Issue ID
Type
Area
Title
Assigned To
Priority
Status
Milestone
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 MacLean3open 
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 ratiosNick Shulman3open20.2
715DefectSkylineProsit not availableBrendan MacLean3open 
714DefectSkylineQuestion about Data upload to panoramaGuest3closed 
713DefectSkylineUnable to view or explore spectral libraries in Skyline DailyNick Shulman3open 
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 Shulman3open 
706DefectSkylinePeptide data not imported for a few peptidesBrendan MacLean3open 
705DefectSkylineToo much audit logging for Refine > Accept PeptidesNick Shulman3open 
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 outagesBrian Pratt3open 
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 Pratt3open 
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
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 lossesBrendan MacLean2resolved19.2
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 PanoramaVagisha3resolved19.2
684DefectSkylineDo not use getContainers to determine if a URL is for a LabKey ServerVagisha3open19.2
683TodoSkylineAdd support for opening .skyp files in SkylineVagisha3resolved19.2
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 peaksKaipo3open 
675TodoSkylineView > Proteins and View > Peptides menu items added and remove View > TargetsBrendan MacLean2resolved19.2
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 bitBrian Pratt3open 
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 systemBrian Pratt3open19.2
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 itemsGuest3closed19.2
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 (http://www.psidev.info/peff)Brian 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 namesVagisha3resolved19.2
626TodoSkylineAdd command-line arguments to select samples to import from multi-injection wiff filesVagisha3resolved19.2
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 interfaceGuest2closed19.2
619TodoSkylineControl of extraction range in MS1 is desirablematt.chambers42@gmail.com3open 
618TodoSkylineProblem accessing MS/MS in method with multiple fragmentation modesGuest3closed 
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
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
581TodoSkylineUsability idea: empty document should have getting-started hint text in the Targets windowBrian Pratt3open 
580DefectSkylinea couple more adduct description syntax variations seen in the wildGuest3closed4.2
579TodoSkylineuse "Natural Sort Order" for filenamesBrian Pratt3open 
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 TimeBrian Pratt3open19.2
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 insteadBrendan MacLean2open 
567TodoSkylineAdd Expand All menu item to Targets View right-click menu when at least 1 parent node is selectedBrendan MacLean3open 
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 librarymatt.chambers42@gmail.com3open 
558TodoSkylineAdd results search paths to Document SettingsKaipo3open 
557DefectSkylineChooseFormatDlg needs a documentation linkGuest3closed4.3
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 importedBrendan MacLean3resolved 
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 MacLean3open 
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 Shulman3open4.3
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 scansGuest2closed4.1
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 modificationsKaipo3open 
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 AutoCopyUSBGuest4closed4.1
525DefectSkylineResults Grid or calibration curveGuest3closed4.1
524TodoSkylineMake it possible to rename replicates through the Document GridGuest3closed4.1
523TodoSkylineMake it easy to connect raw data file sample information to annotations in SkylineBrendan MacLean2resolved4.3
522TodoSkylineAdd a way to add annotations to a document from the command-lineGuest2closed4.1
521TodoSkylineAdd CE recognition to transition list importKaipo4open 
520TodoSkylineMake ctrl-Page Up ctrl-Page Down retreat or advance all document panes at onceBrendan MacLean3open 
519TodoSkylineSynchronize zooming for RT and Area plotsGuest3closed4.1
518DefectSkylineResolve issue of hard-coding Waters CE equationsKaipo4open 
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 annotationsGuest1closed4.1
514TodoSkylineExpand neutral loss support to allow for charged losses from the precursorBrendan MacLean3open 
513DefectSkylineFix ExclusionUseDIAWindow setting to consider IsolationWindow.MethodStart and MethodEndGuest3closed 
512TodoSkylineAdd summary statistics for q valuesritach3open20.2
511TodoSkylineRequest for customizable bulk peak removalGuest2closed4.1
510TodoSkylineUpdates to iRT standards necessaryGuest3closed3.7
509TodoSkylineremoove limit of 200aa or increase this number for analysis top-down or middle-down dataGuest3closed3.7
508DefectSkylineMake SkylineCmd.exe return non-zero when a line starting with "Error:" is outputGuest2closed4.1
507DocumentationSkylineSkyline Menu for all terminology.Guest3closed3.7
506TodoSkylineAdd Cone Voltage optimization support for Waters triple quadrupolesGuest3closed3.7
505TodoSkylineAdd RF Lens optimization for Thermo triple quadrupoleKaipo3open 
504TodoSkylineAdd support for CE optimization for PRM on Waters Xevo QTOFKaipo3open 
503TodoSkylineImprove document minimizing and command-line supportBrendan MacLean2open4.3
502TodoSkylineImprove UnimodCompiler to preserve modification more than one decimal place for modifications that require more to disambiguateGuest2closed4.1
501DefectSkylineImprove BlibBuild handling of multiple searches on the same raw data filesGuest3closed3.7
500DefectSkylineInstrument tab not limiting time for extraction based on RT predictionNick Shulman3open4.3
499TodoSkylineMass error replicate comparison does not support split graphBrendan MacLean3resolved4.3
498DefectSkylineTheoretical peptide z ion does not matchGuest3closed3.7
497DefectSkylineIgnore full-scan settings for retention time prediction when importing SRM dataNick Shulman3open19.2
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
492DefectSkylineAnother library building errorBrendan MacLean2resolved 
491DefectSkylineIssue with building spectral libraryGuest3closed3.6
490DefectSkylineID lineGuest3closed3.6
489DefectSkylineImporting negative ion transitions from Masshunter (small molecules)Guest2closed3.6
488DefectSkylinePeptide uniqueness change should probably ignore automanage states, or at least offer toBrian Pratt3open3.6
487DefectSkylinemake automanage status of each node knowable (ideally changeable) in DocumentGridBrian Pratt3resolved4.3
486TodoSkylineCome up with clearer way of informing a user that iRT regression was not good enoughNick Shulman2open 
485TodoSkylineAdd Help > Check for UpdatesGuest3closed3.6
484TodoSkylineAdd confidence intervals for slope and intercept in calibration regressionsNick Shulman3open4.3
483DefectSkylinePrecursor isotope peaks (M+1, M+2) not automatically shown for small moleculesGuest3closed3.6
482TodoSkylineset negative ion mode for peptidesBrian Pratt3open3.6
481DefectSkylineError trying to access Tool Store in Skyline DailyGuest3closed3.6
480DefectSkylineSkyline Daily does not support Agilent Automation ToolGuest3closed3.6
479DefectSkylineSkyline Daily shows no data when there is data - Agilent QQQGuest2closed3.6
478DefectSkylinePeak Boundary List File Fails to LoadGuest3closed3.5
477TodoSkylineRequest for occupancy proportion report valueBrendan MacLean3resolved 
476DefectSkylineIssues with QuaSARGuest3closed3.6
475DefectSkylineNeed to close and reopen Document Grid after adding new annotationsBrendan MacLean2resolved4.3
474DefectSkylineAsk user about Library settings if changing peptide Filter settingsYuval3open 
473DefectSkylineMissing 2nd transition for some samples_small moleculesBrian Pratt3open3.6
472DefectSkylinemethod export for Quantiva failedGuest3closed3.6
471DefectSkylineMaxQuant library builder fails to understand T(2) modificationGuest2closed3.6
470TodoSkylineAdd TotalAreaMS1Adjusted column to reportsNick Shulman3open4.3
469TodoSkylinedocument grid TransitionResult should show extraction width, as well as drift time and windowBrian Pratt3open19.2
468DefectSkylineS-lens value isn't written to Exported transition list when checkedGuest3closed3.6
467DefectSkylineSkyline-daily (3.5.1.9673, 64-bit) locks up when uploading .raw files.Guest3closed3.6
466DefectSkylineSkylineRunner scriptability improvements: version number and help info from commandline, and non-zero exit code on errorBrian Pratt2resolved19.2
465DefectSkylineGenerating DIA Isolation Schemes with Optimize window placement does not work correctly for odd m/z (or fractional m/z) Window widthsGuest1closed3.6
464TodoSkylineSupport exporting isolation list from command lineGuest3closed3.6
463DefectSkylineAutomating Skyline for HT Proteomics with Skyline RunnerGuest3closed3.6
462DefectSkylineAdd "Thermo TSQ Quantiva" to transition settingsGuest2closed3.6
461DefectSkylineUnable to change transition settingsGuest3closed3.6
460DefectSkylineprovide a means of updating protein metadata to current Uniprot level for document and background proteomeBrian Pratt3open 
459DefectSkylineOnly one chromatogram type in Full-Scan graph for chromatogram clicked in split graph modeNick Shulman3open4.3
458DefectSkylineMRM Chromatogram not ProcessedGuest3closed 
457TodoSkylineAdd access to SpectraST retention times to library implementationGuest3closed3.6
456DefectSkylinereimport after changing full scan settings to "Centroided" doesn't actually perform centroidingBrian Pratt3open19.2
455TodoSkylineAdd option to allow exporting mass errors with File > Export > ChromatogramsBrendan MacLean3open 
454TodoSkylineRemove asymetric isolation scheme support and add ability to specify a marginGuest3closed3.6
453TodoSkylineAdd check box to Digestion tab to allow removal of protein N-terminal MethionineBrian Pratt3open19.2
452DefectSkylineCopy-paste fails to recognize equivalent modifications with different namesBrendan MacLean3resolved 
451TodoSkylineAdd redundant library access to Library ExplorerKaipo3open 
450DefectSkylineSkyline should warn when importing a transition list with values that exceed the current instrument m/z rangeBrian Pratt3open19.2
449DefectSkylineLIBRARY BUILD ERRORGuest2closed3.6
448DefectSkylineAdd optimization step to compound names in Quantiva method/transition list exportGuest3closed3.6
447DefectSkylineChange of e-mail addressGuest3closed3.6
446DefectSkylineidopt not shown when log view activatedTobias Rohde3open4.1
445DefectSkylineDIA-MS on FusionGuest3closed3.2
444TodoSkylineAdd errors and warnings for documents where Full-Scan settings do not match Filter ion typesGuest3closed3.2
443TodoSkylineImprove behavior of Cancel for a re-import or re-score operationBrendan MacLean3open 
442TodoSkylineSkyline should prefer heavy spectra in many casesBrendan MacLean2open 
441TodoSkylineReevaluate Edit > Refine > Advanced for new filtering opportunitiesBrendan MacLean3open 
440DefectBiblioSpecGraceful failure during MaxQuantReader constructorGuest3closed 
439DefectSkylineMS1 Full-Scan import = match with mascot search, ppm values missingGuest3closed3.2
438DefectSkylineMake "Insert Transition List" for small molecules tolerant of empty product ion columnsGuest3closed3.2
437TodoBiblioSpecImprove performance of BlibBuild spectral library building from pepXML/mzXMLGuest2closed3.2
436TodoSkylineAdd TraML as a transition list import formatGuest3closed 
435DefectSkylineProblem handling 'Optimize CE' dataGuest3closed3.2
434TodoSkylineAdd chromatogram export support to command-line interfaceGuest3closed3.2
433DefectSkylineAllow Remove Peak and Apply to All from peptide view with multiple precursorsGuest2closed3.2
432TodoSkylineMake it possible to view instrument-specific scan information from the full-scan viewBrendan MacLean3open 
431TodoSkylineAllow clicking on totals chromatograms to show Full-Scan graphBrendan MacLean3open 
430DefectSkylineCancelling report export leaves a truncated report on diskGuest3closed3.2
429TodoSkylineExtend the Insert Transition List dialog to be as flexible for peptides as it is for small moleculesBrian Pratt3open19.2
428DefectSkylineMulriple injection import error when no scans match document peptides or current filter settingsGuest3closed 
427TodoSkylineCreate Thermo TraceFinder export toolGuest2closed3.6
426TodoSkylineAdd peak area shading to show the area integrated in SkylineGuest2closed3.2
425DefectSkylineHard to figure out how to filter on true/false columns in Document GridGuest2closed3.2
424DefectSkylineColored summary chromatogram disappeared with latest Skyline-daily updateGuest3closed3.2
423DefectBiblioSpecHandle multiple modifications on the same residueGuest4closed 
422TodoSkylineAttempt to make Skyline ignore spectra from incorrect mass analyzer typeBrian Pratt3open3.2
421DefectSkylineImplement cursor changes for the start-up formGuest4closed3.2
420TodoSkylineAdd refinement option for DDA data based on peak IDsBrendan MacLean4open 
419TodoSkylineAdd SkylineRunner support for Edit > Refine > ReintegrateGuest3closed3.2
418TodoSkylineImprove peak removal UIGuest3closed3.2
417TodoSkylineAdd explicit property support for peptidesGuest3closed3.2
416DefectSkylineHaving many disconnected network drives causes the Import Results form to hang for a long timeGuest3closed3.2
415DefectSkylineTransition list import should pick modified sequence column over bare sequence columnGuest3closed3.2
414TodoSkylineAdd the ability to show the center of mass and possibly the target mass for an extraction region in the full-scan graphBrendan MacLean3open 
413DefectSkylineKeep optimization values from being negativeKaipo2open 
412TodoSkylineNeed ways to see isolation windows on full-scan graphsYuval3open 
411DefectSkylineColumn filters do not apply to Export and Copy AllGuest1closed3.1
410DefectSkylineMultiple selection color is too faintGuest3closed3.2
409DefectSkylineSkyline guesses poorly when it encounters AQUA/SILAC labelingKaipo3open 
408DefectSkylineGroup comparison grid and graph can become disconnectedGuest1closed3.2
407DefectSkylineOpening a .sky file in a .zip file can be confusingNick Shulman2open4.3
406DefectSkylineNeed better error message for Waters instruments when multiple RT windows are requiredGuest3closed3.2
405TodoSkylineAdd View > Group Comparisons > Edit List... itemGuest3closed3.2
404TodoSkylineIncreased versioning requested for validated environmentsBrendan MacLean3open 
403TodoSkylineMake it possible to choose top N transitions for quantificationBrendan MacLean1open4.3
402TodoSkylineMake it possible to do group comparison normalization by a replicate annotation valueGuest3closed3.2
401DefectSkylineAssumptionException SummaryPeptidePeakData.GetMzFiltersGuest3closed4.3
400TodoSkylineAdd option to export chromatograms to SkylineRunnerGuest2closed3.6
399DefectSkylineInstrument info not imported from RAW fileGuest3closed3.1
398TodoBiblioSpecInvestigate Mascot score thresholdGuest3closed3.1
397TodoSkylineSupport mzid and pride xml from PeptideShakerGuest3closed3.1
396TodoSkylineNaming convention for peptides in Thermo Quantiva transition list exportGuest3closed3.1
395DefectSkylineException thrown trying to sort Results GridGuest3closed3.1
394DefectSkylineSkyline not in Alt-Tab list when Customize View is showingGuest3closed3.1
393DefectSkylineUse different strategy when we detect slow loading of Thermo files over the networkGuest4closed3.1
392DefectSkylineProblems importing spectral libraries from DDA to iRT librariesGuest3closed3.1
391DefectTopographDiscrepancies in point countEvvie Vincow1resolved3.1
390DefectTopographCannot access individual protein half-lives within TopographGuest0closed3.1
389Todo Finalize AutoQCGuest3closed3.1
388Todo Test ResultsGuest3closed3.1
387TodoSkylineL10N for VS2013/RS9 & team city fail buildsGuest3closed3.1
386Todo Skyline sliderGuest3closed3.1
385TodoSkylineWeb args collector documentationYuval3open 
384Todo Sign Up moduleGuest3closed3.1
383TodoSkylineMonitoring charged losses could be made easierBrendan MacLean3open 
382TodoSkylineImprove modifications for glycansBrendan MacLean3open 
381DefectTopographProtein Key is not displaying the correct informationGuest0closed3.1
380TodoSkylineAdd support for PRM and DIA-with-DDA workflows to Import Peptide Search wizardGuest2closed3.1
379DefectSkylineSmall molecules: Annotations and user-set peaks don't serialize properly for custom moleculesGuest1closed3.1
378TodoSkylineAdd support for IDPicker 3 .idpDB as an a search result format for BlibBuildGuest3closed3.1
377TodoTopographNeed to limit the peptides used in calculating PP enrichment to those from short-lived proteinsGuest1closed3.1
376DefectSkylineBackground Proteome Problems -“Resolving protein details for background proteome not working”Brian Pratt3open 
375DefectSkylineSmall molecules: need negative ion capabilityGuest3closed3.1
374DefectSkylineSmall molecules: users want to import m/z values, not massesGuest3closed3.1
373DefectSkylineSmall molecules: Insert Transition list doesn't construct the tree properlyGuest3closed3.1
372DefectSkylineSmall Molecule issues with transition settingsGuest3closed3.1
371DefectSkylineSmall molecules: need to be able to import and/or set CE, RT and DT for individual precursors and productsGuest3closed3.1
370DefectSkylineSmall Molecule CE Output not workingGuest3closed4.1
369DefectSkyline"An item with the same key has already been added" when adding peptides from a libraryGuest2closed3.1
368TodoSkylineTool Require Multiple R VersionsGuest3closed 
367DefectTopographResults by Cohort feature produces no outputGuest1closed3.1
366DefectTopographMass accuracy cannot be changed for an individual protein/peptideGuest3closed3.1
365DefectSkylineMake peptide matching to background proteome more flexibleGuest3closed3.7
364TodoSkylineAdd PeptideTotalArea and ProteinTotalArea values to reports and graphsNick Shulman3open4.3
363TodoSkylineHandle Mascot Distiller settings which are problematic for SkylineGuest3closed3.1
362TodoSkylineAdd support to Skyline for querying a Mascot Server directly for search resultsmatt.chambers42@gmail.com3open 
361DefectSkylineShrink font before hiding dtop or idotp values on the Peak Areas graphGuest3closed3.1
360DefectSkylineReview all forms with tips and extend AutoPopDelay to 60000 (1 minute)Guest3closed3.6
359DefectSkylineDouble-click to zoom out on chromatogram graphs not reflected in synchronized zoomingTobias Rohde3open 
358DefectSkylineTool Framework Python package installation bugGuest3closed 
357TodoSkylineAdd support for Thermo Fusion method export to SkylineGuest2closed3.1
356TodoSkylineImplement export isolation list for Waters Q-TOFGuest1closed3.1
355TodoSkylineAdd support for RT column to BiblioSpec SSL spectrum matching formatGuest3closed3.1
354DefectSkylineCE optimization library populated with data for labeled peptides does not work for analyte peptidesGuest3closed3.1
353DefectTopographCustom view info lost with upgrade; cannot use Customize ViewGuest2closed3.1
352TodoSkylineAnnotate reporter ions in Library Match graphBrian Pratt2open19.2
351DefectTopographReject/Accept setting does not work from Half-Life tab for a proteinGuest2closed3.1
350DefectTopographCannot click through on peptide names from Half-Life view of proteinGuest3closed3.1
349DefectSkylineAcquired time attribute lost for files on ChorusGuest2closed 
348TodoSkylineImplement intensity threshold for Edit > Refine > AdvancedGuest3closed4.1
347TodoSkylineMore work on full-scan graph for ion labels in unzoomed modeBrendan MacLean2open 
346TodoSkylineMake multi-peptide graphs clickableGuest2closed3.1
345DefectSkylineImport Peptide Search wizard should show full-scan settings no matter whatGuest2closed3.1
344DefectSkylineExclude spectrum source files checkbox present in ImportResultsControl but not functionalGuest2closed3.1
343TodoSkylineTool store display orderKaipo4open 
342DefectSkylineSpectral Library Explorer and MS1 AnalysisBrendan MacLean3open 
341DefectSkylineCentroided spectra show up with profile lines in full-scan graphGuest3closed2.6
340TodoSkylineSupport pasting a list of protein accession numbers directly into Skyline when the document has a background proteomeGuest3closed 
339TodoSkylineSupport charged loss from precursor ionsBrendan MacLean3open 
338TodoSkylineSupport Thermo Crystal library formatGuest3closed3.1
337DefectSkylinemascot v2.4 MS1 import raw dataGuest2closed2.6
335TodoSkylineImprove access to optimization values in Skyline UIBrendan MacLean3open 
334DefectSkylineRT prediction not working for all decoy typesGuest3closed2.6
333TodoSkylineAdd "Exclude precursor isolation window" checkbox to Transition Settings - FilterGuest3closed2.6
332DefectSkylineSkyline crashes while uploading document to a Panorama server with no disk spaceGuest3closed2.6
331TodoSkylineImprove Import Results formYuval3open 
330TodoTopographGroup fly peptides by CG numberGuest3closed2.6
329DefectTopographWorkaround for replicates with 100% turnover to prevent ValueOutOfRange errorGuest3closed2.6
328TodoSkylineImplement support for associating protein FASTA after a document exists as a set of peptide listsGuest3closed 
327DefectSkylineFile | Import | TransitionList... always gives charge state 1 if there is a peptide mass column to the left of the actual m/z columnBrian Pratt3open19.2
326DefectSkylineGroup by peak area graphs should not stack when showing all transitionsBrendan MacLean3resolved4.3
325TodoBiblioSpecAdd support for .idXML as an a search result format for BlibBuildGuest3closed 
324TodoSkylineImprove unexpected error UI to solicit more informationGuest3closed3.1
323DefectSkylineFix PeptideDocNode.CalcBestResult() to use current peak scoring algorithmBrendan MacLean3open 
322DefectSkylineChanging selected file in GraphChromatogram does not update Targets viewBrendan MacLean3open 
321TodoSkylineAdd relative ion abundance columns to reportsNick Shulman3open 
320TodoSkylineAdd support for .sptxt as an a search result format for BlibBuildGuest3closed2.6
319TodoSkylineAdd support for SpectraST retention times to SkylineGuest3closed3.1
318TodoSkylineAdd multi-peptide RT graphGuest3closed 
317TodoSkylineAdd UI to Accept Peptides form to allow specifying a list of proteinsGuest2closed3.2
316DefectSkylineSaving a minimized skyline doc which uses an XHunter library doesn't work if peptide ranking is turned onBrian Pratt3open 
315TodoSkylineImprove support for library scores in SkylineKaipo3open 
314DefectSkylineSupport modifications not associated with an amino acid in SSL format for spectral library buildingGuest2closed3.1
313TodoSkylineAdd separate groups for Live Report viewsGuest3closed3.1
312TodoSkylineAdd Tools > Options - Language tab to v2.5 branchGuest0closed2.5
311DefectSkylineIndexOutOfRangeException UniquePrefixGenerator.GetUniquePrefixGuest3closed2.5
310DefectSkylineIndexOutOfRangeException in GraphChromatogram.DisplayPeptidesGuest3closed2.5
309DefectSkylineProblems running R for MSstats on computers that report successful installationGuest2closed2.5
308DefectSkylineMissing R.exe after MSstats installationGuest3closed3.1
307TodoSkylineGet Skyline window on screen fasterGuest2closed3.1
306DefectSkylineMessage box timeout code should be disabled when pausing a testGuest1closed2.6
305DefectSkylineColumns appear multiple times in PrescursorResults viewGuest1closed2.5
304DefectSkylineProteins added to an existing protDB don't get digestedBrian Pratt3open 
303LocalizationSkylineLOCALIZATION: Create build tool that scans the source for strings without "Not L10N"Guest3closed2.6
302LocalizationSkylineLOCALIZATION: Make SkylineRunner command-line interface localizableGuest3closed2.6
301LocalizationSkylineLOCALIZATION: Several strings have been added since .resx files were given to Language ScientificGuest3closed2.5
300DefectSkylineChange encoding of filepaths in .skyd files from Default to UTF-8Guest3closed2.6
299DefectSkylinechromatogram extraction with .wiff data in TestMS1Tutorial is about 2x slower when run in French or JapaneseGuest3closed2.6
298TodoSkylineAdd accession number and human readable protein name to proteinsGuest2closed2.6
297LocalizationSkylineLOCALIZATION: Live reports toolbar not localizedGuest3closed2.5
296DefectSkylineIrtDb can prevent document from being saveable.Guest2closed2.5
295DefectSkylineInvalidOperationException in TransitionGroupDocNode.CalcMatchingPeakGuest2closed2.5
294DefectSkylinepeak splittingGuest3closed2.6
293DefectSkylineUnhandled exceptionGuest3closed2.6
292TodoSkylineAdd Replicate Comparison order for View > Arrange Graphs > GroupedGuest3closed3.6
291DefectSkylineResults grid last selected customized view needs to be rememberedGuest3closed2.5
290TodoSkylineAdd in-place filtering to Live ReportsGuest3closed3.1
289LocalizationSkylineLOCALIZATION: Report headers cannot be translatedGuest3closed2.6
288DefectSkylineInvalidOperationException in AdlerChecksum.MakeForString if type filename into Import Results File Open DialogGuest2closed2.5
287DefectSkylineArgumentOutOfRangeException in ChromDataSet.SetBestPeakGuest2closed2.5
286DefectSkylineNRE in TransitionPeakPairData<TData>.GetMatchingReferencePairsGuest2closed2.5
285DefectSkyline"An item with the same key has already been added" exception in TargetDecoyGenerator.PopulateDictionaryGuest2closed2.5
284DefectSkylineFix sluggish update of multiple peptides graph after "Select All" on a large documentGuest1closed3.2
283DefectSkylineSynchronized zooming should work for tabbed graphsGuest4closed 
282TodoSkylineAdd new TotalArea values to reportsGuest3closed2.6
281DefectSkylineMSStats (Skyline External Tool) installation is noisy and full of scary warningsBrian Pratt3open 
280DefectSkyline"External Tools | Add" UI is mildly confusing - presents a picklist where it should be a simple textboxGuest4closed 
279DocumentationSkylineMerge QuaSAR GenePattern documentation with Tool Store versionGuest3closed2.2
278DefectSkylineBiblioSpec bug parsing pep.xml from ProspectorGuest3closed2.5
277DefectSkylineAdd ByOnic support to BiblioSpecGuest3closed2.5
276DefectSkylineMaxQuant no matching mod error in BiblioSpecGuest3closed2.5
275DocumentationSkylineCreate External Tools examples for Web Sites and Java ToolsYuval4open 
274DefectSkylineRefactor new Live Reports class names to stop using the product name SkylineGuest3closed3.1
273DefectSkylineDot-product labels clipped in peak area graphsGuest3closed3.1
272DefectSkylineNRE in MS1Probe external toolGuest3closed2.1
271TodoSkylineAdd group-by queries to exported reportsGuest1closed4.1
270TodoSkylineSave window layouts in a way that allows them to be used across documentsBrendan MacLean4open 
269TodoSkylineAllow m/z or ppm tolerance for chromatogram extractionGuest3closed3.1
268TodoSkylineCreate UI to allow hiding/showing replicatesNick Shulman3open 
267TodoSkylineChange Skyline File > Share file extension to .sky.zipGuest3closed2.2
266DefectSkylineFail to create peptide library by using .mzid file from MSGF+ searching result!Guest2closed2.5
265DefectSkylineSkyline won't recognize precursor transitions in certain RAW filesGuest3closed2.1
264TodoBiblioSpecClarify limitation on BlibBuild reading vendor raw files and consider lifting itGuest3closed 
263DefectSkylineToo strict about choosing only one precursor for every MS/MS scan in Targeted MS/MSGuest3closed2.1
262TodoSkylineAdd way to specify charge state when pasting peptide listsBrendan MacLean3open 
261TodoSkylineAdd a raw intensity filter for peaks to Edit > Refine > AdvancedGuest3closed 
260DefectSkylineArgumentOutOfRangeException pasting into calibrate windowGuest2closed2.1
259DefectSkylineNear isobars in spectral library building getting mergedGuest2closed4.1
258DefectSkylineInvalidOperationException clicking on column to sort rows in EditIrtCalcDlg.CalibrateGuest2closed2.1
257DefectSkylineDIA isolation scheme editor needs an instrument method modeGuest3closed2.6
256DefectSkylineFix normalized CE column for Q Exactive isolation list exportGuest2closed2.1
255TodoSkylineCreate ToolReportCache class to make repeated analysis fasterGuest2closed2.1
254TodoSkylinePeak Areas > Peptide Comparison graph should have stacked all transitions displayNick Shulman3open 
253TodoSkylineCreate Document Settings form and implement fold-change statisticsGuest2closed 
252DefectSkylineLight and heavy transitions can be different for several casesGuest3closed3.1
251DefectBiblioSpecBlibFilter crashes, if it cannot find :redundant: in the library LSIDGuest3closed2.1
250TodoSkylineMethod and transition list export for Waters Xevo uses a constant cone voltage of 35Kaipo4open 
249TodoSkylineAdd support for storing optimized CE values in a database file like iRTGuest3closed2.6
248TodoSkylineAdd light to heavy dot-productsGuest3closed2.2
247TodoSkylineAdd modification sites field to Skyline custom reportsNick Shulman4open 
246TodoSkylineEnable scheduled targeted-MS/MS method export on Orbitrap Elite, etc.Guest4closed 
245TodoSkylineSupport MSGF+ pepXML in BlibBuildGuest2closed2.1
244TodoSkylineAdd Thermo Quantiva to Export > Transition List optionsGuest3closed2.1
243TodoSkylineAdd tool tips to some of the graphsTobias Rohde3open4.1
242TodoSkylineAdd option to show only chromatograms for transitions that contribute to total peak areaGuest4closed4.2
241DefectSkylineImprove BlibFilter best spectrum picking for targeted MS/MS dataGuest2closed2.1
240TodoSkylineAdd Row and Column to View > Arrange menuGuest4closed3.1
239DefectSkylineRaw data for certain transitions not being imported from Xevo into SkylineGuest3closed2.1
238TodoSkylineAdd ability to import peptide search to SkylineRunnerGuest3closed3.2
237DefectSkylinePopup pick lists can end up inserting nodes that are out of sync with the settingsBrendan MacLean3open 
236DefectSkylineerror in building spectral libraryGuest3closed2.1
235TodoSkylineAuto-check HTTPS for Panorama server configuration when HTTP is specified and failsGuest3closed2.1
234TodoSkylinePreserve tree expansion in PublishDocumentDlgGuest3closed2.1
233DefectSkylineMove from dictionary to array in pwiz.Skyline.Model.Results.ChromDataCollectorSet.ProcessExtractedSpectrum(Double, ExtractedSpectrum)Guest3closed2.5
232DefectSkylineImprove chromatogram read performance for large full-scan filesGuest3closed3.1
231DefectSkylineFix MSGraph to include annotation boundaries in graph scalingGuest3closed2.1
230TodoSkylineAdd Filter By... menu item with Group By and Order ByGuest3closed3.1
229TodoSkylineAdd ability to specify a list of peptide sequences to BlibBuildGuest2closed2.1
228DefectSkylineWhen re-importing, peak boundaries that have been manually set should recompute integrationNick Shulman2open4.3
227TodoSkylineShow more complete list of error transitions on paste of transition listGuest3closed 
226DefectSkylineNeed better error message when isolation windows conflictGuest3closed2.6
225TodoSkylineStreamline File > Publish to Panorama first useGuest3closed2.1
224DefectSkylineFix SkylineRunner to support multiple instances running at the same timeGuest3closed2.1
223TodoSkylineAdd PPM and resolution options to Transition Settings - Library - Ion match toleranceBrendan MacLean3open4.3
222TodoSkylinePrediction versus confidence intervals in peak area plotsNick Shulman3open3.1
221TodoSkylineAdd retention time prediction indicators to retention time summary graphsTobias Rohde3open 
220TodoSkylineEnable sorting by annotation value in Replicate ComparisonGuest3closed2.1
219DefectSkylineImport results with folder selected does not work as expectedGuest3closed2.1
218TodoSkylineAdd checkbox to Transition Settings - Filter to add neutral loss ionsGuest3closed 
217DefectSkylineImporting a Document with the DIA analysis of same files, different peptidesBrendan MacLean3open 
216TodoSkylineAdd ragged end flag to the Peptide class and expose this value in reportsBrendan MacLean4open 
215TodoSkylineAdd graph properties to allow user control of axis label font size and orientationGuest3closed3.1
214TodoSkylineAmbiguous peptide spectrum matches are removed during library building without any notificationGuest3closed3.1
213DefectSkylineUnhandled InvalidOperationExceptionGuest3closed 
212TodoSkylineAdd filter exclusion for peptide duplicationGuest3closed3.1
211DefectSkylineUnhandled System.NullReferenceException in pwiz.Skyline.Model.Find.BookmarkEnumerator.set_CurrentGuest2closed1.4
210DefectSkylineUnhandled exception in RecordNavBar.UpdateAll()Guest2closed2.1
209TodoSkylineAdd Peptides.StructuralModifiedSequence to custom report fields in SkylineGuest1closed1.4
208TodoSkylineAllow R scripts to act as external tools in SkylineGuest3closed2.1
207TodoSkylineAdd a Prompt for arguments check box to the External tools form in SkylineGuest2closed2.1
206TodoSkylineSkyline should show progress in the status bar when a report is being generated for an external toolGuest2closed2.1
205TodoSkylineAdd Auto-zoom Y-axis sub-menu which includes Best PeakYuval2open4.1
204TodoSkylineAdd Min intensity value to Chromatogram Graph Properties formGuest4closed 
203TodoSkylineTargetedMSMS-BSA_ProteaGuest3closed2.1
202DefectSkylineImprove multiplexing detector to reject multi-precursor isolations that are not really multiplexedGuest3closed2.1
201DefectSkylineNeutral loss ions lost in pivoted report when same non-neutral loss ions are presentGuest3closed1.4
200TodoSkylineAdd File > Import > Replicate Annotations... menu itemGuest3closed2.1
199DefectSkylineEditing annotation values in Results Grid with protein selected has strange grid selection behaviorGuest2closed1.4
198TodoSkylineAdd the ability to incorporate spectral library retention times into scheduling RT predictionGuest3closed2.1
197TodoSkylineAdd ability to annotate replicatesGuest3closed1.4
196DocumentationSkylineCreate a new instructional video on working with full-scan dataGuest3closed 
195DocumentationSkylineWrite a Data Independent Acquisition tutorialGuest3closed 
194DocumentationSkylineWrite an Integration with External Tools tutorialGuest3closed 
193DocumentationSkylineWrite a Command-Line Automation tutorialBrendan MacLean3open 
192DocumentationSkylineWrite a Chromatogram Peak Integration tutorialGuest3closed 
191DocumentationSkylineWrite an Advanced Peptide Modifications tutorialGuest3closed 
190TodoBiblioSpecAdd library building support for Proteome Discoverer native .msf filesGuest3closed 
189TodoBiblioSpecAdd library building support for PRIDE XMLGuest3closed2.1
188DocumentationSkylineTutorials using Thermo RAW data should mention need for English (US) number format settingsGuest4closed2.1
187TodoSkylinePlot Base Peak and TIC chromatogramsGuest3closed2.1
186DefectSkylineFix multi-line error messages for Agilent method exportGuest2closed1.2
185TodoSkylineN- and C-terminal protease combinationsGuest4closed2.1
184TodoSkylineLevey-Jennings Chart for QCGuest3closed 
183TodoSkylineSave internal pane state in .sky.viewGuest3closed 
182DefectSkylineSpiky chromatograms from MSFileReader when two targets have the same Q1 and Q3 but different scheduling windowsGuest3closed2.5
181TodoSkylineAdd Edit > Refine > Rename Proteins formGuest3closed 
180TodoSkylineAdd refinement support for merging repeated proteinsBrendan MacLean2open 
179DefectSkylinelocal copy work-around error when importing thermo TSQ raw filesGuest3closed1.2
178DocumentationSkylineBackgroundGuest3closed1.2
177DefectSkylineHow to import WIFF files for SWATH data?Guest3closed1.2
176TodoBiblioSpecImplement BiblioSpec library building support for MaxQuant AndromedaGuest3closed2.1
175TodoSkylineAllow exporting multiple DIA methods to cover larger mass ranges, using smaller windowsKaipo3open 
174TodoSkylineAdd protein terminal modification support to SkylineBrendan MacLean3resolved 
173TodoBiblioSpecSupport peak list files for ProteinProspector (UCSF)Guest4closed 
172TodoSkylineWhat time does the Skyline version 1.3 release?Guest3closed1.2
171DefectSkylineEdit > Insert > Proteins should ignore white space on pasteBrian Pratt4open19.2
170TodoSkylineCorrect peptide start and end indices to use 1-based indexing instead of 0-base indexingBrendan MacLean3open 
169DefectBiblioSpecBlibBuild status for ProteinPilot (.group.xml) is brokenBrendan MacLean3resolved 
168TodoSkylineCopy Data on retention time copies time of end of peak, instead of peak apexGuest3closed1.2
167TodoSkylineAdd orthogonal peak ranking for MS1 and MS/MS filteringGuest3closed3.5
166DefectSkylineDeclustering potential abbreviated CE under the transition settingsGuest3closed1.2
165DefectTopographUnhandled exception error message on half-lives results pageGuest3closed1.2
164TodoSkylineAdd Max peptide rank field to Refine formGuest3closed2.1
163DefectSkylinewill/is SkyLine MS1 filtering be capable of peak picking in MS-only data?Guest3closed1.2
162TodoSkylineAdd new data file fields to Skyline reportsGuest3closed3.1
161TodoSkylineStore Spectral Library Explorer sort order in the library cache filesGuest3closed 
160TodoSkylineAdd customizable Tools menuGuest3closed2.1
159TodoSkylineSpectral Library Explorer displays duplicate entriesGuest3closed1.2
158DefectSkylineWhen building a library from IdentityE (PLGS) search results the individual transitions are not listedGuest3closed1.2
157DefectSkylineapplying transition filter settings (precursor only) to peptidesGuest3closed1.1
156DefectSkylineDocNode missing resultsGuest3closed1.2
155TodoTopographDepersonalize "Evvie's Filter"Guest4closed1.2
154DefectSkylinecannot import/merge documents in skyline 1.2Guest3closed1.2
153DefectTopographError message during generation of Results by Cohort outputGuest2closed1.2
152DefectTopographManual "reject" is not workingGuest4closed1.2
151DefectSkylineProblem with MANAGE RESULTS > UP/DOWN functionGuest3closed1.2
150DefectSkylineexporting scheduled method using results for peptides with and without previous retention timesNick Shulman3open4.1
149DefectTopographPeptides with only one Leu have average turnover scores lower than 1 when out of rangeGuest4closed1.2
148DefectTopographPlease correct Y-axis label of half-life graphs to read "ln" rather than "log"Guest3closed1.2
147TodoSkylineReplace isolation width on full-scan settings tab with isolation schemeGuest2closed2.1
146DefectSkylinecannot install skyline softwareGuest3closed1.2
145DefectSkylineWrite automated test for iRT tutorialGuest2closed1.2
144TodoSkylineWrite automated test for MS1 Filtering tutorialGuest2closed1.2
143TodoSkylineWrite automated test for Absolute Quantification tutorialGuest2closed1.2
142DefectSkylineQ-Exactive data acquired using Xcalibur 2.2Guest3closed1.2
141DefectTopographSerious apparent discrepancies in half-life valuesGuest1closed1.2
140TodoSkylineAdd support to Edit > Insert > Peptides for not fully cleaved peptides, if protein name is givenBrendan MacLean3resolved 
139DefectSkylineRegarding building spectral library which Skyline can recognise using Mascot(Proteome Discoverer 1.3)Guest3closed1.2
138TodoSkylineAdd report value for spectral library retention timeNick Shulman3open 
137DefectSkylineexport of scheduled methods to waters xevoGuest3closed1.2
136TodoTopographAdd Average Turnover Score cutoff to Half-Lives and Results by Cohort formsGuest2closed1.2
135TodoTopographImplement "decrease in old protein" method of calculating half-lifeGuest2closed1.2
134DefectTopographTopograph fails to generate Results by Cohort outputGuest1closed1.2
133DefectTopographTopograph tries to load peptide analysis when I click on Status drop-downGuest3closed1.2
132DefectSkylinepeak integration and annotation missing after document mergingGuest3closed1.2
131DefectSkylineabsolute quantification of mTRAQ-modified peptidesGuest3closed1.2
130DefectTopographTopograph stops in the middle of generating replicates w/o MS2 IDs, with no error messageGuest1closed1.2
129DefectSkylineClipboard failure in DataGridViewGuest2closed2.1
128DefectTopographTopograph throws exceptions during search for replicates w/o MS2 IDs, and those replicates are not accessibleGuest2closed1.2
127DefectSkylineExpecting only one periodGuest4closed1.2
126DefectSkylineAnnotationsGuest3closed1.2
125DefectTopographTopograph threw exception and crashed during recalculation of resultsGuest3closed1.2
124DefectSkylineSkyline saved file won't open probably because replicates rearrangedGuest3closed1.2
123TodoSkylineCE,DP optimizing: step number and increment valueGuest3closed1.2
122TodoSkylineCollision Cell Exit Potential (CXP) optimizationBrendan MacLean3open4.2
121TodoSkylineenzyme combinations (N and C terminal)Guest3closed1.4
120TodoSkylineAdd original measurement times to .skyd fileGuest3closed 
119TodoSkylineChromatograms display suggestionGuest3closed1.2
118TodoSkylineMake Skyline graph colors customizableGuest3closed3.7
117TodoSkylineAdd a SkylineRunner command-line parameter to import QC data from a directoryGuest2closed1.2
116DefectTopographTopograph failed and gave "contact manufacturer" message on home computerEvvie Vincow2resolved1.2
115TodoSkylineAdd feature to make multiple selection graph multiple precursor or transition chromatogram togetherBrendan MacLean3open 
114TodoSkylineAdd ability to overlay all heavy and light transitionsGuest4closed1.2
113TodoSkylineStrict scientific notation for y-axis intensity scaleGuest3closed3.1
112DefectSkylineAdd PrecursorResults.MaxHeight value to reportsGuest3closed1.2
111TodoSkylineImplement Edit / Refine / ReintegrateGuest2closed2.1
110DefectSkylineBuilding spectral libraries from Mascot results slower than before?Guest3closed1.2
109DefectTopographAUC cutoff value set on the HalfLivesForm is not transmitted to individual half-life tabsGuest3closed1.2
108DefectSkylineInserting a medium-large transition list with a background proteome can appear to hang SkylineBrian Pratt4open 
107TodoSkylineAdd gene name property to proteins and UI to support itGuest3closed2.6
106TodoSkylineSupport new columns in Thermo TSQ transition list user interfaceGuest3closed1.2
105TodoTopographCreate ultra-simple outlier filter (>2 SD)Guest2closed1.2
104TodoSkylineAdd flexible custom naming for Analyst transition listsGuest3closed 
103TodoSkylineImplement support for MS3 full-scan filtering for neutral lossesGuest3closed 
102TodoSkylineAdd Minimize... button to Edit / Manage Results formGuest2closed2.1
101TodoTopographAdd "minimum area under curve" cutoff to Acceptance Criteria dialogGuest3closed1.2
100DefectSkylineAttempted row add in Results Grid without any columnsGuest2closed2.1
99DefectSkylineInvalidOperationException in PreviewReportDlg.SetResultsGuest3closed2.1
98DefectSkylineNullReferenceException in ResultsGrid.UpdateGridNotReplicateGuest3closed1.2
97TodoTopographIncorporate protein identification/localization info from spreadsheet into TopographGuest3closed1.2
96DefectTopographPercent turnover in Results by Cohort does not match value from Half-Life tabGuest1closed1.2
95DefectTopographHalf-Lives view sometimes comes up "blank" (all zero/NaN values)Guest2closed1.2
94DefectSkylineexport image in .emf format can not be read by Adobe IllustratorGuest3closed 
93TodoSkylineAdd custom finder to find transitions that overlapBrendan MacLean3open 
92TodoTopographCreate a feature to view % newly synthesized on the protein levelGuest2closed1.2
91TodoTopographModify the "Evvie's Filter" algorithm to exclude extreme outliers firstGuest2closed1.2
90DefectTopographDuplicate entries in drop-down when using the Find box in the Half-Lives tabGuest4closed1.2
89DefectSkylineFile / Share minimal needs to be aware of retention time informationGuest3closed1.2
88DefectSkylineAdd peptide ID flag to results peak attributesGuest3closed1.2
87DefectSkylineZoom stops responding during analysis of multiple peptides and replicatesGuest3closed2.6
86DefectSkylineUnhandled exception in DataGridViewRowCollection.RowComparer.CompareObjectsGuest2closed1.2
85DefectSkylineResults grid hangs trying to set annotationsGuest1closed1.2
84DefectSkylineCant export MRM transition list to Analyst method fileGuest3closed1.2
83DefectSkylineCan't export .exp method file for Xevo MassLynxGuest3closed1.2
82DefectSkylineglobal setting for synchronizing isotope typesGuest3closed1.2
81DefectSkylineMethodEdit.zipGuest3closed1.2
80TodoSkylineAdd support for opening File / Share ZIP files directlyGuest3closed1.2
79DefectSkylineFind of an annotation name should find all items with the annotation setGuest2closed1.2
78TodoSkylineAdd Advanced button to Find dialog with checkbox list of things to findGuest2closed1.2
77DefectSkylineNullReferenceException in Results GridGuest2closed1.2
76TodoBiblioSpecBlibBuild needs to store file names with same basename as original instrument data filesGuest2closed1.2
75TodoSkylineSkyline should have document-wide grid view (live report)Guest3closed 
74DefectSkylineImprovements to exception postingGuest3closed1.2
73DefectSkylineAdd error message when incompatible isotope modifications are chosenBrendan MacLean4open 
72TodoSkylineImplement MS1 isotope values in reportsGuest3closed1.2
71TodoSkylineImplement File / Print GraphsGuest3closed 
70DefectSkylineOverlapping transitions causes unpredictable results during CE optimizationBrendan MacLean3open 
69DefectSkyline"Pick Children" causes exception when there is only a peptide list (no proteins)Guest3closed1.2
68DefectSkylinePasteTest does not test intended automanage caseGuest4closed1.2
67DefectSkylineBefore shrinking font in replicate plots truncate names when possibleGuest3closed1.2
66TodoSkylineFind View for SkylineGuest2closed1.2
65TodoSkylineAllow multiple note flags per node attached to specific usersGuest3closed 
64DefectSkylineSummary plots should not reset zooming on selection changeGuest3closed3.1
63TodoSkylineAdd quick menu access to custom annotationsGuest3closed 
62DefectSkylineDocument must be fully loaded before it can be savedGuest2closed1.2
61TodoSkylineShould be possible to view a list of files from which a library was createdGuest4closed1.2
60DefectSkylineImport transition list can pick unlikely ions when more likely ions are with m/z match toleranceGuest4closed1.2
59DefectSkylineSynchronized zooming can make it hard to Undo All Zoom/PanGuest3closed 
58TodoSkylineImplement Experiment Templates in SkylineBrendan MacLean3open 
57DefectSkylinePeptide highlighting in tips problems with variable modificationsBrendan MacLean3open 
56DefectSkylinePaste with missing library message strangeGuest3closed1.2
55TodoSkylineAdd option to show both heavy and light transitions as split graph in same viewGuest3closed 
54DefectSkylineForce matching boundaries between light-heavy precursors with Matching modificationsGuest2closed2.1
53DefectSkylineLibrary spectrum chart does not always rank ions correctlyGuest3closed1.2
52DefectSkylineCopy data in multi-paned graph only copies first paneGuest3closed 
51DefectSkylineCE Optimization mass shifts limited to m/z match toleranceGuest4closed 
50TodoSkylineConsider allowing separate scheduling of peptide precursors for CE optimizationGuest4closed 
49DefectSkylinebackground database with two enzymes doesn't work for first enzymeGuest3closed2.6
48TodoSkylineAdd Audit algorithm for detecting transition interferenceNick Shulman3open 
47TodoSkylineAdd isoelectric point as peptide filterBrendan MacLean4open 
46DefectSkylinemove transition selection box so it doesn't cover transition rankings in tree view (please)Guest4closed1.2
45TodoSkylineSupport unlabeled internal standardsGuest3closed 
44TodoSkylineAdd "Show All" right-click menu to tree viewBrendan MacLean3open 
43TodoSkylineNeed an easier way to review transitions not integratedGuest3closed1.2
42TodoSkylineAdd ability to assign meaning and structure to the replicates in a Skyline documentBrendan MacLean3open 
41DefectSkylineEditing protein names for "fully backed" fasta proteins.Guest3closed1.2
40TodoSkylineAllow user to specify new location for missing result filesGuest3closed 
39TodoSkylineRicher Graph PropertiesGuest4closed3.1
38TodoSkylineMake skyline support case-control experiment analysisGuest3closed 
37DefectSkylineMulti-select drag-drop does not work as expectedGuest3closed1.2
36TodoBiblioSpecImport spectral libraries in .csv format (e.g. created from SRM atlas)Guest3closed2.6
35TodoSkylineMake it possible to find note/annotation text from Find dialogGuest3closed1.2
34TodoSkylineAdd new support for ion highlighting options in spectral library graphBrian Pratt3open19.2
33DefectSkylineChemical formula ordering should not effect warning about existing Unimod modificationGuest3closed1.2
32TodoSkylineDelete results for invidiual peptidesGuest3closed 
31TodoSkylineExport inclusion lists for Skyline documents with only MS1 full--scan filteringGuest3closed1.2
30TodoSkylineUse retention time regression to better predict peptide peaks over multiple replicatesGuest3closed1.2
29TodoSkylineImplement support for overlapping light-heavy isotope envelopes in MS1 filteringNick Shulman3open 
28TodoSkylineUse MS/MS with peptide IDs in MS1-only full-scan filteringGuest3closed1.2
27TodoSkylineImplement full-scan method export for QSTAR and Triple-TOF 5600Guest3closed1.2
26TodoSkylineImplement full-scan method export for Waters Q-TOF instrumentsGuest2closed3.1
25TodoSkylineMake Thermo EZ Method transition list format the default even for unscheduled runsGuest3closed 
24TodoSkylineImplement targeted MS/MS methods for Agilent Q-TOFGuest3closed1.2
23TodoSkylineInteresting scenarios for Thermo tools require precursor mass shiftsGuest3closed 
22TodoSkylineMake fragment ion labeling in spectral library not limited to two labels.Guest3closed 
21TodoSkylineAdd refinement option to add missing product ions with matching dataBrendan MacLean3open 
20TodoSkylineImplement command-line interface for SkylineGuest2closed1.2
19TodoSkylineAdd a tip somewhere that shows the ion table for the library spectrumBrendan MacLean4open 
18DefectSkylineChosing the number of unscheduled methodsGuest3closed1.2
17TodoSkylineDynamically size position/count indicators based on transition countsGuest4closed3.1
16DefectSkylineData import dialog scans drives unnecessarilyGuest3closed1.2
15DefectSkylineExport modification assignemtGuest3closed1.2
14DefectSkylineExport method error Xevo TQ-SGuest3closed2.1
13DefectSkylineMissing filtered ion types can have surprising effect on the dot-productBrendan MacLean3open4.3
12TodoSkylineAdd signal-to-noise value in reportsBrendan MacLean4open 
11DefectSkylineBackground proteome build fails with large FASTA fileGuest4closed 
10TodoSkylineAdd reporter ion type for measuring constant mass ions like ITRAQGuest3closed2.6
9TodoSkylineLibrary spectrum graph should offer UI to choose manually specturm matchesBrendan MacLean3open 
8TodoSkylineAdd an Apply To All action to the chromatogram graphsGuest3closed 
7TodoSkylineMake all Results Grid columns available in column picking UI alwaysGuest3closed2.2
6DefectSkylineResults columns should get #N/A when no results availableGuest2closed2.1
5TodoSkylineImplement full-scan method export for Agilent QTOF instrumentsGuest3closed 
4TodoSkylineImplement custom neutral lossesGuest3closed 
3TodoSkylineAdd a way to specificy document level informationGuest3closed1.2
2TodoSkylineSupport second round CE optimizationKaipo4open 
1TodoSkylineImplement custom ion supportGuest2closed3.1