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Reads in peptides and assigned probabilities, such as those computed by PeptideProphet, and computes probabilities that proteins are present in the original sample.
Output formats can be:
As an initial step of analysis, recovers from the database used for search all proteins corresponding to each peptide. This utilizes the program PeptideProphetOutput.
Wrapper for running ProteinProphet with user specified options.
Reads database used for search to compute at one time the percent coverage (what percent of the protein sequence was represented by observed peptides in the dataset) for all identified proteins.
Assorted png files displayed upon clicking the 'Help' button on the ProteinProphet results output.
CGI program which takes user's specifications to write stylsheet (in XSL), which is then passed along to an XML transformer program to generate the desired view of the data, whether that be HTML, tab delimited text, or XML. This is the workhorse for viewing ProteinProphet results, launched upon clicking 'Filter/Sort/Discard checked entries', 'Restore Original', and 'Write Displayed Data Subset to Filt', as well as by ProteinProphet.pl following its analysis.
CGI program which displays all protein entries containing each peptide. Launched by clicking on a peptide weight.
CGI program which displays all search results of specified precursor ion charge and peptide sequence. Launched by clicking on a precursor ion charge/peptide sequence.
CGI program which displays sensitivity and error rates predicted by ProteinProphet as a function of minimum probability threshold. Launched by clicking on 'Sensitivity/Error Info'.
CGI program which displays details of ProteinProphet analysis, as well as input files and run settings. Launched by clicking on 'More Analysis Info'.
CGI program which displays help on how to view ProteinProphet results, displaying Help Images. Launched by clicking on 'Help'.
CGI program which displays what filters were used to generate data subset files. Launched by clicking on 'Dataset Derivation Info'.
CGI program which displays identified peptides overlaid on sequence of protein. Launched by clicking on protein name.
CGI program which displays all protein entries containing each peptide when ProteinProphet run in 'HTML' mode. Launched by clicking on a peptide weight.
CGI program which filters ProteinProphet results when run in 'HTML' mode.
CGI program which restores filtered ProteinProphet results when run in 'HTML' mode.
Versatile program that imports XPRESS and ASAPRatio quantitation information for each identified protein (when ProteinProphet is run in the X or A mode, respectively), as well as record user-updated quantitation information (via clicking on the quantitation ratio). The program reads in and writes out ProteinProphet XML.
CGI program that displays information contributing to computed XPRESS quantitation ratio for protein entry. Launched by clicking on XPRESS protein ratio.
CGI program that updates ProteinProphet XML with user-specified chages. Launched from by clicking on 'Accept Changes'.
CGI program that displays information contributing to computed ASAPRatio quantitation ratio for protein entry. Launched by clicking on ASAPRAtio protein ratio.