Our results indicate in-source fragmentation can be a major source of partially tryptic peptides in LC-MS/MS proteomics and that the impact of these artifacts is much less significant for datadependent measurements of more complex mixtures due to the larger extent of under sampling of low-abundance species. It appears that the impact of trypsin-induced partially tryptic peptides is minimal (< 2%). The majority of the in-source fragments showed much later elution times compared to the predicted time, which is consistent with the larger size of their actual parent ions. By excluding such in-source fragmentation artifacts, one can then much more effectively identify in-vivo or in-vitro proteolytic products, as well as better characterize protease activities.
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