As many people are throwing their opinions, here is my penny=92s worth
of opinion. Peptide mass mapping is and can be very powerful, provided
you have enough number of peptide masses (from the same protein)=20
determined to a good mass accuracy. More than five peptide masses will
be usually required for a greater confidence, because of the
possibilities of modifications (natural or those created
unintentionally during generation of these peptides) and mistakes in the
databases.
More than 50% of the time, the so called =93unknowns=94 turned out to =
be
known proteins (artifacts in protein generation, sample handling (gels,
digestions, etc.)) and this is where the technique is most useful. It
can save enough time and money that you can concentrate your efforts on
=93truly unknowns=94. =20
Peptide mass mapping can be powerful in matching the proteins to the
species it is derived from, unlike a simple homology search. At times,
Edman sequencing of the protein from blots, would identify only as
protein XXX, but mass mapping could even pinpoint the species it would
come from.=20
This technique is only a beginning in the process of getting
information about the =93unknowns=94, but not an end.=20
Viswanatham Katta