centrifugation: A core step that uses high-speed spinning to separate cells or debris from the liquid (supernatant). Speeds of 4,000–6,000 ×g are common for bacterial samples.
- Filtration: Uses membranes with defined pore sizes (e.g., 0.45 µm or 0.22 µm) to remove particulates such as cell debris or microorganisms from protein solutions.
- Solid Phase Extraction (SPE): Occasionally used for peptide clean-up; less common for full-length proteins due to limited selectivity.
Core methods to isolate the protein of interest based on chemical or physical properties:
- Affinity Chromatography: Exploits specific ligand–protein interactions (e.g., Ni-NTA for His-tags, Protein A/G for antibodies).
- Ion Exchange Chromatography (IEX): Separates proteins by net surface charge (strong or weak anion/cation exchangers).
- Hydrophobic Interaction Chromatography (HIC): Separates proteins based on surface hydrophobicity under high-salt conditions.
- Size Exclusion Chromatography (SEC): Separates by molecular size; often used for final polishing or removing aggregates.
Applied after purification to concentrate proteins or prepare for storage/assays:
- Ultrafiltration: Membrane-based size exclusion is used to retain proteins while removing buffer components or concentrating the sample.
- Dialysis: Passive diffusion across a semipermeable membrane to exchange buffers or remove small molecules (e.g. imidazole).
- Desalting Columns: Miniaturized SEC columns used for rapid buffer exchange or salt removal.
- SPE: commonly used for desalting and buffer exchange, especially for peptides and small proteins.
- Precipitation + Centrifugation (e.g. ammonium sulfate): Occasionally used as a crude concentration method.
Protein Purification Case Studies and Application Notes
Other Protein Purification Resources
Browse app notes, user guides, specification documents, and more in our Knowledge Center.
Browse app notes, user guides, specification documents, and more in our Knowledge Center.
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