This new feature is based on our recently developed formalism for combining weighted P-values and a rigorous statistical method for protein identification . The most substantial extension of the RAId package, however, is its protein identification with accurate protein level P- and E-values. To go beyond scoring functions that are sums of independent contributions, we have further implemented in RAId the extreme value distribution (EVD) based method for peptide significance assignment . To extend accurate statistics to more scoring functions, we have also developed via dynamic programming the “all possible peptide” (APP) statistics which is applicable to any scoring function that sums independent contributions, including popular scoring functions such as XCorr , RAId score , Hyperscore , and Kscore . Based on the extension of the central limit theorem (CLT), RAId’s score distribution can be derived theoretically with one parameter for fitting the skewness of the corresponding score histogram per spectrum. An important feature of RAId is its use of spectrum-specific statistics for inferring peptide P- and E-values.
#SEARCHGUI PROTEOMICS DOWNLOAD SOFTWARE#
RAId is a software package for identifying peptides and proteins via analyzing tandem mass spectrometry data.
#SEARCHGUI PROTEOMICS DOWNLOAD CODE#
Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at. The results viewer displays and allows the users to download the analyses results. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. We have constructed a graphical user interface to facilitate the use of RAId on users’ local machines. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. Founded on rigorous statistical methods, RAId’s core program computes accurate E-values for peptides and proteins identified during database searches. RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data.
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