Hi Dave,
both "programs" will help you to find the right proteins which will
match your MS-data. Can't tell much about Sequest, because this is not
longer (?) free. You have to buy it from Finnigan.
Mascot is program from Matrixscience and you can access it free from
their homepage. You can not download it but have free access. You can
search with a peptide fingerprint, with partial sequence information and
with uninterpreted MS/MS data. I often use Mascot when getting data from
our Q-TOF. You can generate a searchfile with your MS-software using
uninterpreted data and loaded this into Mascot, and it will identify
your protein(s).
Markus
Markus Piotrowski
Ruhr-Universitaet Bochum
Dep. Plant Physiology
Germany
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