Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation

Table 4 Top hits produced by searching E. coli flagellin MS data against a curated E. coli flagellin database (CD) and the public databases, Swiss-prot and NCBInr ^a

Strain number	Confirmed serotype	CD (195 sequences) top hit	Swiss-prot (331,337 sequen ces) top hit	NCBInr (25,303,445 sequences) top hit
E169	H1	H1	Shigella flagellin	flagellin [E. coli]
E170	H2	H2	E. coli Elongation factor	flagellin [E. coli]
E171	H3	H3	Salmonnella flagellin	flagellin [E. coli]
E172	H4	H4	E. coli K12 flagellin	flagellin [E. coli]
E173	H5	H5	E. coli K12 flagellin	E. coli flagellar protein FliC
E174	H6	H6	Shigella flagellin	FliC [E. Coli]
EDL933	H7	H7	Shigella flagellin	flagellin [E. coli]
E176	H8	H8	Shigella flagellin	flagellin [E. coli]
E177	H9	H9	Shigella flagellin	flagellin [E. coli]
E659	H10	H10	E. coli K12 flagellin	flagellin [E. coli]
902380	H7	H7	Shigella flagellin	flagellin [E. coli]
050958	H7	H7	Shigella flagellin	flagellin [E. coli]
090414	H7	H7	Shigella flagellin	flagellin [E. coli]
091349	H7	H7	Shigella flagellin	flagellin [E. coli]
091350	H7	H7	Shigella flagellin	flagellin [E. coli]

^aAn Orbitrap system was used with 30 ppm peptide mass tolerance, 0.5 kD MS/MS tolerance, one missed tryptic cleavage for all database searches. Oxidation on methionine and deamidation on glutamine and asparagine were chosen as a possible modification.