Identification of Cat L proteases from ES preparations by MSMS.

Peptide sequences were used to search against Genbank or a translated EST library for the identification of specific Cat L proteases. Single amino acids in bold type in MSMS sequences indicate proteomic identification of single amino acid polymorphisms (SAAP) deviating from published sequences and revealed though a translated EST database. Spots with accession numbers as NFD relate to spots where too few peptides were sequenced preventing isoform and sub-clade identification and were consequently not fully designated (NFD), although the clade could be defined. All data for protein identification, such as percentage coverage and search scores, can be seen in Tables S2 and S3.a)Sequences derived from MSMS analysis were interpreted either, automated or manually (where manually interpreted using Masslynx version 3.5 sequences are denoted by a *). Sequenced amino acids that match exactly with those found in the Genbank database or translated EST database are underlined.b)For MSMS spectra from peptides specific to each Cat L isoform see Figures S6, S7, S8, S9, S10, S11.c)Protein accession numbers correspond to those from Genbank.d)If protein spots were identified in vitro or in vivo they are denoted by •, if they are up or down regulated when compared with the other they are denoted with + or − respectively. The percentage contribution of each identified Cat L protease spot compared to the total Cat L proteases calculated using densitometry are in parentheses below the appropriate symbol (•,+ or −).