Proteolysis is also used in research and diagnostic applications: 
* Cleavage of fusion protein so that the fusion partner and protein tag used in protein expression and purification may be removed. The proteases used have high degree of specificity, such as thrombin, enterokinase, and TEV protease, so that only the targeted sequence may be cleaved.
* Complete inactivation of undesirable enzymatic activity or removal of unwanted proteins. For example, proteinase K, a broad-spectrum proteinase stable in urea and SDS, is often used in the preparation of nucleic acids to remove unwanted nuclease contaminants that may otherwise degrade the DNA or RNA.
* Partial inactivation, or changing the functionality, of specific protein. For example, treatment of DNA polymerase I with subtilisin yields the Klenow fragment, which retains its polymerase function but lacks 5'-exonuclease activity.
* Digestion of proteins in solution for proteome analysis by liquid chromatography-mass spectrometry (LC-MS). This may also be done by in-gel digestion of proteins after separation by gel electrophoresis for the identification by mass spectrometry.
* Analysis of the stability of folded domain under a wide range of conditions.
* Increasing success rate of crystallisation projects
* Production of digested protein used in growth media to culture bacteria and other organisms, e.g. tryptone in Lysogeny Broth.