MacCoss Lab Issues List 

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Issues List : issues 

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Issue ID
Assigned To
 566TodoSkyline add a Hide / Show Title menu item everywhere we have Hide / Show Legend, and make it possible to show a descriptive title everywhere (e.g. molecule name for calibration curve plot)Brian Pratt3open 
565TodoSkylineAccept defined annotation types as valid column headers for small molecule transition listsBrian Pratt3open4.2
564TodoSkylineAdd checkboxes to invert meaning of Edit > Refine > Accept Proteins/PeptidesBrendan MacLean3open4.2
563TodoSkylineNot all document grid columns have descriptions in helpNick Shulman3open4.2
562TodoSkylineImplement Audit Log for Skylinetobiasr2open4.2
561DefectSkylineSkyline-daily loosing peak integrationsNick Shulman3resolved4.1
560TodoSkylineImplement group by graph panes for summary graphstobiasr3open 
559TodoSkylineCannot load msf result file (PD) when building a libraryKaipo3open4.2
558TodoSkylineAdd results search paths to Document SettingsKaipo3open 
557DefectSkylineChooseFormatDlg needs a documentation linkNick Shulman3open4.1
556DefectSkylineIssues with Waters schedule MRM data. Can't load.Guest3closed3.7
555DefectSkylineSkyline assumes /labkey context path when pinging PanoramaVagisha3open4.1
554DefectSkylineAssigning a wrong peak and not following the spectral library retention timeNick Shulman3open4.1
553DefectSkylineSupport Contains filter for report column that looks like textNick Shulman3open4.1
552TodoSkylineSupport multiple replicate selection in summary graph panes and Remove Peaktobiasr3open4.1
551DefectSkylineSkyline file not openingGuest3closed4.1
550DefectSkylineOnly iRT traces are importedKaipo3open4.1
547DefectSkylineXML Error -- Reading mz values; small molecule transition listBrian Pratt3resolved4.1
546DefectSkylineUnable to build spectral libraryGuest3closed4.1
545TodoSkylineAdd Include charge state checkbox to Edit > Insert > PeptidesBrendan MacLean3open4.1
544DefectSkylineDiscrepancies in Heavy and Light Peptide Chromatogram Import RangesGuest3closed4.1
539DefectSkylineHeavy/Light Peptide Chromatogram Import Range DiscrepanciesGuest3closed4.1
538TodoSkylineMulti-peptide calibration curves would be niceNick Shulman3open4.1
537DefectSkylineHow to add a column to the documents or results grid that contains the heavy or ISTD areas? Nick Shulman3open4.1
536DefectSkylinePoints across peak count should scale with chromatogram graph font settingsGuest4closed4.1
535DefectSkylineMS1 chromatograms in scheduled PRM data should get limited to times of matching MS/MS scansNick Shulman2open4.1
534TodoSkylineMulti-peptide graph fixes / enhancementstobiasr2open4.1
533DefectSkylineReporter ion masses must be less than or equal to 5000Guest2closed4.1
532TodoSkylineX!Tandem in SkylineBrendan MacLean3open 
531TodoSkylineInclude Replicate Name as column in exported chromatogramsGuest3closed4.1
530DefectSkylineNIST .msp reader ignores peptide entries with n- or c-terminal modificationsKaipo3open4.1
529TodoSkylineConsider imposing spectrum filtering based on Full-Scan settingsBrendan MacLean3open 
528DefectSkylineColumn header sort messes up peak scoring model training gridGuest3closed4.1
527DefectSkylineDouble-clicking .sky file does not seem to work for Administrator InstallationNick Shulman3open4.1
526TodoSkylineEnhancements to AutoCopyUSBBrendan MacLean3open4.1
525DefectSkylineResults Grid or calibration curveNick Shulman3open4.1
524TodoSkylineMake it possible to rename replicates through the Document GridGuest3closed4.1
523TodoSkylineMake it easy to connect raw data file sample information to annotations in SkylineNick Shulman3open4.1
522TodoSkylineAdd a way to add annotations to a document from the command-lineNick Shulman2open4.1
521TodoSkylineAdd CE recognition to transition list importKaipo4open4.1
520TodoSkylineMake ctrl-Page Up ctrl-Page Down retreat or advance all document panes at onceBrendan MacLean3open4.1
519TodoSkylineSynchronize zooming for RT and Area plotsGuest3closed4.1
518DefectSkylineResolve issue of hard-coding Waters CE equationsKaipo4open4.1
517TodoSkylineAdd Remove Peak and Apply Peak to All menus to retention time graphGuest3closed 
516DefectSkylineManual peak integrations are reset after import of new results fileGuest0closed3.7
515TodoSkylineAdd some way to produce summary statistics to reports by grouping replicate annotationsNick Shulman1open4.1
514TodoSkylineExpand neutral loss support to allow for charged losses from the precursorBrendan MacLean3open 
513DefectSkylineFix ExclusionUseDIAWindow setting to consider IsolationWindow.MethodStart and MethodEndBrendan MacLean3open 
512TodoSkylineAdd summary statistics for q valuesBrendan MacLean3open4.1
511TodoSkylineRequest for customizable bulk peak removalNick Shulman2open4.1
510TodoSkylineUpdates to iRT standards necessaryGuest3closed3.7
509TodoSkylineremoove limit of 200aa or increase this number for analysis top-down or middle-down dataBrendan MacLean3open3.7
508DefectSkylineMake SkylineCmd.exe return non-zero when a line starting with "Error:" is outputGuest2closed4.1
507DocumentationSkylineSkyline Menu for all terminology.Nick Shulman3open3.7
506TodoSkylineAdd Cone Voltage optimization support for Waters triple quadrupolesGuest3closed3.7
505TodoSkylineAdd RF Lens optimization for Thermo triple quadrupoleKaipo3open4.1
504TodoSkylineAdd support for CE optimization for PRM on Waters Xevo QTOFKaipo3open4.1
503TodoSkylineImprove document minimizing and command-line supportNick Shulman2open3.7
502TodoSkylineImprove UnimodCompiler to preserve modification more than one decimal place for modifications that require more to disambiguateNick Shulman2open4.1
501DefectSkylineImprove BlibBuild handling of multiple searches on the same raw data filesGuest3closed3.7
500DefectSkylineInstrument tab not limiting time for extraction based on RT predictionNick Shulman3open3.7
499TodoSkylineMass error replicate comparison does not support split graphNick Shulman3open3.7
498DefectSkylineTheoretical peptide z ion does not matchGuest3closed3.7
497DefectSkylineIgnore full-scan settings for retention time prediction when importing SRM dataNick Shulman3open3.7
496DefectSkylineCannot publish data to Panorama.Guest3closed3.6
495TodoSkylineMore flexibility in View > Arrange Graphs > GroupedYuval3open 
494DefectSkylineCan Skyline Support Waters UNIFI data format .UEP fileBrian Pratt2open3.7
493DefectSkylineiRT standard peptides added to document can gain extra precursorsGuest3closed3.6
492DefectSkylineAnother library building errorKaipo2open4.1
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 DocumentGridNick Shulman3open3.6
486TodoSkylineCome up with clearer way of informing a user that iRT regression was not good enoughKaipo2open4.1
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 moleculesGuest3closed3.6
482TodoSkylineset negative ion modeBrian 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 QQQBrendan MacLean1open3.6
478DefectSkylinePeak Boundary List File Fails to LoadNick Shulman3open3.5
477TodoSkylineRequest for occupancy proportion report valueNick Shulman3open 
476DefectSkylineIssues with QuaSARGuest3closed3.6
475DefectSkylineNeed to close and reopen Document Grid after adding new annotationsNick Shulman2open3.6
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 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 (, 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 errorKaipo2open4.1
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