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Analytical Chemistry

Origin Of Trypsin Makes A Difference

Whether the enzyme comes from cows or pigs is a major source of variation in proteomics experiments

by Celia Henry Arnaud
October 28, 2013 | A version of this story appeared in Volume 91, Issue 43

Most proteomics experiments start with using the enzyme trypsin to cut proteins into smaller pieces at well-defined locations. Because the trypsin catalytic site is well conserved between species, one might expect that one trypsin is as good as another. As it turns out, the source of trypsin matters. Stephen E. Stein of the National Institute of Standards & Technology, Alexey I. Nesvizhskii of the University of Michigan, and coworkers have shown that the origin of trypsin is a significant, previously unrecognized, source of variation in proteomics experiments (J. Prot. Res. 2013, DOI: 10.1021/pr400611h). The researchers used three bovine and three porcine trypsins to digest highly purified human serum albumin for proteomic analysis. Although digestions were reproducible for individual trypsins, the resulting peptide mixtures differed significantly depending on whether the trypsin was of bovine or porcine origin. The bovine trypsins were more likely to miss cleavage sites, whereas the porcine trypsins were more likely to cut the peptides expected from trypsin cleavage into smaller pieces known as semitryptic peptides. Such variations could have a particularly deleterious effect on quantitative proteomics.


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