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841DefectSkylineInsert Transition List with heavy precursors results in document that cannot be opened.Brian Pratt2open 
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 graphsBrian Pratt3open 
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/stepBrian Pratt3open21.1
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 fileNick Shulman2open 
833TodoSkylineShow rdotp in Peak Areas > Replicate Comparison plot when Normalize To > Heavy is chosenritach3open21.2
832DefectSkylineImprove ZedGraph handing of clipboard exceptionsBrendan MacLean3resolved21.2
831DefectSkylineChange or add an option for MS/MS spectrum graph dotp value in mirror plot with Prositritach3open21.2
830TodoSkylineAdd a "High resolution" check box to Transition Settings - Library - Ion match toleranceritach3open21.2
829TodoSkylineChange reports to report 1-based AA positionsBrendan MacLean3resolved21.2
828TodoSkylineMake it possible to see RT with more precision in chromatogram graphsritach3open21.1
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 Shulman3open21.2
824TodoSkylineImplement command-line option --import-peak-boundariessmani3open21.1
823TodoSkylineMake it easier to export FASTA file of the proteins in the targets windowBrian Pratt3open 
822DefectSkylineShow Prosit spectrum always when Mirror is onritach3open21.2
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 pickerBrian Pratt1open21.2
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 Shulman3open21.2
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 itemBrendan MacLean3resolved21.2
809TodoSkylineImplement better searching in Library Explorer for small moleculesBrian Pratt3open 
808TodoSkylineChange Targeted to PRM and add a SureQuant option to Acquisition method listNick Shulman3open21.2
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 missingmatt.chambers42@gmail.com3open21.2
800DefectSkylineBiblioSpec MaxQuant reader should look in parent folders for raw data filesmatt.chambers42@gmail.com3open21.2
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 stickyBrian Pratt3open21.1
795DefectSkylineImport Peptide Search library build with Automatic iRT leaves standard peptides hiddenBrendan MacLean3resolved21.1
794DefectSkylineUnable to deselect (or remove) the Prosit library for library matching in Molecule UIBrian Pratt3open 
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 tabBrendan MacLean2resolved21.1
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 .sky.zip 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 Pratt3open 
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 dataBrian Pratt3open 
778DefectSkylinePasting into the Target window should be on a LongWaitDialogBrian Pratt3open 
777DefectSkylineTraining IMSDB hangs when raw data files are not presentBrian Pratt3open20.2
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 betterritach3open21.1
767DefectSkylinePhase 2 work item for hierarchical clusteringGuest3closed 
766TodoSkylinefurther enhancements to the Import Transition List column pickerBrian Pratt3open 
765DefectSkylineRefactor AuditLog hash calculationritach3open 
764DefectSkylinethe list of pre-made iRT standards should be filtered based on UI mode - don't present peptide standards for small molecules mode and vice versaBrian Pratt3open 
763DefectSkylineEditing iRT standard in Edit iRT Calculator form no longer sets standard to NoneBrendan MacLean3resolved20.2
762DefectSkylineenforce or infer setting ion mobilty units for explicit ion mobility valuesBrian Pratt3resolved 
761DefectSkylineUser would like to force integration of areas that don't have identifiable peaksBrendan MacLean3open 
760DefectSkylineSkyline should probably offer to reimport raw data after user creates or alters an ion mobility libraryBrian Pratt3open 
759DefectSkyline"Use Results" button on the Edit Ion Mobility Library dialog does not fail promptly when raw data is not presentBrian Pratt3open 
758DefectSkylineChromatogram peaks should show IM information as well as RTBrian Pratt3open 
757TodoSkylineadd a display for ion mobility spectrumritach3open 
756TodoSkylineadd support for Thermo mzVault small molecule spectral librariesGuest3closed 
755DefectSkylineImproved handling of ambiguous entries when importing spectral libraries that are .MSP format database dumpsBrian Pratt3open 
754TodoSkylineMake Import Peptide Search wizard smarter about isolation schemesKaipo3open20.2
753DefectSkylineValue list annotations should not allow empty listsBrendan MacLean3resolved20.2
752TodoSkylineAdd option to use 1-based amino acid position numberingKaipo3open21.1
751DefectSkylineWhen creating IM library from results, don't create high energy offsets that are impossible for the equipment (e.g. positive drift time offset - that should only decrease)Brian Pratt3open 
750DefectSkylinesmall molecule accession numbers in Document Grid should be made editableBrian Pratt3open 
749DefectSkylineReimport after adding new transitions causes new transitions to have #N/A peak areasGuest3closed20.2
748DefectSkylineEdit>Insert>TransitionList should issue a warning when ignoring an input line because it duplicates or conflicts with an existing transitionBrian Pratt3open 
747TodoSkylineImport > Assay Library should automatically recognize Water and Ammonia lossesKaipo2open20.2
746DefectSkylineRetention time alignment makes mouse act out of phase on aligned replicate graphsmatt.chambers42@gmail.com3resolved20.2
745DefectSkylinequalification in skylineGuest3closed 
744DefectSkylinequalification 偶发Guest3closed 
743DocumentationBiblioSpecCreate Bibliospec library (.blib) using Tabular text input (.tsv)Guest1closed 
740TodoSkylineChange the scale of the peptide intensityBrendan MacLean3open