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1052DefectSkylineAlphaPeptDeep wording suggestionsBrendan MacLean4open25.2
1051DefectSkylineToo many LongWaitDlgs during AlphaPeptDeep library buildingdshteyn3open25.2
1050DefectSkylineAlphaPeptDeep output files need to be written somewhere outside the Skyline.exe/Tools folderdshteyn2open25.2
1049TodoSkylineUsers need to be able to tell Skyline that they have GC EI dataBrian Pratt3open 
1048DefectSkylineRetention Times - Peptide Comparison graph is not UI mode awareBrian Pratt3open 
1047DefectSkylineimprove SkylineCmd's handling of unrecognized transition list column namesBrian Pratt3open 
1046TodoSkylinecommand line needs the ability to remove named replicates from documentBrendan MacLean3open 
1045TodoSkylineUsers would like settable colors for each moleculeBrendan MacLean3open 
1044TodoSkylineAdd .sdf file support for spectral library creationBrendan MacLean3open 
1043DefectSkylineProvide for manual adjustmen of IM integration as we do for RTBrian Pratt3open 
1042TodoSkylineLibrary Explorer should show iRT information when it is present in a BLIB fileRita Chupalov3open24.2
1041DefectSkylineMSGF+ Installation form does not copy textBrendan MacLean3resolved24.2
1040TodoSkylineImport DIA Peptide Search should suggest using a prespecified isolation scheme based on the dataMatt Chambers3open24.2
1039DefectSkylineImport DDA Peptide Search produces different replicate name sort order than Import DIA Peptide SearchMatt Chambers3open24.2
1038TodoSkylineImport DIA Peptide Search never suggests chromatogram extraction filesMatt Chambers2open24.2
1037DefectSkylineDocuments with lots of mods can get very slow for Import > Transition ListBrendan MacLean3open24.2
1036TodoSkylineMass spec files contain metadata that could usefully be preserved as annotations on replicates in SkylineBrian Pratt3open 
1035TodoSkylineAdd Mirror and Koina menu options to Full-Scan graphBrendan MacLean3open24.2
1034TodoSkylineAdd mirror plot option to chromatogram graphsRita Chupalov3open24.2
1033DefectSkylineFix Normalize To > Heavy Peak Areas - Replicate plot to show rdotp line graphBrendan MacLean2resolved24.2
1032TodoSkylineSkyline needs at least one default report that just gives peak areas for all replicatesNick Shulman3open24.2
1031DefectSkylineMolecule reports show up in Document Settings - Reports when in proteomics modeBrian Pratt3open24.2
1030DefectSkylineSmall molecule improvements are predicted RTBrian Pratt3resolved 
1029TodoSkylineIntegrate Carafe into Peptide Settings - Library - Buildxgwang2open24.2
1028TodoSkylineIntegrate AlphaPeptDeep prediction into Peptide Settings - Library - Buildxgwang2open24.2
1027TodoSkylineSkyline DDA Searches that use Percolator need to calculate all-files-q-valuesBrendan MacLean2resolved24.2
1026DefectSkylinePeak Areas - Relative Abundance includes decoys by defaultRita Chupalov2open24.2
1025DefectSkylineFeature finding should provide information in terms of the expected peptides in a document - what's novel in the search result, what's missingBrian Pratt3open 
1024TodoSkylineSupport transition list "Note" import for all node levels (molecule, precursor, transition)Guest3closed 
1023DefectSkylineArgumentOutOfRangeException scrolling "Ion Types" context menuRita Chupalov2open24.2
1022DefectSkylineidFileName column values are not set in minimized libraries.Vagisha Sharma3open 
1021DefectSkylineDiscourage training mProphet models when explicit peak boundaries are being used from librariesGuest3closed23.2
1020DefectSkylineTransition Full Scan Settings page should discourage user from using retention time filtering with PRMGuest3closed23.2
1019DefectSkylineConfusing behavior of ID lines on chromatograms when library has multiple charge statesNick Shulman3open23.2
1018DefectSkylineAdducts should not attempt formula math when the molecule is described as mass onlyGuest3closed 
1017DefectSkylineMenuitem enabling needs cleanup for Spectrum Match settingsRita Chupalov3open23.2
1016TodoSkylineUse new "Associate Proteins" dialog in other places proteins are associatedMatt Chambers3open 
1015DefectSkylineGlycan idotp values incorrect until close and re-open documentBrendan MacLean3resolved23.2
1014DefectSkylineImmediate Window does not support ESC to focus the Targets ViewBrendan MacLean3open23.2
1013TodoSkylineConsider adding ability to filter MS/MS during DDA import peptide searchMatt Chambers3open23.2
1012DefectSkylineRatio to Heavy not available in small molecule mode until heavy precursors addedBrian Pratt3open23.2
1011DefectSkylineOut of Memory Error for Yeast.hlf in MethodEdit tutorial on Polish systemBrendan MacLean2open23.2
1010TodoSkylineAdd shortcuts for Peptide Settings and Transition SettingsBrendan MacLean2open23.2
1009DefectSkylinebottleneck in spectral library viewer when attempting to access ion mobility valuesBrian Pratt3resolved 
1008DefectSkylineinclude more .D metadata in Skyline replicatesMatt Chambers3open 
1007DefectSkylineModificationMatcher over guesses with Acetyl modificationsBrendan MacLean2resolved23.2
1006DefectSkylineImportTransitionListColumnSelectDlg too trusting of column header namesBrian Pratt3open23.2
1005TodoSkylineAdd support for setting Settings > Integrate All from the command-lineBrendan MacLean2resolved23.2
1004TodoSkylineAdd support for adding modifications from the command-lineBrendan MacLean2open23.2
1003DefectSkylineFix TransitionGroup.GetTransitions() for small molecules to use library information when availableBrendan MacLean3open23.2
1002DefectSkylinetrouble with transition list created with our own document grid exportBrian Pratt3open 
1001DefectSkylineneed exceptiion handling for bad MoleculeMassOffset.SplitFormulaAndMasses inputBrian Pratt3resolved 
1000DefectSkylineWhen reading peptide transition lists we should offer to apply document settings - adding reporter ions, other precursor charges etc.Brendan MacLean3open 
999DefectSkylineInvestigate using ExcludeFromAssay field from DIA-NNBrendan MacLean3open 
998DefectSkylineFix issues with matching DIANN speclib to report TSVMatt Chambers3open 
997DefectSkylineWe should allow adducts with formulaic losses on mass-only molecule description (e.g. don't complain that Adduct "[M-CO2]-" calls for removing more C atoms than are found in the molecule [+331.977251])Guest3closed 
996TodoSkylineFeature detection could be reworked to parallelize tasksBrian Pratt3resolved 
995TodoSkylineImport Peptide Search should default to no decoys when Library.UseExplicitPeakBounds will be usedMatt Chambers3open23.2
994TodoSkylineFile > Import > Peptide Search - FASTA page should have Peptide Settings - Filter optionsMatt Chambers3open23.2
993DefectSkylineWeirdness in the raw data view when switching from IM-containing replicate to non-IM replicateRita Chupalov3open23.2
992DefectSkylineDIA-NN Speclib handling in BlibBuild mishandles n-terminal modsGuest2closed23.2
991DefectSkylineWe should add a "Run" submenu to Skyline's File menu, and move Feature Detection, Encyclopedia, and peptide search engines there from the "Import" menuBrian Pratt3resolved 
990TodoSkylineClean up Transition Settings and IMS arguments in command-line documentationBrian Pratt3open23.2
989TodoSkylineNeed to add new coverage for Peptide Settings changes by command-lineGuest1closed23.2
988DefectSkylineNeed to normalize Transition Settings change command-line outputGuest3closed23.2
987DefectSkylineDisplaying tooltip for protein sometimes takes a really long time when "Enforce Uniqueness" is enabledBrian Pratt3open 
986DefectSkylineMake ion mobility library editor searchableBrian Pratt3open 
985DefectSkylineTarget tree's Find function results window says "Peptide" where it should say "Molecule"Brian Pratt3resolved 
984DefectSkyline"zombie chromatograms" complicate merging of Skyline filesNick Shulman3open 
983DefectSkylinemanually modifying molecule mass does not modify the m/z of precursor transitions belowBrian Pratt3resolved 
982TodoSkylineImproved error message when user tries to File>Open a mass spec data file in SkylineBrian Pratt3open 
981DefectSkylineCE optimization does not work for SCIEX QTOF instrumentsMatt Chambers3open 
979DefectSkylineSupport isotope nomenclature like "[13C]3H7[15N]O2" (that's C'3H7N'O2 in Skyline-speak)Brian Pratt3open 
978DefectSkylineNeed a way to represent targets that were dimers in the IMS stage but broke into monomers in the MS stageBrian Pratt3open 
977DefectSkylineNeed a way to import and display keys other than InChI, SMILES, KEGG etc - e.g. "METLIN ID"Brian Pratt3open 
976DefectSkylineLibrary Explorer: Allow for searching within peptide/molecule descriptionBrian Pratt3open 
975TodoSkylinefeature request: User-editable keyboard shortcuts for menu itemsBrendan MacLean3open 
974DefectSkylineOpenDataSourceDialog WIFF/WIFF2 data type causes file selection to be painfulBrendan MacLean2resolved23.2
973TodoSkylineAdd a way to add annotation definitions to a Skyline document from the command-linehenrytsanford2open23.2
972DefectSkylineFeature: Export mProphet features from commandlinehenrytsanford3open 
971DefectSkylineSmall molecule transition list reader could be more clever about setting formulasBrian Pratt3open 
970TodoSkylineFeature request: Right click on molecule in the molecule tree to “Add to iRT Database”Brendan MacLean3open 
969DefectSkylineTrouble handling transition lists that declare precursor isotopesBrian Pratt3open 
968DefectSkylineNullReferenceException when uploading to a saved Panorama URIVagisha Sharma3open 
967DefectSkylineCreate matching small molecule versions of all standard peptide reports in Document GridGuest3closed 
966TodoSkyline"Mobiligram" display for ion mobility filtered chromatograms (alternate view to our ion mobility heatmap)Rita Chupalov3open 
965TodoSkylineAdd command arg to SkylineRunner.exe to run any instance of Skyline by pathBrendan MacLean3open23.2
964DefectSkylineFeature Request - Surrogate calibration curvesGuest3closed 
963DefectSkylineFeature Request - Remove Replicate/Result from Chromatogram or Replicate Right-click menuBrendan MacLean3open 
962DefectSkylineFind CCS values for targets not found in an IMSDB library without changing existing valuesBrendan MacLean3open 
961TodoSkylineShow units for pressure traces in Skyline chromatograms and enable Panorama to do the sameMatt Chambers3open23.2
960DefectSkylineChinese language update: "Centroided" in the drop down list can be translated as 中心对称的Brendan MacLean2open23.1
959TodoSkylineImprove error message for BlibBuild failuresBrendan MacLean2resolved23.1
958DefectSkylineadd the Skyline version to the "More Info" text in alert dialogsGuest3closed 
957TodoSkylineDuplicated collision energy settings for SCIEX instrumentsRita Chupalov3open 
956DefectSkylineSupport for importing results from the Sage search engineBrian Pratt3open 
955DefectSkyline"Associate Proteins" should not remove unmapped peptides from the document.Guest2closed23.1
954DefectSkylinesome interesting small molecule transition list weirdnessBrian Pratt3open 
953DefectSkylineadd a code inspection test to check that the start page Tutorials tab uses the same links as the Tutorials testsBrian Pratt3open 
952TodoSkylineStrategies for reducing ExceptionWeb reports for already-solved issuesBrian Pratt3open