If you have any doubt whether the issue you are reporting requires a change to the software to fix, please post to the Support Board first instead of the issues list.

Please be thorough in your investigation of all issues, and provide a concise description of the steps necessary to reproduce your issue.  Attach any files that help clarify your issue, or which are necessary to reproduce it.  If the files are large (greater than 10M) or you do not wish to share them publicly, please simply note you have files, and we will arrange with you to transfer them for our investigation.

Learn more about finding and reporting software issues.

[Terms of Use] [Privacy Statement]

View Details
Issue IDTypeAreaTitleAssigned ToPriorityStatusMilestone
790TodoSkylineEdit > Insert > Peptides lacks the ability to add specific precursorsNick Shulman3open 
789DefectSkylineNo longer able to reset settings in Tools > Options > Misc tabNick Shulman2open21.1
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 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 LongWaitDlgBrian Pratt1open21.1
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 clusteringNick Shulman3open 
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 
739DefectSkylinesetup.exe fails on Windows Server 12 and 16Guest3closed 
738DefectSkylineissue to download Skyline 64bitGuest3closed 
737DefectSkylineWebinar #19: Ion Mobility Spectrum Filtering with Skyline some problem encounterGuest3closed 
736DefectSkylineWebinar #19: Ion Mobility Spectrum Filtering with Skyline some problem encounterGuest3closed 
735TodoSkylineSkyline should attempt BlibBuild conversion when confronted with a spectral library whose format is not natively supportedBrian Pratt3open 
734DefectSkylineEnable joining partial .skyd files when the filenames do not have a hashVagisha3open 
733TodoSkylineCan Skyline export the protein intensities?Guest3closed20.2
732DefectSkylineExporting user-defined reports from command lineBrendan MacLean3resolved 
731DefectSkylineVarying small molecule implementations of .MSP format aren't handled well by SkylineBrian Pratt3open 
730DefectSkylinePeak MS1 integration with FAIMSmatt.chambers42@gmail.com2open 
729DefectSkylineConfusing progress indicator behavior on SRM import when targeted transitions are less intense than other unmatched transitions - it just shows greyBrian Pratt3open 
728DefectSkylineAutoQC: retry upload to Panorama if upload fails due to network errorVagisha3open 
727DefectSkylinePanorama upload issuesVagisha3open20.2
726DefectBiblioSpecSkyline nonredundant blib format to MS2 conversionmatt.chambers42@gmail.com3resolved 
725DefectSkylineNeed to improve inference of ionization type when reading small molecule .MSP filesBrian Pratt3resolved 
724DefectSkylineImport multiple files as a single run for iRT calibrationKaipo3open20.2
723DefectSkylinePrecursors per sample injection think's it is transitions per sample injectionBrendan MacLean3open 
722DefectSkylineHow can I put z+1 ions in the fragments list for ETD?Brendan MacLean2open21.1
721DefectSkylineSkyline cannot properly analyze Agilent QQQ with waste diverter in the beginning of the runBrendan MacLean3open 
720DefectSkylineUpload to Panorama fails when There are custom annotations for the TransitionsBrendan MacLean3resolved 
719DefectSkylineCalibration curve of Sodiated Adduct not appearingBrian Pratt3resolved 
718TodoSkylineAllow overlay of QC traces on chromatogramsBrendan MacLean3open 
717DefectSkylineImprove handling of unknown adducts in small molecule transition reader (exception on seeing adduct "[+]" not caught gracefully)Brian Pratt3open 
716DefectSkylineWhen light and heavy precursors have different sets of transitions, all quantifiable transitions should be summed when calculating Light:Heavy ratiosGuest3closed21.1
715DefectSkylineProsit not availableBrendan MacLean3open 
714DefectSkylineQuestion about Data upload to panoramaGuest3closed 
713DefectSkylineUnable to view or explore spectral libraries in Skyline DailyGuest3closed 
712DefectSkylineAcetyl 2H(3) K modification disappears on heavy en medium peptides, when library is created from Maxquantmatt.chambers42@gmail.com2resolved 
711DefectSkylineTroubles with skyline document file upload to LabKey ServerVagisha3open 
710DefectSkylineSkyline Unistall problemsGuest3closed 
709DefectSkylinePotentially possible to do a better job at routing external tool support requests to tool-specific support boardsBrendan MacLean4open 
708DefectSkylineRenaming a molecule in Targets tree causes Skyline to miscalculate mass of transition with heavy label adductBrian Pratt3resolved19.2
707DefectSkylineDefault report names stuck in installation languageNick Shulman3open21.1
706DefectSkylinePeptide data not imported for a few peptidesBrendan MacLean3open 
705DefectSkylineToo much audit logging for Refine > Accept Peptidesritach3open 
704DefectSkylineSkyline silently fails reading FASTA files with sequences in lowercaseBrian Pratt3open 
703DefectSkylineNightly tutorial tests should not always re-download data sets - makes us too vulnerable to temporary outagesGuest3closed 
702DefectSkylineIllegal character is phosphopeptide sequenceBrendan MacLean3resolved 
701DefectSkylineMalfunctioning of the reintegration toolBrendan MacLean3resolved 
700DefectSkylineMalfunctioning of the reintegration toolGuest3closed 
699DefectSkylineMalfunctioning of the reintegration toolGuest3closed 
698TodoSkylineAdd Mass Errors to Spectrum Match graphritach3open 
697DefectSkylineimport wizard should not ask about ion mobility handling if the files to be imported don't contain any IM infoBrian Pratt3resolved 
696DefectSkylinelibrary filename extensions are case sensitive (e.g. Skyline recognizes "foo.msp" but not "foo.MSP")Brian Pratt3resolved19.2
695DefectSkylineFailed importing results DIAGuest3closed 
694DefectSkylineAudit Log records a failed operation and does not roll it backTobias Rohde3open 
693TodoSkylineImprove "Apply Peak to All" peak matchingKaipo3open 
692TodoSkylineChange some default settingsBrendan MacLean3open19.2
691DefectSkylineLimiting Transition Settings - Instrument - Max m/z has unintended consequences on spectral library transition pickingKaipo2open19.2
690DefectSkylineBefore starting a new Import > Results we need to check that Decoys are representative of the TargetsKaipo2open19.2
689DefectSkylineFile > Export > Spectral Library losing information from small molecule documentsBrian Pratt2open19.2