match only if there is a sequence and mass-conserved
domain in a protein from another species.
The success of a search is also sensitive to the
collision energy conditions used to obtain the tandem
mass spectrum. Searches that use spectra from
[CL’]-fibrinopeptide (EGVNDNEEGFFSAR) obtained
under energy conditions varying from 10 to 20 eV are
shown in Table 4. At laboratory collision energies of
10-12.5 eV, the correct sequence is considerably lower
in the rankings. At energies closer to those typically
used for a peptide of this size, the rankings are closer
to the first position (Table 4). In several cases (rows 2,
3, and 5 of Table 4) the number one ranked sequence
was QGVNDNEEGFFSAR, a sequence from the fibrinogen
p-chain precursor. This sequence is identified
because the mass of this peptide sequence is within the
mass tolerance used for the search and the predominant
set of sequence ions observed for
[Glu’l-fibrinopeptide is the y-type ion. Consequently,
the single amino acid difference at the N terminus of
the fibrinogen p-chain peptide does not change the
mass-to-charge ratio values for the y ions of this sequence
and this results in a high score.