Issues List

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927DefectSkylineBibliospec - retain fragment charge values in MGF filesBrian Pratt3open 
926TodoSkylineImplement Bruker Paser support in BlibBuildMatt Chambers2open23.1
925DefectSkylineTargets view hangs during mouse-over with peptides longer than 2000 or soNick Shulman3open 
924DefectSkylineFix ability to provide a protein description in Edit > Insert > PeptidesNick Shulman3open 
923TodoSkylineImplement an interface that allows for multiple algorithms to do peak group assignmentNick Shulman3open 
922DefectSkylineEdit > Find needs to use LongWaitDlg and support cancelNick Shulman3open23.1
921TodoSkylineTransition list reader should identify special ions by m/z the same way it does calculated peptide fragment ionsBrian Pratt3open 
920DefectSkylineWhen Group By fails in replicate comparison graphs you lose the Order By menu itemNick Shulman3open23.1
919DefectSkylineSpectrumLibraryInfoDlg scoring columns should match library build columnsBrendan MacLean3resolved23.1
918DefectSkylinea few issues with "Use Results" in ion mobility librariesBrian Pratt3open23.1
917DefectSkylineIon mobility high energy offset should be applied for all Full Scan MS/MS modes, not just All Ions DIAGuest3closed23.1
916DocumentationSkylineDocument normalization methodsNick Shulman2open22.2
915DefectSkylineLibrary Match and Full-Scan - Right-click menu item order is broken in 22.2Rita Chupalov2open22.2
914DefectSkylineProteomics features still showing in small molecule modeBrian Pratt3open23.1
913TodoSkylineMake Ctrl-A work in Import > Results form to select all files in a folderBrendan MacLean3open22.2
912DefectSkylineAuto-Zoom X Axis > Best Peak does nothing for chromatograms with removed peaksKaipo Tamura3open23.1
911DefectSkylineCalibration Curve graph calculates concentrations on double-blanks (NaN or infinity)Nick Shulman3open23.1
910DefectSkylineSynchonized integration has trouble with removed peaksBrendan MacLean3resolved23.1
909DefectSkylineRed dots for dotp values below the cut-off appear behind barsRita Chupalov3open23.1
908TodoSkylineCommand Line Enhancement Request : Include MS/MS Filtering OptionsBrian Pratt3open23.1
907DefectSkylineViewLibraryDlg right-click menu lagging behind Library Match right-click menuRita Chupalov2open23.1
906DefectSkylineA few details working with Bruker PASER assay library listsBrian Pratt3open22.2
905DefectSkylineIndexOutOfRangeException bringing up GraphFullScan immediately after modifying the documentRita Chupalov3open23.1
904DefectSkylineStore more spectrum and instrument information in .blib files when possibleMatt Chambers2open23.1
903DefectSkylineShow names of default settings, and save settings with document when exporting a transition listKaipo Tamura3open22.2
902TodoSkylineadd an ion mobility range filter in Transition Settings IM tab similar to instrument settings tab's mz range filterBrian Pratt3open 
901DefectSkylineNewly added annotations don't show up in the Rule EditorNick Shulman3open22.2
900DefectSkylineOpening a .skyp file shows no progress until the file is downloadedVagisha Sharma3open22.2
899TodoSkylineAdding targets from DDA library seems useful to be able to specify a number of runs a peptide got ID'd inMatt Chambers3open23.1
898DefectSkylineRecord the Document Grid selection in the Undo/Redo buffer during Document Grid editing eventsBrendan MacLean3resolved22.2
897TodoSkylineMake Ctrl-Z (Undo) and Ctrl-Y (Redo) work in Document GridBrendan MacLean2resolved22.2
896DefectSkylineIMS library "Use Results" should ignore poor quality chromatographic peaksBrian Pratt3open 
895TodoSkyline"Split Graphs" equivalent (stacked MS1 and MS/MS views) for Full Scan viewBrian Pratt3open 
894TodoSkylineMake "Use Results" isolation scheme work for Import > Peptide Search of DIAKaipo Tamura2open22.2
893TodoSkylineNeed a way to turn off switching replicates in retention times - regression plotRita Chupalov3open22.1
892DefectSkylineExport > Transition / Isolation List with scheduling seems broken for counting multiple methodsGuest1closed21.2
891DefectSkylineAdjusting peak boundaries with non-quantitative transitions is confusingNick Shulman3open22.2
890DefectSkylineAudit log Skyline Version upgradeKaipo Tamura3open22.1
889TodoSkylineMake more instrument parameters available on Files in the Document GridMatt Chambers3open22.1
888DefectSkylineFile > Import > Peptide Search with existing library reports the build settings in the Audit LogBrendan MacLean2resolved22.2
887DefectSkylineSmooth handling of .skyp file for server lacking credentialsVagisha Sharma3open22.1
886DefectSkylineAutoQC Loader stops scrolling log text area after a wrapped lineVagisha Sharma3open22.1
885DefectSkylineDotp line graph points should be clickable for changing the active replicateRita Chupalov3open22.1
884DefectSkylineSome user are really unhappy that they can't type transition lists into Skyline like they used to doBrian Pratt3open 
883DocumentationSkylineUpdate tutorials with new library building interfaceGuest2closed 
882TodoSkylineClean out apparent IMS related cruft in Full Scan tabGuest3closed 
881DefectSkylineMove Bruker timsTOF method export into BuildMethodKaipo Tamura3open 
880TodoSkylineSSL format changes for Feature DetectionBrian Pratt3open22.1
879DefectSkylineNeed some way to show user FAIMS information in raw scan view, to demystify jagged chromatograms before IM filters are appliedBrian Pratt3open 
878DefectSkylineNeed to handle retention time shifts for deuterated internal standardsBrian Pratt3open 
877DefectSkyline"How Skyline Calculates Peak Areas and Heights" tip could use updatingBrendan MacLean3open 
876DefectSkylineTypo in "Skyline Small Molecule Method Development and CE Optimization" tutorialNat Brace3open 
875DefectSkylineThe adduct pick list (as used in Modify... in Targets tree) should include [M+] and [M-]Guest3closed 
874DefectSkylineDefault Win32 MAX_PATH value of 260 is too small for some usersBrian Pratt3open 
873DefectSkylineFeature request: single molecule/peptide re-integrationBrendan MacLean3open 
872DefectSkylineDocument created by an m/z-only transition list should not depend on list orderGuest3closed22.1
871DefectSkylineClean up the interaction of small molecule transition list imports and Transition Settings that affect precursor isotope ([M+1], [M+2] etc) creationBrian Pratt1open22.1
870TodoSkylineImplement special peak statistics for DDA MS/MSGuest1closed22.2
869TodoSkylineAdd a Prosit RT calculator parallel to SSRCalcKaipo Tamura3open 
868TodoSkylineConsider generating a dictionary of less common isotopes instead of hardcoding them piecemeal in response to user requestsBrian Pratt3open 
867TodoSkylinePossible Improvements to Edit>Insert>TransitionListBrian Pratt3open22.1
866DefectSkylineProvide option in Skyline to upload a minimized library to PanoramaGuest3closed22.1
865DefectSkylineAdding heavy mods in Peptide Settings does not add "Ratio to Heavy" normalization to Quantification tabGuest1closed21.2
864DefectSkylineVarious issues reading this small molecule transition list with heavy label formulasGuest3closed22.1
863DefectSkylineProblem loading a small mol document with isotope labels - Skyline complains that they aren't known modifications (which should not matter)Guest3closed22.1
862DefectSkyline"Importing Results..." window should resize its multi-file progress control when there's a vertical scrollbar in use (currently cuts off the "Cancel" buttons and looks funny)Guest3closed22.1
861TodoSkylineImplement better peptide to protein assignment strategies for target selectionMatt Chambers2open22.1
860DefectSkylineSupport more than one fragment specification per line in transition list column picker, for small molecules at leastBrian Pratt3open 
859DefectSkylineAdd peak apex CCS to Transition ResultNick Shulman3open22.1
858DefectSkylinemake "ImportPeptideSearch with the IMS filtering visible" a form view that can be shown in the SkylineTester Forms tabGuest3closed22.1
857DefectSkylineImportTransitionListColumnSelectDlg lags a bit when associate proteins checkedBrendan MacLean3resolved21.2
856DefectSkylineWhen training a "Default" peak scoring model, the model should be able to use feature scores that are present for some but not all peptidesGuest3closed22.1
855DefectSkylineLog scale with median normalization does not mention the normalization in the y-axis labelBrendan MacLean3resolved22.2
854DefectSkylinePeak Areas - Replicate Comparison - Normalize to strangely chooses poorlyBrendan MacLean2resolved21.2
853DefectSkylineRemove peak should make dotp annotations and line missingGuest1closed21.2
852DefectSkylineFull-Scan graph no longer auto-scales the y-axis when clicking arrow buttonsBrendan MacLean2resolved21.2
851TodoSkylineRename auto trained peak scoring modelsKaipo Tamura3open22.1
850DefectSkylineFix performance issue with ion moblity filtering in library viewerBrian Pratt3open22.1
849DefectSkylineFailure opening .sky file saying audit log entry has been modifiedBrendan MacLean2resolved21.2
848DefectSkylineShow a better error message if check for Panorama server failsVagisha Sharma1open23.1
847DefectSkylineAdd option to use explicit RT instead of measured for exporting scheduled methodsKaipo Tamura3open 
846DefectSkylineTrouble exporting polarity-switching QQQ method from Skyline to Agilent-6495CKaipo Tamura3open 
845DefectSkylineUser says Agilent 6495C can go down to a dwell time of 0.5ms, but we insist on integer dwell times in UIKaipo Tamura3open 
844DefectSkylineLibraries should load without error even if the directory that the library is in is not writeable.Guest2closed21.2
843DefectSkylineUpdate "_elementMasses" in MaxQuantReader.cppGuest2closed21.2
842TodoSkylineAdd a setting for RT annotation display to Chromatogram graph right-click > properties formGuest2closed 
841DefectSkylineInsert Transition List with heavy precursors results in document that cannot be opened.Guest2closed 
840DefectSkylineis M+Na precursor being handled properly in display of split graphs and heat maps, and is it being used properly in SONAR extraction?Guest3closed 
839DefectSkylineInconsistent representation of "squared" in IM peak display on chromatogram graphsGuest3closed 
838DefectSkylineinitial zoom on ion mobility heat map should not default to zero as lower rangeGuest3closed21.1
837DefectSkylineImport Peptide wizard "Configure Full-Scan Settings" IMS stuff should have its own page/stepGuest3closed21.1
836DefectSkylineCertain TransitionSettings>Library tab controls dealing with product ion filtering should be declared as proteomicGuest3closed21.2
835DefectSkylineAudit verification error after minimizing and sharing Skyline documentRita Chupalov3open 
834DefectSkylinePrecursors for the same peptide with same precursor m/z get lost in the .skyd fileGuest2closed 
833TodoSkylineShow rdotp in Peak Areas > Replicate Comparison plot when Normalize To > Heavy is chosenGuest3closed21.2
832DefectSkylineImprove ZedGraph handing of clipboard exceptionsGuest3closed21.2
831DefectSkylineChange or add an option for MS/MS spectrum graph dotp value in mirror plot with PrositRita Chupalov2open22.1
830TodoSkylineAdd a "High resolution" check box to Transition Settings - Library - Ion match toleranceRita Chupalov2open22.1
829TodoSkylineChange reports to report 1-based AA positionsGuest3closed21.2
828TodoSkylineMake it possible to see RT with more precision in chromatogram graphsBrian Pratt3closed22.1