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a protein has been fragmented and mass spectra taken, the question of
what to do with the data presents itself. The mass data itself would
be of little use were it not for the many protein databases which exist.
Of course, it is possible to spend years looking at every single entry
in every single database. That, for obvious reasons, would be impractical.
Fortunately, there exist several programs, some operated by individual
databases, some operated independently, that allow the user to enter
their experimental masses and search for proteins with matching masses,
within a particular error range. You may access several of these databases
from within the case study, or via the "more information" area.
You should read any "instruction" or "read me" pages before attempting
to use any database. They are put there for a reason-- these searches
are not terribly intuitive, and it may take several attempts before
you are comfortable enough with the terminology and interface to understand
what parameters will give you the best results. There are some features
in common among the most popular searches. You should be able to choose
the enzyme used to cleave your protein (tryspin was used in this case
study; it is also often the default choice). Many digests require some
sort of cysteine modification (to break disulfide bridges; in this case
study, carbamidomethylation), which must be taken into account when
masses are measured. You may also choose how narrow a margin of error
you want to search within, as well as the minimum number of peptides
to match. You can even limit your searches to a certain species, if
you are positive about the source of your sample (which is obviously
not a feature you should invoke for this case study). One warning: be
sure that you know the difference between "average mass" and "monoisotopic
mass" when you enter your experimental data.
Once again, be sure to read any "Getting Started" or "Help" files before
actually using a database; they should contain information that is not
only relevant to the specific program, but can also save you lots of
time and frustration.
Here are the search engines you could use to do peptide mass mapping.
All links are good as of May 8, 2003.
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