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Identifying proteins
Using protein databases
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Using protein databases

Once 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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