ProDBWiki/DeveloperDocumentation/reduceSearches
Reduce Searches
Idea
To get good results with a mascot search, you choose many different search parameters. For example more than one database, 0 - 5 or more missed cleavage sites, a wide spectra for the peptide tolerance and small steps (50-100pmm in 10ppm steps). With every parameter more, the number of searches increases. Rapidly you have 100 or more searches for one scan. And if you want to analyse more than one scan, you can wait very long for your results.
If you choose the Reduce Searches, you can decrease the number of searches. This function tries which parameters give the best results and minimizes the searches. At first it only iterates over the missed cleavage sites and saves the best one. Then it iterates over the peptide tolerance (the missed cleavage site is always the best one) and saves the best combination from missed cleavage site and peptide tolerance. For all other searches these parameters are used and only the remaining parameters are iterated. By the use of this tool, you can reduce the number of searches to less than 10.
How to use
What Did I Do
Author: Nicole de la Chaux