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Issue IDTypeAreaTitleAssigned ToPriorityStatusMilestone
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
688TodoSkylineAdd Product Loss Formula column to Edit > Insert > Transitions for small moleculesBrian Pratt2open19.2
687TodoSkylineImplement support for charged losses where Skyline currently has only neutral lossesNick Shulman2open19.2
686TodoSkylineImplement a better system for assigning a version which is not web installedmatt.chambers42@gmail.com2open19.2
685DefectSkylineShow progress in LongWaitDlg for Skyline document import on PanoramaVagisha3open19.2
684DefectSkylineDo not use getContainers to determine if a URL is for a LabKey ServerVagisha3open19.2
683TodoSkylineAdd support for opening .skyp files in SkylineVagisha3open19.2
682DefectSkylineImport peptide search from Start page differs from File > Import > Peptide SearchBrendan MacLean2resolved19.1
681TodoSkylineExport method sorted by m/zKaipo3resolved 
680TodoSkylineAdd access to some of the explicit values added for small molecules to peptide transition list importBrendan MacLean3open 
679TodoSkylineMake drift time predictor training available for use from command-lineBrian Pratt3open 
678DefectSkylineUnhandled error when importing peak boundaries for document with no result filesNick Shulman4open 
677TodoSkylineAdd PEP (localFDR) as another score beside q values for mProphet picked peaksBrendan MacLean3open 
675TodoSkylineView > Proteins and View > Peptides menu items added and remove View > TargetsNick Shulman2open19.2
674TodoSkylineWork out a way for an interactive tool to know Skyline is closing or has closedBrendan MacLean3open19.2
673DefectSkylineOrder By > Annotation in summary plots got brokenBrendan MacLean2resolved19.1
672DefectSkylineQuerying UniProt for SGD Yeast FASTA information having problemsBrendan MacLean1resolved19.2
671TodoSkylineImprove small molecule peak boundaries importBrian Pratt3open19.2
670DefectSkylineSkylineTester's tutorial demo mode should roll forever, and slow down a bitBrendan MacLean3open19.2
669TodoSkylineConsider adding explicit window size for CCS and/or IM for transition list importBrian Pratt3open19.2
668DefectSkylineUI mode selection capability should be available in the menu systemBrendan MacLean3open19.2
667DefectSkylineInclude fragment ion annotation when "Copy Data" from Library Match tabBrendan MacLean3open 
666DefectSkylineThe "Add small molecule test nodes" checkbox on SkylineTester is obsolete and confusing, should be removedBrian Pratt3resolved 
665DefectSkylineReplicate Label Fonts on Graph Axis too smallBrendan MacLean3resolved 
664TodoSkylineAdd "Only max precursor peak" checkbox below "Max peptide peak rank" field in Refine > Advanced - Results tabpvvemul3open19.2
662TodoSkylineAdd View > Peptides > By menu itemsBrendan MacLean3open19.2
661TodoSkylineUpdate unimod.xml which is now about 2 years oldBrendan MacLean3open19.2
660TodoSkylinerevisit changes around ReSharper 2019.1 issues with false null check warningsBrian Pratt3open19.2
659DefectSkylineneed better handling of typing mistakes (or partially completed typing) when user is renaming a peptideBrian Pratt3open19.2
658DefectSkylinenonstandard (or at least non-intuitive) keystroke handling causes exceptionBrian Pratt3open19.2
657DefectSkylineRecord BlibBuild command-line arguments in LibInfo tablematt.chambers42@gmail.com3open19.2
656TodoSkylineadd diaPASEF supportBrian Pratt3open19.2
655DefectSkylineadjust behavior of "Explicit Retention Time" to match user expectationsBrian Pratt3open19.2
654TodoSkylineAdd support for PEFF extended FASTA format ( Pratt3open19.2
653TodoSkylineImplement arbitrary peptide proportion groupingBrendan MacLean2resolved19.2
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.com3resolved4.3
647DefectSkylineProblems with annotations in reportsGuest2closed19.2
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.com3open 
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 documentGuest3closed 
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 accessmatt.chambers42@gmail.com3resolved4.3
627TodoSkylineImport results from multi-injection wiff files that have the same sample/injection namesVagisha3open19.2
626TodoSkylineAdd command-line arguments to select samples to import from multi-injection wiff filesVagisha3open19.2
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 desirablematt.chambers42@gmail.com3open 
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 filesGuest2closed4.3
609TodoSkylineImplement a way to remove peaks from a set of PrecursorResults selected in the Document GridGuest3closed4.3
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 Pratt3resolved19.2
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