====== How to ====== ===== Creation/Suppression===== * create a [[DbConnection|connection to a database]] * [[createProject|create an hEIDI Project]] * [[openSession|open a MS Identification session]] to explore MSIdb content * [[createContext|create new contexts to organize and compile identification results]] * [[how_to:loadProject|reopen an existing hEIDI Project]] * [[deleteContext|delete context(s)]] * [[fillIdentInfo|get Sample/Run informations from ePims]] ===== Visualization ===== * [[browseContextProtGroups|Browse all context's protein groups]] * [[peptideView|visualize all context's peptides]] * [[viewProtgroups|visualize protein groups ]] information details * [[graphicalPlotPeptides|generate a graph (histograms, plots...) on peptides features]] * [[accessIdentificationInfos|access identification general informations (parse parameters, filters, statistic, FDR)]] * [[editIdentificationInfos|view and edit identification informations (general information ans run/sample)]] * [[accessspectralcountdata|run and/or view spectral count data]] * :!: **New** [[accessadjustedspectralcountdata|run and/or view adjusted spectral count data]] * [[accessProperties|access object properties, show/hide columns in a tree view, filter columns in a tree view]] ===== Save, import and export ===== * [[exportContext|export identified proteins & peptides from a context]] * [[exportComparison|export a comparison result]] * [[saveComparison|save/load a comparison result]] * [[saveToMSIdb|save modifications back to the MSIdb]] * [[exportSqlResult|export an SQL result to a file]] * [[spectrumMatchFeeder|populate MSI database with spectra]] * [[generateAMTdb|[AMT] generate a new AMT database from a context]] * [[includeUmcInAmtDb|[AMT] include UMCs in AMTdb]] (see Import UMCs into MSIdb) * [[exportPride|[PRIDE] export context to PRIDE XML format]] * [[exportPrideLog|[PRIDE] view PRIDE log]] * [[exportAdHocExport|[Ad-hoc export] on-demand exports]] * [[exportadhocexport_ppmswleaves|[Ad-hoc export] export Protein Groups, Peptides and Leaves]] * [[exportAdHocExport_N15|[Ad-hoc export, N15] export 15N data]] * [[importUmcToMsiDb|[AMT] Import UMCs into MSIdb]] =====Algorithm and other operation ===== * [[proteinGrouping|group proteins within a context]] * [[proteinFiltering|filter proteins or protein groups]] * [[resetProteinFiltering|reset protein/protein group filter]] * [[compareMultiContexts|compare several contexts]] * [[compareContextWithExtAccession|compare a context with an external accession list]] * [[accessspectralcountdata|run and/or view spectral count data]] * [[idfFilters|check that all identifications have been filtered with the same parameters]] * [[writeSqlQueries|write SQL Queries to explore database]] * [[changeTypicalProtein|change typical protein]] * [[alignRetentionTime|[AMT] align retention time]] * [[recomputeRetentionTime|[AMT] recompute retention time]] * [[batchProcessing| make batch processing]] * [[computeFalsePositiveRate|Compute False Positive Rate]]