Please be thorough in your investigation of all issues, and provide a concise description of the steps necessary to reproduce you 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.

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

Learn more about finding and reporting software issues.

[Terms of Use] [Privacy Statement]

View Details
Issue IDTypeAreaTitleAssigned ToPriorityStatusMilestone
599DefectSkylineFailing importing Agilent GC-MS/MS SRM data after upgrade to 18257Brian Pratt3open4.2
597TodoSkylineUsers would like to be able to tile all chromatograms in a scrollable pane for ease of inspectionBrendan MacLean3open4.2
596TodoSkylineWhen using a spectral library with ion mobility info, we should direct user's attention to the "Use Spectral Library Ion Mobility Values" settingBrian Pratt3open4.2
595DefectSkylineLoss of adjusted peak boundaries after copy pasteBrendan MacLean3open4.1
594DefectSkylineThe MS1 "precursor [M-1]" ion should have Quantitative property off by defaultBrendan MacLean3resolved4.1
593DefectSkylinecannot find spectal libraryBrendan MacLean3open4.1
592DefectSkylinesmall molecule targets don't connect with spectral libraries unless created from spectral librariesBrian Pratt3open4.1
591TodoSkylineMove AutoQC code into Skyline.CommandLine to allow running its functionality without the UIVagisha3open4.2
590DefectSkylineSpectrumMill mzXMLs not loading "no scans match current filter settings"Guest3closed4.1
589DefectSkylineModify Skyline output for data analysis using MSstatsBrendan MacLean3resolved4.1
588DefectSkylineDuplicate vs repeated peptidesBrendan MacLean4open4.1
587DefectSkylineSkylineRunner Instant CrashGuest3closed4.1
586DefectSkylinePivot Editor causes SkylineWindow deactivationNick Shulman3open4.2
585DefectSkyline1 raw file used with 2 skyline template issueGuest3closed4.1
584TodoSkylineAudit log improvementsTobias Rohde3open4.2
583DefectSkylineLibrary Match view should show the same metadata (RT, IM , ?) seen in Library ExplorerBrendan MacLean3open4.2
582DefectSkylineUsability idea: use Library Match window even when document wasn't populated from a libraryBrian Pratt3open4.2
581DefectSkylineUsability idea: empty document should have getting-started hint text in the Targets windowAlex MacLean3open4.2
580DefectSkylinea couple more adduct description syntax variations seen in the wildBrian Pratt3open4.2
579DefectSkylineuse "Natural Sort Order" for filenamesAlex MacLean3open4.2
578DefectSkylineBackground proteome fileBrendan MacLean3open4.1
577DefectSkylineFailed to import MassLynx (centered) Q-TOF raw dataBrendan MacLean3open4.1
576DefectSkylineCreating Reports: atomic composition (formula) does not contain stable isotope infoBrian Pratt3resolved4.1
575DefectSkylineError opening file in skyline-dailyNick Shulman3resolved4.1
574DefectSkylineError downloading small molecule tutorial fileBrendan MacLean3resolved4.1
573TodoSkylineAdd -> refine window missing OK / Cancel buttonsBrian Pratt0open 
572TodoSkylineAdd View > Peak Areas > Regression plotsBrendan MacLean3open4.2
571DefectSkylineissue with normalization ratioBrian Pratt1open4.1
570TodoSkylineChromatogram extraction should respect Explicit Retention Time Window and not just Explicit Retention TimeBrendan MacLean3open4.2
569DefectSkylineTrouble in importing Altis SRM data in skyline dailyBrendan MacLean1open4.1
568TodoSkylineFor Import of columnar text where we currently guess the column meanings show a grid to choose insteadAlex MacLean2open4.2
567TodoSkylineAdd Expand All menu item to Targets View right-click menu when at least 1 parent node is selectedAlex MacLean3open4.2
566TodoSkyline add a Hide / Show Title menu item everywhere we have Hide / Show Legend, and make it possible to show a descriptive title everywhere (e.g. molecule name for calibration curve plot)Brian Pratt3open 
565TodoSkylineAccept defined annotation types as valid column headers for small molecule transition listsBrian Pratt3open4.2
564TodoSkylineAdd checkboxes to invert meaning of Edit > Refine > Accept Proteins/PeptidesBrendan MacLean3open4.2
563TodoSkylineNot all document grid columns have descriptions in helpBrendan MacLean3resolved4.2
562TodoSkylineImplement Audit Log for SkylineTobias Rohde2open4.2
561DefectSkylineSkyline-daily loosing peak integrationsGuest3closed4.1
560TodoSkylineImplement group by graph panes for summary graphsTobias Rohde3open 
559TodoSkylineCannot load msf result file (PD) when building a libraryKaipo3open4.2
558TodoSkylineAdd results search paths to Document SettingsKaipo3open 
557DefectSkylineChooseFormatDlg needs a documentation linkNick Shulman3open4.1
556DefectSkylineIssues with Waters schedule MRM data. Can't load.Guest3closed3.7
555DefectSkylineSkyline assumes /labkey context path when pinging PanoramaVagisha3open4.1
554DefectSkylineAssigning a wrong peak and not following the spectral library retention timeNick Shulman3resolved4.1
553DefectSkylineSupport Contains filter for report column that looks like textBrendan MacLean3resolved4.1
552TodoSkylineSupport multiple replicate selection in summary graph panes and Remove PeakTobias Rohde3open4.1
551DefectSkylineSkyline file not openingGuest3closed4.1
550DefectSkylineOnly iRT traces are importedKaipo3open4.1
547DefectSkylineXML Error -- Reading mz values; small molecule transition listBrian Pratt3resolved4.1
546DefectSkylineUnable to build spectral libraryGuest3closed4.1
545TodoSkylineAdd Include charge state checkbox to Edit > Insert > PeptidesBrendan MacLean3open4.1
544DefectSkylineDiscrepancies in Heavy and Light Peptide Chromatogram Import RangesGuest3closed4.1
539DefectSkylineHeavy/Light Peptide Chromatogram Import Range DiscrepanciesGuest3closed4.1
538TodoSkylineMulti-peptide calibration curves would be niceNick Shulman3open4.1
537DefectSkylineHow to add a column to the documents or results grid that contains the heavy or ISTD areas? Nick Shulman3open4.1
536DefectSkylinePoints across peak count should scale with chromatogram graph font settingsGuest4closed4.1
535DefectSkylineMS1 chromatograms in scheduled PRM data should get limited to times of matching MS/MS scansNick Shulman2open4.1
534TodoSkylineMulti-peptide graph fixes / enhancementsTobias Rohde2open4.1
533DefectSkylineReporter ion masses must be less than or equal to 5000Guest2closed4.1
532TodoSkylineX!Tandem in SkylineBrendan MacLean3open 
531TodoSkylineInclude Replicate Name as column in exported chromatogramsGuest3closed4.1
530DefectSkylineNIST .msp reader ignores peptide entries with n- or c-terminal modificationsKaipo3open4.1
529TodoSkylineConsider imposing spectrum filtering based on Full-Scan settingsBrendan MacLean3open 
528DefectSkylineColumn header sort messes up peak scoring model training gridGuest3closed4.1
527DefectSkylineDouble-clicking .sky file does not seem to work for Administrator InstallationNick Shulman3open4.1
526TodoSkylineEnhancements to AutoCopyUSBAlex MacLean4open4.1
525DefectSkylineResults Grid or calibration curveNick Shulman3open4.1
524TodoSkylineMake it possible to rename replicates through the Document GridGuest3closed4.1
523TodoSkylineMake it easy to connect raw data file sample information to annotations in SkylineNick Shulman3open4.1
522TodoSkylineAdd a way to add annotations to a document from the command-lineNick Shulman2open4.1
521TodoSkylineAdd CE recognition to transition list importKaipo4open4.1
520TodoSkylineMake ctrl-Page Up ctrl-Page Down retreat or advance all document panes at onceBrendan MacLean3open4.1
519TodoSkylineSynchronize zooming for RT and Area plotsGuest3closed4.1
518DefectSkylineResolve issue of hard-coding Waters CE equationsKaipo4open4.1
517TodoSkylineAdd Remove Peak and Apply Peak to All menus to retention time graphGuest3closed 
516DefectSkylineManual peak integrations are reset after import of new results fileGuest0closed3.7
515TodoSkylineAdd some way to produce summary statistics to reports by grouping replicate annotationsNick Shulman1open4.1
514TodoSkylineExpand neutral loss support to allow for charged losses from the precursorBrendan MacLean3open 
513DefectSkylineFix ExclusionUseDIAWindow setting to consider IsolationWindow.MethodStart and MethodEndBrendan MacLean3open 
512TodoSkylineAdd summary statistics for q valuesBrendan MacLean3open4.1
511TodoSkylineRequest for customizable bulk peak removalNick Shulman2open4.1
510TodoSkylineUpdates to iRT standards necessaryGuest3closed3.7
509TodoSkylineremoove limit of 200aa or increase this number for analysis top-down or middle-down dataBrendan MacLean3open3.7
508DefectSkylineMake SkylineCmd.exe return non-zero when a line starting with "Error:" is outputGuest2closed4.1
507DocumentationSkylineSkyline Menu for all terminology.Nick Shulman3open3.7
506TodoSkylineAdd Cone Voltage optimization support for Waters triple quadrupolesGuest3closed3.7
505TodoSkylineAdd RF Lens optimization for Thermo triple quadrupoleKaipo3open4.1
504TodoSkylineAdd support for CE optimization for PRM on Waters Xevo QTOFKaipo3open4.1
503TodoSkylineImprove document minimizing and command-line supportNick Shulman2open3.7
502TodoSkylineImprove UnimodCompiler to preserve modification more than one decimal place for modifications that require more to disambiguateNick Shulman2open4.1
501DefectSkylineImprove BlibBuild handling of multiple searches on the same raw data filesGuest3closed3.7
500DefectSkylineInstrument tab not limiting time for extraction based on RT predictionNick Shulman3open3.7
499TodoSkylineMass error replicate comparison does not support split graphNick Shulman3open3.7
498DefectSkylineTheoretical peptide z ion does not matchGuest3closed3.7
497DefectSkylineIgnore full-scan settings for retention time prediction when importing SRM dataNick Shulman3open3.7
496DefectSkylineCannot publish data to Panorama.Guest3closed3.6
495TodoSkylineMore flexibility in View > Arrange Graphs > GroupedYuval3open 
494DefectSkylineCan Skyline Support Waters UNIFI data format .UEP fileBrian Pratt2open3.7
493DefectSkylineiRT standard peptides added to document can gain extra precursorsGuest3closed3.6