Certain wavelengths of light are absorbed by or transmitted through a solution when a light is passed through it. The color of the solution is due to the transmitted light. Different chemicals have different absorption spectra. For instance, several amino acids absorb light in the UV region. By virtue of this, they (and proteins containing them) can be detected in an optically clear solution. The vitamin riboflavin is another example. It appears yellow in solution, but absorbs light in the blue region.

Photometry involves the qualitative and quantitative use of absorption spectra in the UV, visible and infrared regions to characterize components in solutions. Solution conditions such as pH or salt concentration can influence the absorption spectra of some compounds. The concentration of a compound in a solution can be determined using photometry and a standard curve prepared from a known concentration standard. Sometimes indirect colorimetric assays are used to quantify colorless substances in solution. In a colorimetric assay, the color of the solution results from a chemical reaction of a reagent with the compound of interest. Proteins are often detected by colorimetric assays such as the Biuret or Folin-Ciocalteu assays.

Chromatography involves the separation of solution components on a solid phase support based on differential affinity of substances for the solid phase over a mobile phase (liquid or gas). Solutes are resolved by differential migration during passage through a porous medium. Many types of chromatography exist including gas, paper, thin layer, high pressure and column.

Perhaps the most widely used type of chromatography involves the use of a column packed with separatory material. The material may separate substances based on size, charge or affinity. Size separation occurs when the solutes must pass over a column filled with particles that act as a molecular sieve. Large molecules pass through the column faster as they cannot enter the pores of the spongelike packing granules. Smaller molecules take a more tortuous journey through the granules in their path, thus having a much longer transit time through the column.

Ion exchange chromatography takes advantage of the molecular charge of the solutes and uses a charged packing medium. For instance, most proteins have a net negative charge that can be exploited to purify them using a positively charged packing material. Likewise, affinity chromatography can be used to remove specific components from a complex solution. For instance, a packing resin that has insulin bound to it can be used to extract insulin binding proteins from a complex cell lysate.

Atoms have a central nucleus that contains small particles, protons and neutrons, surrounded by a cloud of electrons. The nuclear charge (the number of protons in the nucleus) determines the chemical properties of an atom. Atoms with a constant nuclear charge but with varied masses (caused by differences in the number of neutrons) are called isotopes of an atom. Unstable isotopes may spontaneously undergo nuclear transformation of mass and charge. This process results in the emission of specific radioactive particles. These particle emitting isotopes are called radioisotopes and can be used to track biological reactions and processes via the detection of the emitted particles. Radioisotopic assays are very sensitive. However, radioactivity is harmful to DNA and extreme care must be taken in working with and disposing of radioisotopes. Biochemically important isotopes include 3H, 14C, 32P, and 35S.

Electrophoresis encompasses all techniques where charged molecules migrate in an electric field through solutions. Often, the aqueous ionic solution is carried in a solid or matrix support and the samples are applied to the matrix in spots as in agarose or polyacrylamide gel electrophoresis. The mobility or rate of movement of a molecule increases with increased applied voltage or increased net charge of the molecule. The mobility of a molecule decreases with increased molecular size and shape because of friction with the supporting material.

Isoelectric focusing involves separating molecules according to their isoelectric point (pI), the pH where they are electrically neutral, using electrophoresis. In this method, ampholytes, stable molecules that carry a charge at a particular pH, are embedded in a solid matrix. When an electrical current is applied, the ampholytes migrate to their isoelectric pH. An applied protein will also migrate to its isoelectric point. The resultant gel can be stained for the presence of proteins that will be organized in visible bands. Comparison of the sample lanes to standard lanes containing proteins of known size and pI yields information about the sample proteins.