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867TodoSkylinePossible Improvements to Edit>Insert>TransitionListBrian Pratt3open22.1
866DefectSkylineProvide option in Skyline to upload a minimized library to PanoramaVagisha Sharma3open22.1
865DefectSkylineAdding heavy mods in Peptide Settings does not add "Ratio to Heavy" normalization to Quantification tabNick Shulman1open21.2
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)Brian Pratt3open22.1
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.chambers42@gmail.com2open22.1
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 tabBrian Pratt3resolved22.1
857DefectSkylineImportTransitionListColumnSelectDlg lags a bit when associate proteins checkedBrian Pratt3open21.2
856DefectSkylineWhen training a "Default" peak scoring model, the model should be able to use feature scores that are present for some but not all peptidesNick Shulman3open22.1
855DefectSkylineLog scale with median normalization does not mention the normalization in the y-axis labelNick Shulman3open21.2
854DefectSkylinePeak Areas - Replicate Comparison - Normalize to strangely chooses poorlyNick Shulman2open21.2
853DefectSkylineRemove peak should make dotp annotations and line missingritach1resolved21.2
852DefectSkylineFull-Scan graph no longer auto-scales the y-axis when clicking arrow buttonsritach2open21.2
851TodoSkylineRename auto trained peak scoring modelsKaipo3open22.1
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 Sharma3open22.1
847DefectSkylineAdd option to use explicit RT instead of measured for exporting scheduled methodsKaipo3open 
846DefectSkylineTrouble exporting polarity-switching QQQ method from Skyline to Agilent-6495CKaipo3open 
845DefectSkylineUser says Agilent 6495C can go down to a dwell time of 0.5ms, but we insist on integer dwell times in UIKaipo3open 
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 documentritach3open 
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 chosenritach3resolved21.2
832DefectSkylineImprove ZedGraph handing of clipboard exceptionsGuest3closed21.2
831DefectSkylineChange or add an option for MS/MS spectrum graph dotp value in mirror plot with Prositritach3open22.1
830TodoSkylineAdd a "High resolution" check box to Transition Settings - Library - Ion match toleranceritach3open22.1
829TodoSkylineChange reports to report 1-based AA positionsGuest3closed21.2
828TodoSkylineMake it possible to see RT with more precision in chromatogram graphsBrian Pratt3closed22.1
827DefectBiblioSpecX! Tandem point mutations not understood by BlibBuildKaipo2open21.2
826DefectSkylineChoosing an existing standard during Assay Library import fails to add library spectrum to BLIBKaipo3open21.2
825TodoSkylineSDRF ReportsNick Shulman3open22.1
824TodoSkylineImplement command-line option --import-peak-boundariesBrendan MacLean3resolved22.1
823TodoSkylineMake it easier to export FASTA file of the proteins in the targets windowBrian Pratt3open 
822DefectSkylineShow Prosit spectrum always when Mirror is onritach3open22.1
821TodoSkylineExpand multiple selection handling in chromatogram graphs to handle precursorsKaipo3open 
820DefectSkylineIon Mobility Library editor should offer to wipe CCS value when IM value is alteredBrian Pratt3open 
819TodoSkylineImplement new option to synchronize integrationKaipo2open21.2
818TodoSkylineBlibBuild needs to write more information to .blib filesmatt.chambers42@gmail.com2open 
817TodoSkylineSmall molecule support for Import > Transition > List column pickerGuest1closed21.2
816TodoSkylineFile>Share should offer to include a selection of raw filesBrian Pratt3open 
815TodoSkylineSettings UI should offer choices when a change is made that would break consistencyBrendan MacLean3open21.2
814TodoSkylineNeed a way to more easily run all tests that produce audit logsBrendan MacLean3open21.2
813DefectSkylinetidy up user-facing notation for mass-only fragments, and adjust sense of "[M-]", "[M+2]" etc to means "inherently charged, m/z to mass conversion is simple multiplication, no particles lost/gained"Brian Pratt3open 
812TodoSkylineCalculate and store peak skewness/asymmetry valueNick Shulman2open22.1
811DefectSkylinedeal with the TODO from commit "When adding small molecule library values to a document, just ignore any fragment peaks with absurdly small or large m/z values"Brian Pratt3open 
810DefectSkylineManage Reports - Copy button still has "Open View Editor" menu itemGuest3closed21.2
809TodoSkylineImplement better searching in Library Explorer for small moleculesGuest3closed 
808TodoSkylineChange Targeted to PRM and add a SureQuant option to Acquisition method listGuest3closed21.2
807DefectSkylineFix/Improve File > Export > Spectral LibraryKaipo3open21.2
806DefectSkyline"Column1", "Column2" etc generated headers in the column picker should be localized.Guest3closed 
805DefectSkylineStopping SkylineTester does not abort the second run of SkylineNightlyBrian Pratt3open 
804TodoSkylineImplement simple filtering for MSP file importBrian Pratt3open 
803TodoSkylineRetain previous iRT values in iRT databasesKaipo2open21.2
802TodoSkylineAdd "Synchronize Integration" optionKaipo3resolved21.2
801DefectSkylineBiblioSpec MaxQuant reader should look for all necessary raw data files and issue a block error about any that are missingGuest3closed21.2
800DefectSkylineBiblioSpec MaxQuant reader should look in parent folders for raw data filesGuest3closed21.2
799TodoSkylineImprove Library Match behavior when precursor not selectedKaipo3open21.2
798TodoSkylineWhen missing chromatograms but we have a RT prediction, we should graph thatNick Shulman3open21.2
797TodoSkylineTransitions Split Graph confusing for multiple precursor chargesNick Shulman3open21.2
796DefectSkylineImport Transition List column picker is too stickyGuest3closed21.1
795DefectSkylineImport Peptide Search library build with Automatic iRT leaves standard peptides hiddenGuest3closed21.1
794DefectSkylineUnable to deselect (or remove) the Prosit library for library matching in Molecule UIGuest3closed 
793TodoSkylineCreate a way to limit the set of replicates immediately under analysis without removing replicatesNick Shulman3open 
792DefectSkylinetrying to type an adduct description into the Modify... popup is maddening, cursor location keeps jumping back to start of lineBrian Pratt3open 
791DefectSkylineInconsistencies in Small Molecule UI mode make it difficult to reopen a closed Targets windowBrian Pratt3resolved 
790TodoSkylineEdit > Insert > Peptides lacks the ability to add specific precursorsNick Shulman3open 
789DefectSkylineNo longer able to reset settings in Tools > Options > Misc tabGuest2closed21.1
788DefectSkylineNeed better handling for IO problems in library loadBrian Pratt3open 
787TodoSkylineCustom graph background colors - or maybe just Dark Mode - for SkylineBrian Pratt3open 
786DefectSkylineIon mobility library "use results" algorithm improvementsBrian Pratt3open 
785DefectSkylineTransition Settings - Ion Mobility - Fixed width value not saved when it is all that changesBrian Pratt2open21.1
784DefectSkylineImprovements to associating raw files with files (for support, Panorama, ???)Brendan MacLean3open 
783DefectSkylinesmall molecule transition list reader should be more tolerant of missing values for InChIKey etc, and should explain properly when it rejects a mismatchBrian Pratt3open22.1
782DefectSkylineallow small molecule precursors to support the full range of retention time matching options found in the isotope modification formBrian Pratt3open 
781DefectSkylineallow user to select which files are used in ion mobility library "Use Results"Brian Pratt3open 
780DefectSkylineshow m/z value in Ion Mobility Library editor windowBrian Pratt3open 
779DefectSkylineAdapt ion mobility library editor "Use Results" to work with FAIMS dataGuest3closed 
778DefectSkylinePasting into the Target window should be on a LongWaitDialogGuest3closed 
777DefectSkylineTraining IMSDB hangs when raw data files are not presentGuest3closed20.2
776DefectSkylineStandard industry teminology for CCS has landed on "Collision Cross Section", we call it "Collisional Cross Section" and should change thatBrian Pratt3open 
775DefectSkylinefollow up on possible improper parenting of MessageDlgBrian Pratt3open 
774DefectSkylineadd an error sense to ion mobility filtering in chromatogram extraction, akin to what we do in the RT dimensionBrian Pratt3open 
773DefectSkylineImportTransitionListColumnSelectDlg needs a better code page for textBrian Pratt3open 
772DefectSkylineImportTransitionListColumnSelectDlg.CheckForErrors() needs to use a LongWaitDlgGuest1closed21.1
771DefectSkylineMSP reader should be aware same peptide mods as the rest of SkylineBrian Pratt3open 
770TodoSkylineAllow user to select RT display units - currently fixed at minutes, seconds is desirable tooritach3open 
769TodoSkylineSupport parent ion scanning for Sciex (and Thermo?)Brian Pratt3open 
768TodoSkylineUpdate audit log to use SHA-256 or betterritach4open