FAS1-4 mutations cause alternative HtrA1 degradation. The introduction of an in vivo relevant mutation in the FAS1 domain of TGFBIp influenced its degradation by HtrA1. The major cleavage sites, represented by more than eight spectra in the LC-MS/MS analysis, became more abundant in mutant proteins associated with the LCD phenotype (A546T, A546D, A546D/P551Q, and V624M). Cleavage sites appeared in and near the amyloidogenic 571–588 region in FAS1-4. Samples were analyzed in technical triplicate.