A Simple Outline of Methods for Protein Isolation and Purification (2023)

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  • Endocrinol Metab (Seoul)
  • v.32(1); 2017 Mar
  • PMC5368116

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A Simple Outline of Methods for Protein Isolation and Purification (1)

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Endocrinol Metab (Seoul). 2017 Mar; 32(1): 18–22.

Published online 2017 Feb 28. doi:10.3803/EnM.2017.32.1.18

PMCID: PMC5368116

PMID: 28256117

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At the summer workshop of the Korean Endocrine Society held in 2016, some examples of protein experiments were discussed in the session entitled “All about working with proteins.” In contrast to what the title suggested, it was unrealistic to comprehensively discuss all protein analytical methods. Therefore, the goal was to outline protein experimental techniques that are useful in research or in bench work. In conversations with clinicians, however, I have always felt that researchers who do not engage in bench science have different demands than those who do. Protein research tools that are useful in bench science may not be very useful or effective in the diagnostic field. In this paper, I provide a general summary of the protein analytical methods that are used in basic scientific research, and describe how they can be applied in the diagnostic field.

Keywords: Chromatography, Molecular imaging, Immunoenzyme techniques


As a simple example, let us think about how to obtain a protein of interest. Proteins can be obtained from a wide variety of samples. For diagnostic purposes, they may be obtained from a patient's cells or tissues, whereas for experimental use on the bench, the proteins may originate from microorganisms or from cell lines derived from insects, vertebrate animals, or plants. In any case, endogenous proteins that we do not want are present in a much greater quantity than the proteins we do want. Regardless of the source, is not easy to isolate a specific protein for several reasons, some of which are presented below.

First, no generalized property can be applied in protein purification. In the case of nucleic acids (DNA or RNA), one can employ selective adsorption techniques using silica residues with positive charges, since nucleic acids have negative charges from their phosphodiester bonds. The development of specialized methods of nucleic acid purification, such as miniprep and midiprep, was made possible by the fact that all nucleic acid molecules are highly negatively charged. In contrast, the applicability of selective adsorption to proteins is limited for several reasons. Hydrophobicity or specific electrostatic properties can be found in a diverse range of molecules, including lipids, nucleic acids, and sugars. However, some proteins may have strong surface charges or specialized functional groups that can be useful for purification. For example, a purification method with phosphocellulose has been used for DNA-binding proteins that have many positively charged residues. Nonetheless, this does not guarantee high purity or loss-free purification. Unlike DNA, protein purification requires multiple steps, rather than a simple one-step procedure. As will be described later, fractionation during the isolation process and use of the proper column type during the purification process enable successful purification [1].

Second, the amount of the protein of interest tends to be quite small. Intracellular protein concentrations are known to be in the range of 300 mg/mL. However, this value refers to the total amount of proteins in a cell. Since the number of active proteins in cells is in the tens of thousands, most proteins are present in negligible quantities except for some housekeeping gene products. In some cases, the target proteins may be present in picomolar or femtomolar concentrations. Proteins such as keratins can be used as biomarkers for cancer diagnosis because they are overexpressed proteins. The typical analytical instruments used in biophysics are less sensitive than one might think. Spectroscopic or calorimetric methods usually require protein samples with concentrations ranging from 0.01 to 1 mM (or to tens of mg/mL). Therefore, most proteins directly derived from living organisms cannot be analyzed using those methods. In mass spectrometry, it is possible to analyze samples in femtogram units. However, mass spectrometry is not a panacea, because the ionization efficiency may be not high enough to obtain a useful signal, depending on the nature of the peptide fragments.

Third, there is no way to amplify proteins. In the case of nucleic acids, amplification is possible, to the point that even a trace amount obtained in a biological sample can be used for further analysis. Polymerase chain reaction (PCR) amplifies DNA sequences, and RNA sequences can also be amplified by reverse transcription PCR. In contrast, if a protein is not overproduced at the beginning of the experiment, it may be lost continuously during the experiment, to the point that it is not detectable at the final analytical stage.

Fourth, contamination issues are inevitable. This is related to the second and third problems discussed above. More specifically, certain proteins make up an exceptionally large share of the proteins present in cells. Intermediate filament proteins and histones are proteins that appear as contaminants when analyzing trace proteins by mass spectrometry. Samples from human patients pose especially severe problems. These samples may be attached to blood vessels, or may be a mixture of lesions and healthy tissue. Lipid molecules, blood cells, and/or blood plasma may already be present in excess. Proteins that are classified as noise are present in much greater quantities than the target protein, which often makes data analysis difficult.

Fifth, proteins are unstable. It is well known that RNA is quickly degraded, but proteins are also degraded by enzymes both in vivo and in vitro. It is not easy to block all proteolytic activity by adding protease inhibitors to a test tube. If the temperature, pH, or salt concentration is not suitable, proteins are likely to be denatured. If the experimental conditions of the buffer are not optimal, the proteins may aggregate before or after the analysis. In proteins with cysteine residues, the structure may be destroyed by undesired oxidation-reduction reactions. Experts familiar with protein purification emphasize that researchers should not leave proteins in the refrigerator for a long time because proteins are unstable macromolecules.


The simplest way to solve all the above problems for researchers is to use overexpression, or enrichment. The rule of thumb for protein experiments is to obtain as much protein as possible at the beginning of the experiment. As discussed above, proteins are inevitably lost over the course of the experiment because of their chemical and/or biological instability. Given these practical limitations, it is important to obtain as much protein as possible at the beginning of the process.

With this in mind, let us start our discussion of protein isolation by addressing methods for the high-efficiency isolation of proteins with little loss [2]. Choosing the best protein isolation method depends on the properties of the source sample (e.g., whether the sample is liquid or solid). Supposing that a solid sample contains a large number of cells, a process must be used for homogenizing the tissues and lysing the cells. In the case of tissue samples, mechanical homogenization methods are useful. Methods for lysing cells range from physical methods, such as heat treatment and sonication, to chemical methods, such as treatment with a detergent solution.

Detergents that increase the solubility of proteins can be used most effectively by taking into consideration the conditions of the experimental medium, especially the buffer. Using appropriate detergents, proteins that are difficult to extract (membrane proteins or nuclear proteins) can also be obtained in desirable amounts. In addition, chaotropic reagents, such as urea and guanidine hydrochloride, can be used to increase the efficiency of extraction because they break down the structure of the protein and dissolve well in water. However, treatment with chaotropic reagents usually requires high salt concentrations. Therefore, if not removed using membrane dialysis, the high salt concentration can cause problems in further steps of the experiment. The salt removal process itself can lead to loss of the protein. One should consider both the advantages and disadvantages of using chaotropic reagents when designing an experimental procedure.

In the case of liquid samples, a decision should be made about whether to obtain the dissolved protein or to extract it from the cells it is contained in. In order to extract the protein from the cells where it is present, it is necessary to isolate the cells by centrifugation. In particular, centrifugation using media with different densities may be useful to isolate proteins expressed in specific cells. For example, to obtain only the immune cells from bodily fluids or to separate adipocytes or keratinocytes from skin tissue, centrifuging the liquid containing the cells in a high-density medium may precipitate the desired cells depending on the density of each constituent cell. Density-gradient ultracentrifugation is additionally applicable for eliminating undesired cellular impurities or obtaining certain cell organelles.

If a soluble protein is obtained from bodily fluids, it is treated similarly to a cell lysate from solid samples. Protein solutions are generally dilute when they undergo analysis. Thus, it is necessary to perform an enrichment process, such as concentration or precipitation. The traditional techniques of salting out and heat denaturation have the advantage of being very simple. In addition, the precipitated protein is very stable, meaning that this process may be used as a means of increasing the shelf life of a protein. Salting out is a method of lowering the solubility of proteins through competing solubility in water using salts that are more soluble in water, such as ammonium sulfate. Since proteins precipitate at a specific concentration of salt, this procedure also has the advantage that the desired proteins can be separated from other proteins and precipitated.

Instead of using salts, it may be desirable to use isoelectric precipitation by lowering the pH. Isoelectric precipitation can be performed when the pH reaches at isoelectric point (pI) of the target protein. Each protein has a different pI value, meaning that isoelectric precipitation can be used as a fractionation method as well. Generally, this method is also very simple since a mineral acid or trichloroacetic acid (TCA) is titrated until the target protein is obtained through precipitation. When changing the pH or salting out is not preferable, polymers such as polyethylene glycol or organic solvents such as methanol or acetone can be used to promote precipitation. If required, a cocktail of precipitating reagents (e.g., a mixture of acetone and TCA) can be developed.

However, the isolation technique should be chosen with the method of analysis in mind, as the isolation step may cause denaturation of the protein or require additional steps such as salt removal. The centrifugal membrane concentration method is a useful single-step method of concentrating a protein. However, it is important to keep in mind that this method may exhibit problems involving clogging when used with highly concentrated proteins, and such problems decrease the efficiency of the concentration procedure and increase the loss of the protein.


After enrichment, purification is necessary. Proteins for analytic experiments must be pure enough to have a high signal-to-noise ratio. Methods for purifying target proteins from dirty mixtures vary widely, but preparation-grade purification is most commonly achieved using chromatography [1,2]. Since, as discussed above, proteins do not have a generalized purification method (unlike nucleic acids), the type of chromatography to be used depends entirely on the physical and chemical properties of the target protein. Proteins are usually purified by liquid chromatography (LC), and fast protein LC and high-performance LC can be chosen depending on whether the goal is preparation or quantitative analysis. For proteins, it is possible to use the following techniques either in a single step or sequentially: hydrophobic interaction column chromatography, size exclusion chromatography, ion exchange column chromatography, and affinity chromatography.

If it is not necessary to prepare a large quantity of the target protein, electrophoresis is a possibility. Electrophoresis separates proteins according to their molecular size. If the molecular weight of the target protein is known, the approximate band position on the gel can be cut and be used for further analysis like mass spectrometry. In general, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) provides 1-dimensional (1D) results when analyzing proteins by size. Instead of directly loading the protein sample when performing SDS-PAGE, it is possible to perform 2-dimensional (2D) electrophoresis by performing isoelectric focusing and loading the resultant gel tube with proteins separated according to their pI values. Gels developed in 2D have much better resolution than gels developed in 1D, making this a favorite technique in proteomics.

If the target protein is too small for the band (1D) or spot (2D) to be easily stained after electrophoresis, a Western blot using antibodies can be performed. In order to perform Western blotting, it is necessary to have an antibody specific to the target protein. In recent years, Western blotting has become possible in most cases due to the commercial availability of a very wide range of antibodies.

It is also possible to separate and purify proteins using antibodies. Immunoprecipitation is a good enrichment method for proteins. Since antibody binding is specific, most of the final products are obtained only from the target protein of the antibody. Either protein A-conjugated or protein G-conjugated agarose, which bind to most antibodies, can be used in most cases, meaning that virtually any kind of antibody can be applied to obtain a small amount of target protein through several rounds of centrifugation.

The enzyme-linked immunosorbent assay (ELISA) technique is a sensitive assay method using antibodies. ELISA is an enzyme-amplified reaction for antigens present in trace amounts in bodily fluids. Using ELISA, both the presence of the target protein and quantitative information about it can be obtained without purification. Of course, if enough antibodies are present, it is possible to identify the amount and location of proteins in tissues and cells in situ via immunohistochemistry or immunofluorescent labeling.

Antibodies are usually obtained from rats or rabbits. If the antibody is obtained from camelids, a unique antibody protein known as a single-chain antibody or nanobody can be obtained [3,4]. A typical antibody usually consists of four polypeptide chains per molecule, whereas a camelid antibody has two chains per antibody molecule. Since the antigen-binding site of a camelid antibody is composed of a single chain, the cloning and the production process are simpler than those of regular antibodies. As antibody design studies evolve, the use of single-chain antibodies will become more common.

Instead of using antibodies, it may be desirable to use an aptamer for the target protein [5]. Aptamers are nucleic acid molecules that bind specifically to their target proteins. Aptamers can be obtained by screening RNA or DNA macromolecules for binding to target molecules (usually through a method known as SELEX [systematic evolution of ligands by exponential enrichment]). Aptamers are likely to replace antibodies because they are very easy to synthesize in vitro.

In recent years, techniques for identifying target proteins in which mass spectrometry and LC are combined have become very common. Mass spectrometry, of course, has the limitation of only allowing qualitative analysis. Metabolic labeling can be used for quantitative analyses, but only in controllable culture conditions in bench work. Nevertheless, it is becoming an accurate and reliable protein analysis method since sequence information can be obtained even from trace amounts of target proteins. Recently, mass spectrometry imaging (also known as imaging mass spectrometry) has been studied as a way of detecting and analyzing proteins directly in specific locations in cells or tissues by imaging mass profiles (or maps) on 2D samples [6,7]. This technique is very similar to finding a neurotransmitter in a specific section of the brain using magnetic resonance imaging. If this technique is generalized, it will be possible to detect the presence or absence of a target protein in situ just by looking at the tissue or cell. In other words, it may become possible to determine the presence or absence of a desired biomarker quickly and accurately even in a complex situation (e.g., when no appropriate antibody exists or the sample is a mixture of normal tissue and lesion tissue).


Much work must still be done in collecting and analyzing proteins, requiring considerable research on the part of bench scientists. As long as proteins continue to be used as the major biomarkers for diagnosing diseases, scientists will make every effort to develop easier methods for protein research. I am confident that communication both among bench scientists and between bench scientists and clinicians will be a major driving force in future protein research.


CONFLICTS OF INTEREST: No potential conflict of interest relevant to this article was reported.


1. Burgess RR, Deutscher MP. Methods in enzymology: guide to protein purification. 2nd ed. Vol. 436. San Diego: Academic Press; 2009. [Google Scholar]

2. Janson JC. Protein purification: principles, high resolution methods, and applications. Hoboken: John Wiley & Sons; 2011. [Google Scholar]

3. Wang Y, Fan Z, Shao L, Kong X, Hou X, Tian D, et al. Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications. Int J Nanomedicine. 2016;11:3287–3303. [PMC free article] [PubMed] [Google Scholar]

4. Konning D, Zielonka S, Grzeschik J, Empting M, Valldorf B, Krah S, et al. Camelid and shark single domain antibodies: structural features and therapeutic potential. Curr Opin Struct Biol. 2016;45:10–16. [PubMed] [Google Scholar]

5. Ozalp VC, Kavruk M, Dilek O, Bayrac AT. Aptamers: molecular tools for medical diagnosis. Curr Top Med Chem. 2015;15:1125–1137. [PubMed] [Google Scholar]

6. Schwamborn K, Kriegsmann M, Weichert W. MALDI imaging mass spectrometry: from bench to bedside. Biochim Biophys Acta. 2016 Oct 31; doi:10.1016/j.bbapap.2016.10.014. [Epub] [PubMed] [CrossRef] [Google Scholar]

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Articles from Endocrinology and Metabolism are provided here courtesy of Korean Endocrinology Society


What are the methods of protein isolation and purification? ›

For proteins, it is possible to use the following techniques either in a single step or sequentially: hydrophobic interaction column chromatography, size exclusion chromatography, ion exchange column chromatography, and affinity chromatography.

What are the steps in protein isolation? ›

A protein isolation procedure can be viewed as a combination of steps where the protein progresses in purity with each step: (1) identification and acquisition of a source, (2) extraction from the source, (3) separation from nonprotein components such as nucleic acids and lipids, (4) concentration of the bulk protein ...

What is the most common method for protein purification? ›

The most widely used method for protein purification is affinity chromatography, which separates proteins based on their specific interaction with a matrix. It is one of the most effective techniques, since it takes advantage of the incorporation of a structure of choice (called a tag) onto the protein.

What is the purpose of isolation and purification of proteins? ›

Protein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms. Protein purification is vital for the characterization of the function, structure and interactions of the protein of interest.

What is the difference between isolation and purification? ›

Isolation is a separation technique in which we can obtain a purified compound. Therefore we can call it “purification” as well. In this technique, we can remove all the foreign or contaminating substances in order to isolate the desired compound. To get a highly pure compound, we can do a series of extractions.

What are the different types of protein isolate? ›

Two common forms are whey isolate and whey concentrate. Whey isolate undergoes different processing than whey concentrate, which results in the isolate containing more protein with less carbs and fat per serving.

What do you mean by purification of protein? ›

Protein purification can be defined as a series of steps that are carried out in order to obtain and study the desired protein from a complex mixture. Isolating a protein will help in the analysis of the protein's: Size and structure. Binding affinity. Biological activity.

What is an example of protein isolate? ›

Protein isolate from different plant and animal sources • Proteins that are utilised in food processing are of various origins, and can roughly be classified into animal proteins (gelatins), vegetable proteins (e.g. peanut protein, soy protein, wheat proteins, Almond protein, canola meal protein etc.), and animal ...

What are the four major methods of purification? ›

4 Methods to Purify Your Water
  • 1 – Boiling. Boiling water is the cheapest and safest method of water purification. ...
  • 2 – Filtration. Filtration is one of the effective ways of purifying water and when using the right multimedia filters it's effective in ridding water of the compounds. ...
  • 3 – Distillation. ...
  • 4 – Chlorination.

What are the general methods of purification? ›

The common methods of purification comprise distillation, crystallization, extraction, chromatographic, electrophoresis and other methods. In some cases, volatile and other impurities can be removed simply by heating.

What is the conclusion of protein purification? ›


Protein purification involves extraction and purification. In extraction process, there are different procedures to disrupt cells or tissues as well as different extraction solvents, depending on the nature of the cells or tissues.

What is the purpose of isolation method? ›

Patients must be placed in isolation to prevent the spread of infectious diseases. Those who are kept in strict isolation are often kept in a special room at the facility designed for that purpose.

Why is the isolation method necessary? ›

The isolation prevents dangerous voltages from passing to the operator in the event of an electrical fault/failure or during a surge from lightning. They are also important in preventing fire hazards, breaking ground loops, and eliminating transient noise in electrical systems.

What are 3 examples of isolation? ›

Isolation can involve staying at home for lengthy periods of time, having no access to services or community involvement, and little or no communication with friends, family, and acquaintances.

What are the three types of purification? ›

There are three methods of water purification: reverse osmosis (RO), distillation, and ultraviolet (UV). Here's a breakdown of how these methods work to purify water.

What is the difference between protein isolate and protein? ›

The main difference between the two is the amount of protein contained per scoop of protein powder. Isolate protein contains about 90 per cent of protein per scoop and a negligible amount of fat and lactose. On the other hand, protein concentrates contain 25 to 89 per cent protein (depending on the brand you buy).

What's the difference between way and isolate protein? ›

Although both Whey Protein and Whey Isolate are both derived from the same milk concentration, Whey Isolate is simply whey protein that has been filtered in a process to help remove the lactose in the powder itself. This is to create a leaner and lower fat protein source.

What is the difference between isolate protein? ›

Both whey protein concentrate and whey protein isolate have important benefits, but whey protein isolate is a purer form of whey protein and has a higher percentage of protein — sometimes much higher — than whey concentrate.

What are the 4 steps of protein purification? ›

There are four basic steps of protein purification: 1) cell lysis, 2) protein binding to a matrix, 3) washing and 4) elution.

What factors are important for protein purification? ›

Some known parameters like molecular weight, theoretical isoelectric point, the composition of amino acids, extinction coefficient help to increase the rate of successful protein purification. From the homologous protein structure, some variables like pH and salt concentrations are expected.

What is purification the process of? ›

Purification Process:

The purification process involves the removal of several germs, bacteria, impurities by using disinfecting agents. The impurified water causes many health issues. To maintain public as well as domestic hygiene many physical as well as chemical methods are used.

Where does protein isolate come from? ›

It's made from skim milk, whereas whey and casein powders are made from the whey and casein portions of milk, respectively. Milk protein isolate is made from skim milk powder through filtration processes. It has a similar protein composition to milk, with 80% of its protein from casein and 20% from whey.

What is the simplest purification method? ›

Fractional distillation is one of the simplest purification techniques whereby solutions can be separated into their pure components based on boiling point.

What is the 7 step purification process? ›

7 Steps of Water Purification
  1. Ion Exchange and Coagulation. The ion exchange and coagulation phase is the initial aspect of the water purification process. ...
  2. Sedimentation. ...
  3. Filtration and Granular Activated Carbon. ...
  4. Disinfection. ...
  5. Carbon Filters. ...
  6. Reverse Osmosis. ...
  7. Store Purified Water.
Aug 2, 2021

Which is the best purification method and why? ›

The best method for water purification is reverse osmosis. Reverse osmosis consists of four units. Polypropylene filter that removes the 50 microns pore size impurities. Polypropylene filter which removes 1 to 5 microns pore size impurities.

Which is the latest technique for purification isolation? ›

Chromatography is the best and latest technique for the isolation, purification and separation of organic compounds. Was this answer helpful?

What are the four most common methods for separation and purification? ›

The most common methods for purification fall into four broad categories—extraction, distillation, crstallization and chromatography. Each are based on slightly different chemical principles in some respects overlapping, in others complementary.

Which of the following method is used for purification? ›

Chlorination is a method used for purifying water.

What are the methods of protein isolation and separation in proteomics? ›

Three methods for separation of complex protein or peptide samples are preferred in proteomics: denaturing polyacrylamide gel electrophoresis (PAGE) or sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis, and high-performance liquid chromatography (HPLC).

What is the meaning of protein purification methods? ›

Protein purification can be defined as a series of steps that are carried out in order to obtain and study the desired protein from a complex mixture. Isolating a protein will help in the analysis of the protein's: Size and structure. Binding affinity. Biological activity.

What is the method of isolation and purification of organic compound? ›

Steam Distillation

This is a convenient method for the separation and purification of organic compounds from non- volatile organic or inorganic impurities.

Which is the best technique for isolation purification and separation? ›

Chromatography is the most useful and the latest technique of separation and purification of organic compounds.

What are the different types of protein detection methods? ›

There are two methods that are commonly used to identify proteins: Edman Degradation and Mass Spectrometry.

What are the two major methods proteins can be separated? ›

Let us suppose that you have found a protein of interest as a band/spot on a gel or as a peak from an HPLC separation, and you wish to determine its molecular identity. Two methods, Edman degradation and mass spectrometry, are commonly used for this purpose.

What is the summary of protein purification? ›

Protein purification is a series of processes intended to isolate and purify a single protein or complex from cells, tissues, or whole organisms. Protein purification is vital for the characterization of the function, structure, and interactions of the protein of interest.

Which method is used for purification? ›

Crystallization is the most commonly used method for the process of purification of solids. In this method, impure substances are dissolved in a minimum amount of water and then filtered.

What are the five 5 methods used for isolation compound? ›

The majority of isolation procedures still utilize simple extraction procedures with organic solvents of different polarity, water and their mixtures. The methods include maceration, percolation, Soxhlet extraction, ultrasound-assisted extraction and turbo-extraction.

What are methods of isolation? ›

There are two main ways to isolate organisms. Streaking for isolation on an agar plate involves the successive dilution of organisms until you have the cells at a low enough density that single cells are physically isolated spatially to give rise to recognizable individual colonies.

Which technique is only used for isolation or purification of cultures? ›

Streak Plate Method:

Most commonly used method to isolate pure cultures of bacteria. A small amount of mixed culture is placed on the tip of an inoculation loop/needle and is streaked across the surface of the agar medium.

What are the methods of isolation technique and which one is most common? ›

Answer and Explanation:
  • Plating- This includes the dilution of a mixture of microbes until only few is left in the suspension. ...
  • Streaking - This method is the most widely used technique in the isolation of microbes. ...
  • Single technique - This technique is the most ideal method in obtaining pure culture.

What are the three types of isolation technique? ›

There are three categories of Transmission-Based Precautions: Contact Precautions, Droplet Precautions, and Airborne Precautions.


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