User:Nohic/sandbox

RAId (Robust Accurate Identification) is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence using strong statistics. It have been developed in the National Center for Biotechnology Information (NCBI) part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH).

Applications
This software is using rigorous statistics to identify proteins from original peptides sequence databases.

Database
The unique protein database structure of RAId integrate post-translational modifications (PTMs), single amino acid polymorphisms (SAPs) and their associated diseases.

Scoring
RAId is using different scoring functions (RAId-Score (RAIdDbS ), Hyperscore, K-score and XCorr ).

For each peptides from the database an E-Value is computed giving statistical significance during the protein identification.

The proportion of false discoveries (PFD) is define by XXX

$$PDF = \frac{Ec * N\sigma}{R(E\leq Ec)}$$where $$R(E\leq Ec)$$ is the number of peptides with E-value $$\leq Ec$$, Ec the E-value cut off,