What Is Protein Purification? From Bench to Biotech

The history of protein purification is a captivating journey that spans centuries, reflecting the evolution of scientific knowledge and technological progress. It began in the late 1600s, when scientists like Robert Boyle and Antonie van Leeuwenhoek initiated the study of bodily fluids, including blood and urine. However, they had limited means to isolate or characterize proteins during this era.

By the 19th century, significant advancements in chemistry and biochemistry had been made, providing the foundation for protein purification. In 1838, the term "protein" was coined by Jöns Jacob Berzelius, recognizing its prime importance in living organisms. A year later, Gerardus Johannes Mulder proposed that proteins were composed of essential chemical elements, including carbon, hydrogen, oxygen, and nitrogen.

By the end of the 19th, into the early 20th century, the groundwork for protein purification techniques was laid. Eduard Buchner’s discovery in 1897 that yeast extracts could ferment sugar was a pivotal step toward understanding enzymes. In 1926, James B. Sumner successfully crystallized the enzyme urease, proving that proteins could be purified to a crystalline form.

The mid-20th century brought significant progress by introducing groundbreaking techniques such as ion exchange chromatography and gel filtration chromatography. The achievements of Archer John Porter Martin and Richard Laurence Millington Synge in chromatography earned them the Nobel Prize in 1952, propelling the field forward.

Protein purification continued to transform as we moved from the 20th century into the present. The advent of recombinant DNA technology allowed for the production of proteins in various expression systems, simplifying large-scale purification. Techniques like affinity chromatography, mass spectrometry, and recombinant protein expression became instrumental in the precision and efficiency of protein purification.

Protein purification remains central to molecular biology, biochemistry, and biotechnology. The process has become more streamlined with innovations in automation, microfluidics, and high-throughput methods. Emerging technologies like cryo-electron microscopy (cryo-EM) are revolutionizing the structural characterization of purified proteins.

In this post, we’ll cover:

  • What is protein purification?
  • How does protein purification work?
  • Types of protein purification methods
  • Equipment used in the purification process

What Is Protein Purification?

Protein purification isolates a specific protein of interest from a complex mixture of biological material, such as cell extracts or culture supernatants. The goal is to obtain a highly pure form of the desired protein while removing contaminants effectively. The significance of protein purification is profound in various fields of science, including:

  • Biological research: Purified proteins are essential for understanding specific biomolecules' structure, function, and regulation. Researchers use purified proteins to study enzymatic reactions, signaling pathways, and protein-protein interactions, contributing to advancements in biology and medicine.
  • Biotechnology: In the biotechnology and pharmaceutical industries, protein purification is vital for producing therapeutic drugs, vaccines, and recombinant proteins. It ensures the safety, efficacy, and consistency of these products.
  • Structural biology: Protein purification is critical in determining protein structures using techniques like X-ray crystallography, NMR spectroscopy, or cryo-electron microscopy. High-purity samples are necessary for accurate structural analysis.
  • Drug discovery and development: Purified proteins are used in high-throughput screening assays to identify potential drug candidates. Understanding the function of target proteins is crucial in drug discovery and development.

What are the Objectives of Protein Purification?

Understanding the objectives of protein purification is essential for efficient resource allocation, quality control, and experimental design. It ensures that the purification process is tailored to meet specific goals, whether they involve obtaining highly pure protein, maximizing yield, preserving protein activity, or meeting criteria for downstream experiments and applications. 

This clarity enhances the overall efficiency and success of protein purification, contributing to more effective research and biotechnological advancements. The primary objectives of protein purification are as follows:

  1. Obtain high purity in samples: The main goal is to isolate the protein of interest in a highly pure form, removing other molecules and contaminants.
  2. Separate from contaminants: Proteins are often present in complex mixtures with other biomolecules, such as nucleic acids, lipids, and other proteins. Purification aims to separate the target protein from these contaminants.
  3. Maintain protein integrity: The purification process should not alter the protein's structure, activity, or biological function. The protein should remain in its native state whenever possible.
  4. Quantify and concentrate: Determining the concentration of the purified protein is essential for subsequent experiments. Concentrating the protein to higher levels can be necessary.
  5. Reliable and reproducible results: The purification process should be reliable and reproducible, allowing for consistent results in research or production.

How Does Protein Purification Work?

Protein purification involves separating a target protein from contaminants by applying size exclusion, ion exchange, affinity, hydrophobicity, or isoelectric point. 

Various factors, including the specificity of the method, sample complexity, protein stability, yield-purity trade-offs, scale, and reproducibility, influence success in protein purification. Understanding these factors is crucial for designing effective purification strategies.

Protein of Interest vs. Contaminants

The primary objective of protein purification is to isolate a specific protein of interest from a complex mixture containing various contaminants. The protein of interest is the target biomolecule, and its purity and quality are crucial for downstream applications in research, diagnostics, or biotechnology. Contaminants, on the other hand, are unwanted biomolecules present in the initial sample.

These contaminants include other proteins, nucleic acids, lipids, small molecules, and cellular debris. Separating the protein of interest from these contaminants is the central challenge in protein purification.

Key Factors Affecting Purification

Several factors influence the success of protein purification:

  • Specificity of separation method: The choice of purification method depends on the specific characteristics of the protein of interest, such as size, charge, and binding partners. Selecting the most appropriate method is critical for successful separation.
  • Sample complexity: The complexity of the initial sample, including the number and types of contaminants, affects the purification strategy. More complex samples may require multiple purification steps.
  • Protein stability: Some proteins may be sensitive to pH, temperature, or salt concentration changes. Maintaining the stability of the protein during purification is essential to preserve its structure and function.
  • Yield vs. purity: Balancing the yield (amount of purified protein obtained) with the desired purity level is essential. Higher purity often requires more extensive purification steps but may result in lower yields.
  • Scale of purification: The scale of purification can vary from small laboratory-scale experiments to large industrial processes. The equipment and techniques used must be suitable for the desired scale.
  • Factors that affect reproducibility: Achieving consistent results across multiple purification runs is essential. Column packing, buffer preparation, and standard operating procedures greatly contribute to accuracy and reproducibility.

Understanding and considering these factors are vital for successful protein purification because they directly impact the purified protein's quality, quantity, and reliability. Failing to account for these factors can lead to suboptimal results, impure samples, protein denaturation, or the loss of valuable material.

Effective protein purification is essential for scientific research and applications in biotechnology, pharmaceuticals, and medical diagnostics, where the purity and integrity of proteins are critical to their functionality and effectiveness.

Overview of the Protein Purification Process

In general, the protein purification process involves several steps. Each is integral to obtaining a pure and functional protein. Let's break down this process step by step:

  1. Cell lysis
  2. Supernatant collection
  3. Clarification
  4. Protein concentration
  5. Purification protocol
  6. Characterization
  7. Storage and analysis

Cell Lysis

Cells are broken open using various methods, such as mechanical disruption (homogenization), chemical lysis (detergents, enzymes), or sonication (ultrasonic waves). The choice of method depends on the type of cells and the protein of interest.

The lysis method must effectively release the target protein while preserving its structure and activity. It is best to take care to avoid excessive denaturation or degradation.

Supernatant Collection

After cell lysis, the resulting mixture, often referred to as a lysate, is obtained. This lysate is then subjected to centrifugation, which separates cellular debris and unbroken cells from the soluble fraction called the supernatant. The supernatant contains the target protein along with other cellular components.


In some cases, additional clarification steps are necessary to remove large particles and impurities from the supernatant. Clarification techniques may include additional low-speed centrifugation or filtration through membranes with specific pore sizes.

Protein Concentration

Once the supernatant is sufficiently clarified, the next step is often protein concentration. Protein concentration can be achieved using techniques like ultrafiltration or ammonium sulfate precipitation, allowing for a higher concentration of the target protein in a smaller volume.

Purification Protocol

At the core of protein purification is separating the target protein from the remaining impurities. Various purification methods can be employed. The specific choice of method depends on the certain characteristics of the protein, its affinity for particular ligands, and the desired level of purity.

The characteristics to consider include the properties and attributes of the target protein itself, such as its size, charge, hydrophobicity, and structural stability. Additionally, understanding the protein's affinity for specific ligands or affinity tags plays a crucial role in method selection. Equally significant is the desired level of purity, which guides the purification process and determines the choice of purification techniques. 

By considering these characteristics, researchers can tailor their protein purification strategy to effectively separate and isolate the protein of interest from impurities, ensuring the success of the purification process.


After purification, it's essential to characterize the purified protein to confirm its identity, purity, and integrity. Standard characterization techniques include SDS-PAGE, western blotting, mass spectrometry, spectroscopy, and more. These methods verify that the protein is the target of interest and assess its structural and functional properties.

Storage & Analysis

Finally, the purified proteins are stored under appropriate conditions to maintain stability and functionality. These proteins are then ready for use in various downstream experiments, such as enzymatic assays, structural studies, or applications in biotechnology.

Types of Protein Purification Methods

Several types of protein purification methods are designed to isolate proteins based on different properties. Here are some of the most commonly used methods:

Various Chromatographic Methods

Chromatography is a widely used method for protein purification, exploiting various properties of proteins. It involves passing a sample through a stationary phase, where different proteins interact differently and are subsequently separated.

  • Affinity chromatography: Affinity chromatography isolates specific proteins by exploiting interactions with immobilized ligands or antibodies. It's ideal for highly pure, target-specific protein purification.
  • Ion exchange chromatography: Ion exchange chromatography separates proteins based on charge properties, with cation and anion exchange methods available for diverse charge interactions.
  • Size exclusion chromatography: Size exclusion chromatography separates proteins by molecular size, allowing the isolation of larger proteins while removing smaller ones and contaminants.
  • Reverse phase chromatography: Reverse phase chromatography utilizes hydrophobic interactions to separate proteins with differing hydrophobicity, beneficial for hydrophobic protein or peptide purification.
  • Hydroxyapatite chromatography: Hydroxyapatite chromatography separates proteins by interacting with the column, making it useful for nucleic acid-binding proteins and a milder alternative to ion exchange chromatography.
  • Hydrophobic interaction chromatography (HIC): HIC separates proteins based on hydrophobicity, making it suitable for purifying proteins sensitive to denaturation or high salt concentrations.


Centrifugation techniques play an important role in protein purification by separating components of a mixture based on their size, shape, and density. Several centrifugation methods are used in protein purification, each serving specific purposes. Here’s an overview of some common centrifugation techniques:

  • Ultracentrifugation: A high-speed centrifugation technique is used to separate particles, including proteins and subcellular organelles, based on density. Ultracentrifuges can achieve very high speeds, creating strong centrifugal forces that effectively separate particles in a sample. This method is often used for isolating cellular organelles like mitochondria, nuclei, and ribosomes and for sedimenting large protein complexes.
  • Differential centrifugation: Differential centrifugation is a series of steps performed at varying speeds to separate particles and organelles based on sedimentation rates. The sample is spun at low speeds to remove large debris and unbroken cells. The supernatant is then collected and subjected to higher-speed centrifugation to isolate progressively smaller particles. This technique helps fractionate organelles and proteins from a complex mixture, such as a cell lysate.
  • Gradient centrifugation: Gradient centrifugation uses density gradients, often sucrose or cesium chloride solutions, to separate particles based on their density. The sample is layered on top of the gradient. During centrifugation, particles migrate through the gradient until they reach their equilibrium position based on density. Gradient centrifugation can be used for purifying proteins and macromolecular complexes by separating them from contaminants based on differences in buoyant density.
  • Isopycnic centrifugation (Equilibrium Centrifugation): In isopycnic centrifugation, particles are separated solely based on density, with no density gradient in the centrifuge tube. All particles migrate until they reach a position in the tube where the surrounding medium has the same density as the particle. This technique helps researchers study the buoyant density of macromolecules or separate particles with similar densities.

Precipitation Techniques

Two common precipitation techniques include ammonium sulfate precipitation and salting out. Ammonium sulfate is a commonly used salt in protein purification. It works by reducing the solubility of proteins in a solution.

In this method, increasing concentrations of ammonium sulfate are gradually added to the protein solution under controlled conditions, typically at low temperatures. As the ammonium sulfate concentration increases, proteins with lower solubility at higher salt concentrations begin precipitating out of the solution.

The degree of precipitation depends on the specific ammonium sulfate saturation level, which can be adjusted to target the desired protein fraction. After precipitation, the protein precipitate can be collected by centrifugation or filtration, and further purification steps can be employed to isolate the protein of interest.

Salting out involves salts, often sodium chloride or ammonium sulfate, to reduce protein solubility. Adding a high salt concentration to the protein solution disrupts the water molecules surrounding the protein, leading to reduced solubility.

The proteins then aggregate and precipitate out of the solution as larger complexes. The choice of salt and its concentration can be adjusted to control the degree of protein precipitation and selectivity. After precipitation, the protein precipitate can be separated from the solution using centrifugation or filtration. Salting out is a simple and effective method for protein purification, often used as an initial step to remove impurities and concentrate proteins.

Liquid-Liquid Extraction

Liquid-liquid extraction relies on differential solubility, where proteins partition between two immiscible liquid phases, typically aqueous and organic phases. This partitioning is driven by the proteins' affinity for the solvent that best matches their properties, such as hydrophobic or hydrophilic characteristics.

The process involves creating a biphasic system by mixing an organic solvent with an aqueous buffer. The protein-containing sample is then added and mixed, allowing the proteins to distribute between the phases. Hydrophobic proteins migrate into the organic phase, while hydrophilic ones remain in the aqueous phase. After phase separation, the phase containing the target protein is collected and subjected to further purification or concentration.

Liquid-liquid extraction is especially valuable as an initial purification step when dealing with complex samples or when contaminants, lipids, or hydrophobic molecules need removal. Careful selection of the organic solvent and buffer is crucial to ensure successful protein partitioning.

Protein Tagging

Protein tagging is a widely used method in protein purification that involves attaching short peptide sequences, known as tags, to a target protein. These tags serve as handles for easy purification and identification of the protein. The His-Tag (histidine tag) and the GST-Tag (glutathione S-transferase tag) are two commonly employed tags.

The His-Tag typically consists of 6-10 consecutive histidine residues and has a strong affinity for specific metal ions, such as nickel (Ni²⁺) and cobalt (Co²⁺). In the purification process, the His-Tagged protein is introduced into a chromatography column containing immobilized metal ions (IMAC), allowing for selective binding of the target protein while contaminants pass through. This method is known for its high specificity and yield, making it a preferred choice for purifying recombinant proteins.

On the other hand, the GST-Tag involves fusing the target protein with the glutathione S-transferase enzyme. In purification, the GST-Tagged protein binds specifically to a resin containing glutathione. After binding, the column is washed to remove impurities, and the GST-Tagged protein is eluted using reduced glutathione. GST-Tag purification is recognized for its high yield and mild elution conditions, preserving the integrity and activity of the purified protein. This method is beneficial for studying protein-protein interactions and enzyme assays.

Both His-Tag and GST-Tag systems provide efficient ways to purify recombinant proteins, and the choice depends on factors such as the properties of the target protein and the desired level of purity for specific research or biotechnological applications. These tags simplify protein purification processes and are indispensable tools in various molecular biology and biotechnology areas.


Dialysis removes small molecules, salts, or low molecular weight impurities from a protein solution. It involves placing the protein-containing sample in a semipermeable membrane, typically a dialysis bag or tubing, with pores small enough to retain the protein but large enough to allow the passage of smaller molecules.

Once the sample is enclosed within the dialysis membrane, it is immersed in a suitable buffer or solvent. Over time, through diffusion, the smaller molecules and impurities move out of the dialysis bag and into the surrounding buffer. Meanwhile, the protein of interest remains within the bag, effectively exchanging the sample's original buffer or solution with the desired buffer for downstream applications.

Dialysis is a gentle and effective method for changing the buffer, concentrating a protein solution, or removing unwanted contaminants, and it is handy when harsher purification methods might denature or damage the protein. It is commonly employed in biochemical and biophysical research to prepare samples for experiments, such as structural studies, enzymatic assays, and biophysical analyses.


Sonication disrupts cell membranes, homogenizes samples, and assists in various biochemical processes. It involves the application of high-frequency sound waves or ultrasonic vibrations to a protein sample.

During sonication, ultrasonic waves generate tiny bubbles in the sample, rapidly expanding and collapsing. These micro-explosions create intense localized shear forces and cavitation, effectively breaking down cells, cell walls, or cellular structures to release proteins. Sonication is particularly useful for lysing cells to obtain a cell lysate containing the desired proteins.

Additionally, sonication can be employed to homogenize protein samples, disrupt protein aggregates or complexes, and facilitate the solubilization of proteins in various buffers or solutions. It is crucial for preparing protein samples for downstream analyses, such as gel electrophoresis, chromatography, and other biochemical assays. It ensures uniform and efficient sample processing.

Equipment Used in Protein Purification

Protein purification involves a range of specialized equipment designed to separate, analyze, and purify proteins efficiently. These diverse tools—chromatography systems and columns, centrifuges, electrophoresis apparatus, spectrophotometers, etc.—cater to various aspects of the purification process, ensuring precise and reliable results.

  • Liquid Chromatography (LC) systems: LC systems, including high-performance liquid chromatography (HPLC), are robust protein separation and purification tools. They utilize columns and solvents to achieve high-resolution separation based on various protein properties.
  • Centrifuges: Centrifuges separate cellular debris and other solid components from protein solutions. They work by spinning samples at high speeds, causing particles to settle at the bottom, leaving a clear supernatant.
  • Electrophoresis equipment: Electrophoresis apparatus, like SDS-PAGE or native PAGE systems, separate proteins based on size and charge. Proteins migrate through a gel matrix under an electric field, forming distinct bands that can be further analyzed or isolated.
  • Spectrophotometers: Spectrophotometers measure the absorbance of light by proteins at specific wavelengths. This is crucial for determining protein concentration and assessing purity.
  • Sonicators: Sonicators use high-frequency sound waves to disrupt cell membranes, homogenize samples, and assist in solubilizing proteins. They are useful for lysing cells and breaking down cellular structures.
  • Dialysis membranes: Dialysis membranes exchange or remove buffer components from protein solutions. They consist of semipermeable materials that allow small molecules to pass through, making them suitable for buffer exchange and concentration.

Selecting the appropriate equipment for protein purification involves considering factors like the protein’s properties, purification objectives, sample complexity, sensitivity, available resources, budget, and compatibility.

Each piece of equipment serves specific roles: chromatography for precise separation, spectrophotometers for accurate concentration measurements, or centrifuges for debris removal. The choice should align with the project’s goals, lab capabilities, and desired results, ensuring efficient and successful protein purification processes.

Reagents & Consumables

Reagents and consumables are essential in protein purification as they facilitate protein stability, solubility, separation, and analysis. They help maintain the integrity of the protein throughout the purification process and enable accurate quantification and characterization, ensuring successful and reliable results in research and biotechnology applications.

  • Buffers: Buffers maintain the pH and ionic strength of the protein solution, which is necessary for protein stability and activity during purification.
  • Detergents: Various detergents help solubilize membrane proteins and disrupt lipid interactions, aiding in the extraction and purification of these proteins.
  • Protease inhibitors: Protease inhibitors prevent enzymatic degradation of proteins during purification, safeguarding their integrity.
  • Imidazole: Imidazole is used in affinity chromatography to elute His-tagged proteins by competing for binding sites on the resin.
  • Agarose: Agarose gels are utilized in gel filtration chromatography to separate proteins based on size.
  • Coomassie stain: These stains are employed for visualizing proteins after electrophoresis, aiding in their identification and quantification.
  • Labeling reagents: Labeling reagents are used to attach fluorescent or radioactive tags to proteins, enabling their detection and tracking in assays.
  • Substrates: Substrates are specific molecules used in enzyme assays to measure enzyme activity or kinetics.
  • Salt solutions: Salt solutions are used to adjust salt concentrations in buffer systems, aiding in protein precipitation, solubility, and binding interactions during purification processes.

Characterization of Purified Proteins

Various characterization methods enable researchers to comprehensively study purified proteins, offering insights into their structure, purity, modifications, and functional properties, contributing to a deeper understanding of biological processes and facilitating advancements in various fields of science and medicine. Some of the most common include:

  • SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis): SDS-PAGE is a widely used technique that separates proteins based on their molecular weight. By denaturing proteins with SDS and subjecting them to an electric field within a polyacrylamide gel, proteins migrate and form distinct bands according to their size. This method provides insight into protein purity, subunit composition, and integrity.
  • Western blotting: Also known as immunoblotting, this technique detects specific proteins within a complex mixture. It involves transferring proteins from a gel to a membrane, which is then probed with antibodies targeting the protein of interest. This method aids in protein identification and quantification, making it invaluable for studying protein expression and localization.
  • Mass spectrometry: Mass spectrometry is used to determine proteins' precise mass and composition. It identifies proteins by analyzing the mass-to-charge ratio of their ions, providing information about protein sequence, post-translational modifications, and potential contaminants.
  • Isoelectric focusing (IEF): IEF is a technique that separates proteins based on their isoelectric point (pI), the pH at which they have no net charge. Proteins migrate through a pH gradient gel until they reach their pI, where they stop moving. This method helps elucidate protein charge heterogeneity and purity.
  • Protein concentration determination: Accurate measurement of protein concentration is vital for various applications. Using techniques like the Bradford or BCA assay, spectrophotometry is commonly employed to determine protein concentration based on light absorption, providing essential data for downstream experiments.
  • Post-translational modifications: Characterizing post-translational modifications (PTMs) is crucial in understanding protein function. Techniques like mass spectrometry and phosphoprotein staining reveal PTMs such as phosphorylation, glycosylation, and acetylation, shedding light on how these modifications impact protein activity and cellular processes.

Wrap-Up & Takeaways

Protein purification is a fundamental process in biochemistry and biotechnology, aiming to isolate specific proteins from complex mixtures. It involves techniques like chromatography, centrifugation, and electrophoresis, supported by reagents and consumables.

The choice of method depends on factors like protein properties and purification objectives. Characterization techniques such as SDS-PAGE, Western blotting, mass spectrometry, and isoelectric focusing validate the purity and integrity of purified proteins.

Protein purification holds immense significance as it provides highly pure proteins critical for understanding their structure, function, and interactions. Researchers employ purified proteins in enzymatic assays, signaling pathway studies, and protein-protein interaction analyses, advancing knowledge in biology and medicine. Enzyme purification, in particular, is pivotal in drug development, diagnostic assays, and biotechnological applications.

Protein purification techniques continually evolve, driven by the demand for enhanced specificity, speed, and yield. Innovations include affinity chromatography with novel ligands, improved column materials, and automated systems.

Advancements in mass spectrometry and protein analytics enable more precise characterization of purified proteins. Furthermore, research focuses on sustainable and cost-effective purification methods to address environmental concerns and resource constraints.

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