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Issue ID
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Title
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 508DefectSkylineMake SkylineCmd.exe return non-zero when a line starting with "Error:" is outputNick Shulman3open3.7
507DocumentationSkylineSkyline Menu for all terminology.Nick Shulman3open3.7
506TodoSkylineAdd Cone Voltage optimization support for Waters triple quadrupoleskaipot@u.washington.edu3open3.7
505TodoSkylineAdd RF Lens optimization for Thermo triple quadrupolekaipot@u.washington.edu3open3.7
504TodoSkylineAdd support for CE optimization for PRM on Waters Xevo QTOFkaipot@u.washington.edu3open3.7
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 disambiguatekaipot@u.washington.edu2open3.7
501DefectSkylineImprove BlibBuild handling of multiple searches on the same raw data filesBrendan MacLean3resolved3.7
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 matchBrendan MacLean3resolved3.7
497DefectSkylineIgnore full-scan settings for retention time prediction when importing SRM dataNick Shulman3open3.7
496DefectSkylineCannot publish data to Panorama.Brendan MacLean3resolved3.6
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 precursorsBrendan MacLean3resolved3.6
492DefectSkylineAnother library building errorkaipot@u.washington.edu3open3.6
491DefectSkylineIssue with building spectral librarykaipot@u.washington.edu3open3.6
490DefectSkylineID lineGuest3closed3.6
489DefectSkylineImporting negative ion transitions from Masshunter (small molecules)Brian Pratt2resolved3.6
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 DocumentGridNick Shulman3open3.6
486TodoSkylineCome up with clearer way of informing a user that iRT regression was not good enoughkaipot@u.washington.edu3open3.6
485TodoSkylineAdd Help > Check for UpdatesBrendan MacLean3open3.6
484TodoSkylineAdd confidence intervals for slope and intercept in calibration regressionsNick Shulman3open3.6
483DefectSkylinePrecursor isotope peaks (M+1, M+2) not automatically shown for small moleculesBrian Pratt3resolved3.6
482TodoSkylineset negative ion modeBrian Pratt3open3.6
481DefectSkylineError trying to access Tool Store in Skyline DailyGuest3closed3.6
480DefectSkylineSkyline Daily does not support Agilent Automation ToolBrendan MacLean3resolved3.6
479DefectSkylineSkyline Daily shows no data when there is data - Agilent QQQBrendan MacLean1open3.6
478DefectSkylinePeak Boundary List File Fails to LoadNick Shulman3open3.5
477TodoSkylineRequest for occupancy proportion report valueNick Shulman3open 
476DefectSkylineIssues with QuaSARBrendan MacLean3open3.6
475DefectSkylineNeed to close and reopen Document Grid after adding new annotationsNick Shulman2open3.6
474DefectSkylineAsk user about Library settings if changing peptide Filter settingsYuval2open3.6
473DefectSkylineMissing 2nd transition for some samples_small moleculesBrian Pratt3open3.6
472DefectSkylinemethod export for Quantiva failedBrendan MacLean3open3.6
471DefectSkylineMaxQuant library builder fails to understand T(2) modificationGuest2closed3.6
470TodoSkylineAdd TotalAreaMS1Adjusted column to reportsNick Shulman3open3.6
469TodoSkylinedocument grid TransitionResult should show extraction width, as well as drift time and windowBrian Pratt3open3.6
468DefectSkylineS-lens value isn't written to Exported transition list when checkedBrian Pratt3open3.6
467DefectSkylineSkyline-daily (3.5.1.9673, 64-bit) locks up when uploading .raw files.Brendan MacLean3open3.6
466DefectSkylineSkylineRunner scriptability improvements: version number and help info from commandline, and non-zero exit code on errorkaipot@u.washington.edu2open3.6
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 linekaipot@u.washington.edu3resolved3.6
463DefectSkylineAutomating Skyline for HT Proteomics with Skyline RunnerGuest3closed3.6
462DefectSkylineAdd "Thermo TSQ Quantiva" to transition settingskaipot@u.washington.edu2open3.6
461DefectSkylineUnable to change transition settingsNick Shulman3resolved3.6
460DefectSkylineprovide a means of updating protein metadata to current Uniprot level for document and background proteomeBrian Pratt3open3.6
459DefectSkylineOnly one chromatogram type in Full-Scan graph for chromatogram clicked in split graph modeNick Shulman3open3.6
458DefectSkylineMRM Chromatogram not ProcessedBrendan MacLean3open 
457TodoSkylineAdd access to SpectraST retention times to library implementationkaipot@u.washington.edu3open3.6
456DefectSkylinereimport after changing full scan settings to "Centroided" doesn't actually perform centroidingBrian Pratt3open3.6
455TodoSkylineAdd option to allow exporting mass errors with File > Export > ChromatogramsBrendan MacLean3open 
454TodoSkylineRemove asymetric isolation scheme support and add ability to specify a marginBrendan MacLean3open3.6
453TodoSkylineAdd check box to Digestion tab to allow removal of protein N-terminal MethionineBrian Pratt3open3.6
452DefectSkylineCopy-paste fails to recognize equivalent modifications with different namesBrendan MacLean3open3.6
451TodoSkylineAdd redundant library access to Library Explorerkaipot@u.washington.edu3open 
450DefectSkylineSkyline should warn when importing a transition list with values that exceed the current instrument m/z rangeBrian Pratt3open3.6
449DefectSkylineLIBRARY BUILD ERRORkaipot@u.washington.edu2open3.6
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 activatedYuval3open3.6
445DefectSkylineDIA-MS on FusionGuest3closed<3.2>
444TodoSkylineAdd errors and warnings for documents where Full-Scan settings do not match Filter ion typesBrendan MacLean3open<3.2>
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 constructorkaipot@u.washington.edu3resolved 
439DefectSkylineMS1 Full-Scan import = match with mascot search, ppm values missingGuest3closed<3.2>
438DefectSkylineMake "Insert Transition List" for small molecules tolerant of empty product ion columnsBrian Pratt3open<3.2>
437TodoBiblioSpecImprove performance of BlibBuild spectral library building from pepXML/mzXMLGuest2closed<3.2>
436TodoSkylineAdd TraML as a transition list import formatkaipot@u.washington.edu3open 
435DefectSkylineProblem handling 'Optimize CE' dataGuest3closed<3.2>
434TodoSkylineAdd chromatogram export support to command-line interfaceGuest3closed<3.2>
433DefectSkylineAllow Remove Peak and Apply to All from peptide view with multiple precursorsGuest2closed<3.2>
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 diskGuest3closed<3.2>
429TodoSkylineExtend the Insert Transition List dialog to be as flexible for peptides as it is for small moleculesBrian Pratt3open<3.2>
428DefectSkylineMulriple injection import error when no scans match document peptides or current filter settingsGuest3closed 
427TodoSkylineCreate Thermo TraceFinder export toolYuval2open3.6
426TodoSkylineAdd peak area shading to show the area integrated in SkylineGuest2closed<3.2>
425DefectSkylineHard to figure out how to filter on true/false columns in Document GridNick Shulman2open<3.2>
424DefectSkylineColored summary chromatogram disappeared with latest Skyline-daily updateGuest3closed<3.2>
423DefectBiblioSpecHandle multiple modifications on the same residuekaipot@u.washington.edu3open<3.2>
422TodoSkylineAttempt to make Skyline ignore spectra from incorrect mass analyzer typekaipot@u.washington.edu3open<3.2>
421DefectSkylineImplement cursor changes for the start-up formGuest4closed<3.2>
420TodoSkylineAdd refinement option for DDA data based on peak IDsBrendan MacLean4open 
419TodoSkylineAdd SkylineRunner support for Edit > Refine > ReintegrateGuest3closed<3.2>
418TodoSkylineImprove peak removal UIGuest3closed<3.2>
417TodoSkylineAdd explicit property support for peptidesGuest3closed<3.2>
416DefectSkylineHaving many disconnected network drives causes the Import Results form to hang for a long timeGuest3closed<3.2>
415DefectSkylineTransition list import should pick modified sequence column over bare sequence columnGuest3closed<3.2>
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 negativekaipot@u.washington.edu3open<3.2>
412TodoSkylineNeed ways to see isolation windows on full-scan graphsYuval2open3.6
411DefectSkylineColumn filters do not apply to Export and Copy AllGuest1closed3.1
410DefectSkylineMultiple selection color is too faintBrendan MacLean3resolved<3.2>
409DefectSkylineSkyline guesses poorly when it encounters AQUA/SILAC labelingkaipot@u.washington.edu3open<3.2>