Food Biochemistry and Food Processing

406 Part III: Muscle Foods

Vilhelmsson et al. (2004) were able to attain an
identification rate of about 80% using a combination
of search algorithms that included the open-access
Mascot program (Perkins et al. 1999) and a licensed
version of Protein Prospector MS-Fit (Clauser et al.
1999), searching against both protein databases and
a database containing all salmonid nucleotide se-
quences. In those cases where both the protein and
nucleotide databases yielded results, a 100% agree-
ment was observed between the two methods.
A more direct, if rather more time consuming,
way of obtaining protein identities is by direct se-
quence comparison. Until recently, this was accom-
plished by N-terminal or internal (after proteolysis)
sequencing by Edman degradation of eluted or elec-
troblotted protein spots (Erdjument-Bromage et al.
1999, Kamo and Tsugita 1999). Today, the method
of choice is tandem mass spectrometry (MS/MS). In
the peptide mass fingerprinting discussed above,
each peptide mass can potentially represent any of a
large number of possible amino acid sequence com-
binations. The larger the mass (and longer the se-
quence), the higher is the number of possible combi-

nations. In MS/MS one or several peptides are sepa-

rated from the mixture and dissociated into frag-

ments that then are subjected to a second round of

mass spectrometry, yielding a second layer of infor-

mation. Correlating this spectrum with the candidate

peptides identified in the first round narrows down

the number of candidates. Furthermore, several short

stretches of amino acid sequence will be obtained

for each peptide, which, when combined with the

peptide and fragment masses obtained, enhances the

specificity of the method even further (Chelius et al.

2003, Wilm et al. 1996, Yu et al. 2003b). Mass spec-

trometry methods in proteomics are reviewed in

Yates (1998).

SEAFOOD PROTEOMICS AND

THEIR RELEVANCE TO

PROCESSING AND QUALITY

Two-dimensional electrophoresis–based proteomics

have found a number of applications within food sci-

ence. Among early examples are such applications

as characterization of bovine caseins (Zeece et al.

Figure 18.5.A trypsin digest mass spectrometry fingerprint of a rainbow trout liver protein spot, identified as
apolipoprotein A I-1 (S. Martin, unpublished). The open arrows indicate mass peaks corresponding to trypsin self-
digestion products and were, therefore, excluded from the analysis. The solid arrows indicate the peaks that were
found to correspond to expected apolipoprotein A I-1 peptides.