Issues List

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892DefectSkylineExport > Transition / Isolation List with scheduling seems broken for counting multiple methodsKaipo1open21.2
891DefectSkylineAdjusting peak boundaries with non-quantitative transitions is confusingNick Shulman3open22.1
890DefectSkylineAudit log Skyline Version upgradeKaipo3open22.1
889TodoSkylineMake more instrument parameters available on Files in the Document Gridmatt.chambers42@gmail.com3open22.1
888DefectSkylineFile > Import > Peptide Search with existing library reports the build settings in the Audit LogNick Shulman3open22.1
887DefectSkylineSmooth handling of .skyp file for server lacking credentialsKaipo3open22.1
886DefectSkylineAutoQC Loader stops scrolling log text area after a wrapped lineVagisha Sharma3open22.1
885DefectSkylineDotp line graph points should be clickable for changing the active replicateritach3open22.1
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 BuildMethodKaipo3open 
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/MSNick Shulman1open22.1
869TodoSkylineAdd a Prosit RT calculator parallel to SSRCalcKaipo3open 
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.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 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 labelNick Shulman3open21.2
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 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 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 Prositritach2open22.1
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 BlibBuildKaipo2open22.1
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-boundariesGuest3closed22.1
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 integrationBrendan MacLean2resolved21.2
818TodoSkylineBlibBuild needs to write more information to .blib filesGuest2closed 
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 MacLean3open22.1
814TodoSkylineNeed a way to more easily run all tests that produce audit logsGuest3closed21.2
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 LibraryBrendan MacLean3resolved21.2
806DefectSkyline"Column1", "Column2" etc generated headers in the column picker should be localized.Guest3closed 
805DefectSkylineStopping SkylineTester does not abort the second run of SkylineNightlyGuest3closed 
804TodoSkylineImplement simple filtering for MSP file importBrian Pratt3open 
803TodoSkylineRetain previous iRT values in iRT databasesGuest2closed22.1
802TodoSkylineAdd "Synchronize Integration" optionGuest3closed21.2
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 selectedBrendan MacLean3resolved22.1
798TodoSkylineWhen missing chromatograms but we have a RT prediction, we should graph thatNick Shulman3open22.1
797TodoSkylineTransitions Split Graph confusing for multiple precursor chargesNick Shulman3open22.1
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