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Issue IDTypeAreaTitleAssigned ToPriorityStatusMilestone
655DefectSkylineadjust behavior of "Explicit Retention Time" to match user expectationsBrian Pratt3open19.2
654TodoSkylineAdd support for PEFF extended FASTA format (http://www.psidev.info/peff)Brian Pratt3open19.2
653TodoSkylineImplement arbitrary peptide proportion groupingNick Shulman2open19.2
652TodoSkylineControlling the (#) suffix added to replicate filenames from a .wiff ImportBrendan MacLean3resolved4.3
651TodoSkylineDocument Settings - Reports should have buttons to manage the list or add a new reportNick Shulman3open 
650TodoSkylineAdd a menuitem to turn off MIDAS triggered spectra annotationsBrendan MacLean3open 
649TodoSkylineNeed a way for external tools to produce annotations that get imported into the current documentNick Shulman3open19.2
648DefectSkylineError when building a library from MetaMorpheus results (*.mzID)matt.chambers42@gmail.com3open4.3
647DefectSkylineProblems with annotations in reportsNick Shulman2open19.2
646DefectSkylineProblem to build library from MaxQuantmatt.chambers42@gmail.com3resolved4.3
645DefectSkylineMaxQuant mod parser will fail when first two letters are shared between 2 different modsmatt.chambers42@gmail.com3open4.3
644TodoSkylineAdd ability to set a minimum and maximum when generating optimization valuesBrendan MacLean3open4.3
643DefectSkylineProblem interpreting modification format found in NIST phospho librariesBrian Pratt3open19.2
642DefectSkylineBiblioSpec unicode filepath supportmatt.chambers42@gmail.com3resolved4.3
641DocumentationSkylineHow to assign report template name in Command-line argumentGuest3closed4.3
640DefectSkylineUnable to process chromatograms for the moleculematt.chambers42@gmail.com3resolved4.3
633DefectSkylineUsability idea: when we fail to open a Skyline document, check to see if it actually IS a Skyline documentGuest3closed4.3
632DefectSkylineFailure importing SRM runsmatt.chambers42@gmail.com3open4.3
631TodoSkylineFinding *.dat files from the spectral librarymatt.chambers42@gmail.com4resolved4.3
630DefectSkylinerdotp uses Statistics.Angle() when it should be using NormalizedContrastAngleSqrt()Brendan MacLean2open19.2
629DefectSkylineNo import due to overlapping chromatogram start times?matt.chambers42@gmail.com2open4.3
628TodoSkylineThermo RAW attribute accessNick Shulman3open4.3
627TodoSkylineImport results from multi-injection wiff files that have the same sample/injection namesVagisha3open4.3
626TodoSkylineAdd command-line arguments to select samples to import from multi-injection wiff filesVagisha3open4.3
625TodoSkylineLipid quant using Skyline and LipidSearchmatt.chambers42@gmail.com3open4.3
624TodoSkylineAudit log format changesTobias Rohde3open4.3
623TodoSkylineAdd command-line arguments to support background proteome creation and addingBrendan MacLean3open4.3
622DefectSkylineBuilding CCS containing libraryBrian Pratt2open19.2
621TodoSkylineChange default centroiding value to summed intensity from trapezoidal areaBrendan MacLean2resolved4.3
620TodoSkylineExpose refinement options through command-line interfaceBrendan MacLean2open4.3
619TodoSkylineControl of extraction range in MS1 is desirableBrendan MacLean3open 
618TodoSkylineProblem accessing MS/MS in method with multiple fragmentation modesBrendan MacLean3resolved 
617TodoSkylineDecoy generation should only maintain C-terminus when it matches the enzyme cleavage patternBrendan MacLean3open 
616TodoSkylineRequest for instrument serial numbers as data file attribute in Skyline reportsBrendan MacLean3open 
615TodoSkylineAdd more information to multi-peptide chromatogram labelsTobias Rohde4open4.3
614TodoSkylineInclude CSRF token when SkylineNightly posts to LabKey ServerVagisha3resolved4.2
613DefectSkylineAdd clarifier "(in min.)" to axis legends of Skyline graphs showing duration through timeBrendan MacLean3open4.3
612TodoSkylineSupport Pressure Traces in Skyline .skyd filesNick Shulman2open4.2
611DefectSkylineIndexOutOfRangeException switching spectrum type between MS1 and MS/MS in DDA mode fileBrendan MacLean2resolved4.2
610TodoSkylineFix MaxQuant library builder to extract original spectra from source data filesBrendan MacLean2resolved4.3
609TodoSkylineImplement a way to remove peaks from a set of PrecursorResults selected in the Document GridBrendan MacLean3resolved4.3
608DefectSkylineConflict with transition Ion exception when two precursors have the same charge state, and transitions with the same mass.Guest3closed4.3
607DefectSkylinePeak area graph Group By should allow Analyte ConcentrationBrendan MacLean3resolved4.3
606DefectSkylineLists need better audit loggingBrendan MacLean1resolved4.2
605TodoSkylineResize Previous Files Bar on Start PageBrendan MacLean3open4.3
604DefectSkyline.NET 4.7.2 install on Wwindows 10 1803Guest4closed4.2
603DefectSkylinePrompt user about removing unused chromatograms when uploading document to PanoramaNick Shulman3open4.3
602DefectSkylineEnable using the Document Grid to filter and sort Replicate Comparison and Peptide Comparison graphsNick Shulman3open4.3
601DocumentationSkylineNumber of data points per LC peak vs cycle time in scheduled MRMGuest3closed4.2
600DefectSkylineSkyline-Daily Small molecules: Filter to screen out false positives based on number and proportion of transitions.Brendan MacLean3open4.2
599DefectSkylineFailing importing Agilent GC-MS/MS SRM data after upgrade to 18257Guest3closed4.2
597TodoSkylineUsers would like to be able to tile all chromatograms in a scrollable pane for ease of inspectionGuest3closed4.2
596TodoSkylineWhen using a spectral library with ion mobility info, we should direct user's attention to the "Use Spectral Library Ion Mobility Values" settingBrian Pratt3open19.2
595DefectSkylineLoss of adjusted peak boundaries after copy pasteBrendan MacLean3open4.1
594DefectSkylineThe MS1 "precursor [M-1]" ion should have Quantitative property off by defaultGuest3closed4.1
593DefectSkylinecannot find spectal libraryGuest3closed4.1
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 MSstatsGuest3closed4.1
588DefectSkylineDuplicate vs repeated peptidesGuest4closed4.1
587DefectSkylineSkylineRunner Instant CrashGuest3closed4.1
586DefectSkylinePivot Editor causes SkylineWindow deactivationNick Shulman3open4.2
585DefectSkyline1 raw file used with 2 skyline template issueGuest3closed4.1
584TodoSkylineAudit log improvementsTobias Rohde3resolved4.2
583DefectSkylineLibrary Match view should show the same metadata (RT, IM , ?) seen in Library ExplorerBrendan MacLean3open4.3
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 wildGuest3closed4.2
579DefectSkylineuse "Natural Sort Order" for filenamesAlex MacLean3open4.2
578DefectSkylineBackground proteome file not loading shows error message with OK buttonBrendan MacLean3resolved4.3
577DefectSkylineFailed to import MassLynx (centered) Q-TOF raw datamatt.chambers42@gmail.com3resolved4.1
576DefectSkylineCreating Reports: atomic composition (formula) does not contain stable isotope infoBrian Pratt3resolved4.1
575DefectSkylineError opening file in skyline-dailyGuest3closed4.1
574DefectSkylineError downloading small molecule tutorial fileGuest3closed4.1
573TodoSkylineAdd -> refine window missing OK / Cancel buttonsBrian Pratt0open 
572TodoSkylineAdd View > Peak Areas > Regression plotsTobias Rohde3open4.3
571DefectSkylineissue with normalization ratioGuest1closed4.1
570TodoSkylineChromatogram extraction should respect Explicit Retention Time Window and not just Explicit Retention TimeBrendan MacLean3open4.2
569DefectSkylineTrouble in importing Altis SRM data in skyline dailymatt.chambers42@gmail.com1resolved4.1
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 Pratt3open19.2
564TodoSkylineAdd checkboxes to invert meaning of Edit > Refine > Accept Proteins/PeptidesBrendan MacLean3open 
563TodoSkylineNot all document grid columns have descriptions in helpGuest3closed4.2
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 linkBrendan MacLean3resolved4.3
556DefectSkylineIssues with Waters schedule MRM data. Can't load.Guest3closed3.7
555DefectSkylineSkyline assumes /labkey context path when pinging PanoramaGuest3closed4.1
554DefectSkylineAssigning a wrong peak and not following the spectral library retention timeGuest3closed4.1
553DefectSkylineSupport Contains filter for report column that looks like textGuest3closed4.1
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