Peptide analysis by LC-MS/MS allowing differentiation between BKV-VP1 subtypes. MS/MS analysis of a tryptic peptide corresponding to aa 39-63 of VP1 distinguished between subtypes (Figure 2A-C). Each panel shows the amino acid sequence for the relevant viral subtype detected in a clinical isolate. Measured and predicted masses (in brackets) of the b and y fragment ion series are shown within each spectrum. Amino acids that differ between the subtypes and the corresponding b and y fragment ions are indicated in red. (A) The first peptide (TGVDAITEVECFLNPEMGDPDENLR) corresponds to the subtypes Ia, Ib-1 and Ic. (B) The second peptide (TGLDAITEVECFLNPEMGDPDENLR) is specific for subtype Ib-2, whereas (C) the last peptide (TGVDAITEVECFLNPEMGDPDNDLR) is observed in subtype IV only. Subtype Ib-2 (panel B) is distinguishable from the other subtypes by the presence of a leucine residue instead of a valine residue at position 41, resulting in a corresponding mass difference of +14 Da in the b ion series from b3 onwards. Subtype IV (panel C) differs from all subtype I variants (panels A and B) by the presence of asparagine and aspartate instead of glutamate and asparagine at positions 60 and 61 resulting in a corresponding mass difference of +14 Da in the y ion series from y4 onwards.