Computational Survey of Sequence Specificity for Protein Terminal Tags Covering Nine Organisms and Its Application to Protein Identification

In 1998, Wilkins et al. (J. Mol. Biol. 1998, 278, 599–608)
reported high specificity in terminal
regions (terminal tags) of 15 519 proteins from five organisms
and proposed a methodology for identifying proteins by terminal tags.
However, their examined sequence data were not based on complete genome
sequences. Here, we examined current proteome data (217 249
entries from UniProt 2013_6 complete/reference proteome for nine organisms
including human) in terms of the specificity of terminal tags and
their computational annotation. One example from the results indicated
that the specificity of N-terminal tags plateaued at 28% at a length
of six residues for human; even when using both N- and C-terminal
tags, specificity was merely 66%. In order to determine the cause
of these low specificities, the annotation of proteins sharing terminal
tags with other proteins was examined. The results suggested that
a large majority were phylogenetically or functionally related, whereas
nonrelated proteins sharing terminal tags made up less than 1% of
human proteome data. On the basis of these findings, we constructed
the terminal tag sequence database ProteinCarta (http://ms3d.jp/software/proteincarta/), which includes all terminal tags of proteomes from the nine organisms
analyzed here, in order to confirm the specificity of terminal tags
and to identify the parent protein.