ProDBWiki/DeveloperDocumentation/ReduceSearchSpace

Reduce Search Space

Idea

You have mass spectra data and you want to do a search against a database to get the possible names of the protein. On the Mass Spectra Data: MS Query site you can choose between different search parameters and which search tool you want to use (mascot or emowse). If you want to get a better score (for example, when no significant hit is found) you can reduce the search space. That means, at first you do a "normal" search against a database of your choice. After that, the program automatically generates a new database (name: prodb-tmp) with the sequences of the hits from the first search. Then a new search is created with the same search parameters as before only the database changes. Now the programm searches against the new generated database (prodb-tmp). After all searches are completed, you can view the results.

How To Use

When you are on the "Mass Spectra Data: Search" site, you can choose the scan for the search. After clicking on "Peptide Mass Fingerprint" you are forwarded to the search form (Mass Spectra Data: MS Query). Here you can choose your search parameters. For reducing the search space, you have to select reduce search space from the dropdown menu Search for mixture. Also you have to choose how many hits are allowed, this has to be at least ten (out of these hits the new database is generated). Above the dropdown menu you can choose if you want the reduce always or only when no significant hits are found. All the other search parameters can be choosen like normal. After clicking on Search, the search will be submited. After the search you can see the results if you click on results. The search space reduce takes place for every search parameter.

What did I do

At first I changed the graphical user interface in msanalysis.cgi. After that I wrote a new function create_search_for_reduce in msanalysis.cgi, so that after the first search

Creating a New Database

Author: Nicole de la Chaux