| | | | | | | |
---|
936 | Todo | Skyline | Thermo Eclipse and Fusion Lumos method export | Kaipo Tamura | 3 | resolved | 23.1 |
935 | Defect | Skyline | Capture injection time as sample-scoped chromatogram | Brendan MacLean | 3 | open | |
934 | Todo | Skyline | Enable optimization method export for more TOF instruments | Kaipo Tamura | 2 | open | |
933 | Todo | Skyline | Thorium method export | Kaipo Tamura | 2 | open | |
932 | Todo | TestResults | Summarize/graph pass1 iteration count for tests | Kaipo Tamura | 4 | open | |
931 | Todo | Skyline | Agilent MH 12 method export | Kaipo Tamura | 2 | open | |
930 | Todo | Skyline | Export isolation list (DIA) for Bruker timsTOF | Kaipo Tamura | 4 | open | |
929 | Defect | Skyline | When explicit ion mobility values are used, the reported CCS value should be adjusted appropriately in the resulting chromatogram extractions | Brian Pratt | 3 | open | |
928 | Defect | Skyline | AssumptionException saving document with protein groups sometimes | Guest | 2 | closed | 23.1 |
927 | Defect | Skyline | Bibliospec - retain fragment charge values in MGF files | Brian Pratt | 3 | open | |
926 | Todo | Skyline | Implement Bruker Paser support in BlibBuild | Matt Chambers | 2 | open | 23.1 |
925 | Defect | Skyline | Targets view hangs during mouse-over with peptides longer than 2000 or so | Nick Shulman | 3 | open | |
924 | Defect | Skyline | Fix ability to provide a protein description in Edit > Insert > Peptides | Nick Shulman | 3 | open | |
923 | Todo | Skyline | Implement an interface that allows for multiple algorithms to do peak group assignment | Nick Shulman | 3 | open | |
922 | Defect | Skyline | Edit > Find needs to use LongWaitDlg and support cancel | Nick Shulman | 3 | open | 23.1 |
921 | Todo | Skyline | Transition list reader should identify special ions by m/z the same way it does calculated peptide fragment ions | Brian Pratt | 3 | open | |
920 | Defect | Skyline | When Group By fails in replicate comparison graphs you lose the Order By menu item | Nick Shulman | 3 | open | 23.1 |
919 | Defect | Skyline | SpectrumLibraryInfoDlg scoring columns should match library build columns | Brendan MacLean | 3 | resolved | 23.1 |
918 | Defect | Skyline | a few issues with "Use Results" in ion mobility libraries | Brian Pratt | 3 | open | 23.1 |
917 | Defect | Skyline | Ion mobility high energy offset should be applied for all Full Scan MS/MS modes, not just All Ions DIA | Guest | 3 | closed | 23.1 |
916 | Documentation | Skyline | Document normalization methods | Nick Shulman | 2 | open | 22.2 |
915 | Defect | Skyline | Library Match and Full-Scan - Right-click menu item order is broken in 22.2 | Rita Chupalov | 2 | open | 22.2 |
914 | Defect | Skyline | Proteomics features still showing in small molecule mode | Brian Pratt | 3 | open | 23.1 |
913 | Todo | Skyline | Make Ctrl-A work in Import > Results form to select all files in a folder | Brendan MacLean | 3 | open | 22.2 |
912 | Defect | Skyline | Auto-Zoom X Axis > Best Peak does nothing for chromatograms with removed peaks | Kaipo Tamura | 3 | open | 23.1 |
911 | Defect | Skyline | Calibration Curve graph calculates concentrations on double-blanks (NaN or infinity) | Nick Shulman | 3 | open | 23.1 |
910 | Defect | Skyline | Synchonized integration has trouble with removed peaks | Brendan MacLean | 3 | resolved | 23.1 |
909 | Defect | Skyline | Red dots for dotp values below the cut-off appear behind bars | Rita Chupalov | 3 | open | 23.1 |
908 | Todo | Skyline | Command Line Enhancement Request : Include MS/MS Filtering Options | Brian Pratt | 3 | open | 23.1 |
907 | Defect | Skyline | ViewLibraryDlg right-click menu lagging behind Library Match right-click menu | Rita Chupalov | 2 | open | 23.1 |
906 | Defect | Skyline | A few details working with Bruker PASER assay library lists | Brian Pratt | 3 | open | 22.2 |
905 | Defect | Skyline | IndexOutOfRangeException bringing up GraphFullScan immediately after modifying the document | Rita Chupalov | 3 | open | 23.1 |
904 | Defect | Skyline | Store more spectrum and instrument information in .blib files when possible | Matt Chambers | 2 | open | 23.1 |
903 | Defect | Skyline | Show names of default settings, and save settings with document when exporting a transition list | Kaipo Tamura | 3 | open | 22.2 |
902 | Todo | Skyline | add an ion mobility range filter in Transition Settings IM tab similar to instrument settings tab's mz range filter | Brian Pratt | 3 | open | |
901 | Defect | Skyline | Newly added annotations don't show up in the Rule Editor | Nick Shulman | 3 | open | 22.2 |
900 | Defect | Skyline | Opening a .skyp file shows no progress until the file is downloaded | Vagisha Sharma | 3 | open | 22.2 |
899 | Todo | Skyline | Adding targets from DDA library seems useful to be able to specify a number of runs a peptide got ID'd in | Matt Chambers | 3 | open | 23.1 |
898 | Defect | Skyline | Record the Document Grid selection in the Undo/Redo buffer during Document Grid editing events | Brendan MacLean | 3 | resolved | 22.2 |
897 | Todo | Skyline | Make Ctrl-Z (Undo) and Ctrl-Y (Redo) work in Document Grid | Brendan MacLean | 2 | resolved | 22.2 |
896 | Defect | Skyline | IMS library "Use Results" should ignore poor quality chromatographic peaks | Brian Pratt | 3 | open | |
895 | Todo | Skyline | "Split Graphs" equivalent (stacked MS1 and MS/MS views) for Full Scan view | Brian Pratt | 3 | open | |
894 | Todo | Skyline | Make "Use Results" isolation scheme work for Import > Peptide Search of DIA | Kaipo Tamura | 2 | open | 22.2 |
893 | Todo | Skyline | Need a way to turn off switching replicates in retention times - regression plot | Rita Chupalov | 3 | open | 22.1 |
892 | Defect | Skyline | Export > Transition / Isolation List with scheduling seems broken for counting multiple methods | Guest | 1 | closed | 21.2 |
891 | Defect | Skyline | Adjusting peak boundaries with non-quantitative transitions is confusing | Nick Shulman | 3 | open | 22.2 |
890 | Defect | Skyline | Audit log Skyline Version upgrade | Kaipo Tamura | 3 | open | 22.1 |
889 | Todo | Skyline | Make more instrument parameters available on Files in the Document Grid | Matt Chambers | 3 | open | 22.1 |
888 | Defect | Skyline | File > Import > Peptide Search with existing library reports the build settings in the Audit Log | Brendan MacLean | 2 | resolved | 22.2 |
887 | Defect | Skyline | Smooth handling of .skyp file for server lacking credentials | Vagisha Sharma | 3 | open | 22.1 |
886 | Defect | Skyline | AutoQC Loader stops scrolling log text area after a wrapped line | Vagisha Sharma | 3 | open | 22.1 |
885 | Defect | Skyline | Dotp line graph points should be clickable for changing the active replicate | Rita Chupalov | 3 | open | 22.1 |
884 | Defect | Skyline | Some user are really unhappy that they can't type transition lists into Skyline like they used to do | Brian Pratt | 3 | open | |
883 | Documentation | Skyline | Update tutorials with new library building interface | Guest | 2 | closed | |
882 | Todo | Skyline | Clean out apparent IMS related cruft in Full Scan tab | Guest | 3 | closed | |
881 | Defect | Skyline | Move Bruker timsTOF method export into BuildMethod | Kaipo Tamura | 3 | open | |
880 | Todo | Skyline | SSL format changes for Feature Detection | Brian Pratt | 3 | open | 22.1 |
879 | Defect | Skyline | Need some way to show user FAIMS information in raw scan view, to demystify jagged chromatograms before IM filters are applied | Brian Pratt | 3 | open | |
878 | Defect | Skyline | Need to handle retention time shifts for deuterated internal standards | Brian Pratt | 3 | open | |
877 | Defect | Skyline | "How Skyline Calculates Peak Areas and Heights" tip could use updating | Brendan MacLean | 3 | open | |
876 | Defect | Skyline | Typo in "Skyline Small Molecule Method Development and CE Optimization" tutorial | Nat Brace | 3 | open | |
875 | Defect | Skyline | The adduct pick list (as used in Modify... in Targets tree) should include [M+] and [M-] | Guest | 3 | closed | |
874 | Defect | Skyline | Default Win32 MAX_PATH value of 260 is too small for some users | Brian Pratt | 3 | open | |
873 | Defect | Skyline | Feature request: single molecule/peptide re-integration | Brendan MacLean | 3 | open | |
872 | Defect | Skyline | Document created by an m/z-only transition list should not depend on list order | Guest | 3 | closed | 22.1 |
871 | Defect | Skyline | Clean up the interaction of small molecule transition list imports and Transition Settings that affect precursor isotope ([M+1], [M+2] etc) creation | Brian Pratt | 1 | open | 22.1 |
870 | Todo | Skyline | Implement special peak statistics for DDA MS/MS | Guest | 1 | closed | 22.2 |
869 | Todo | Skyline | Add a Prosit RT calculator parallel to SSRCalc | Kaipo Tamura | 3 | open | |
868 | Todo | Skyline | Consider generating a dictionary of less common isotopes instead of hardcoding them piecemeal in response to user requests | Brian Pratt | 3 | open | |
867 | Todo | Skyline | Possible Improvements to Edit>Insert>TransitionList | Brian Pratt | 3 | open | 22.1 |
866 | Defect | Skyline | Provide option in Skyline to upload a minimized library to Panorama | Guest | 3 | closed | 22.1 |
865 | Defect | Skyline | Adding heavy mods in Peptide Settings does not add "Ratio to Heavy" normalization to Quantification tab | Guest | 1 | closed | 21.2 |
864 | Defect | Skyline | Various issues reading this small molecule transition list with heavy label formulas | Guest | 3 | closed | 22.1 |
863 | Defect | Skyline | Problem loading a small mol document with isotope labels - Skyline complains that they aren't known modifications (which should not matter) | Guest | 3 | closed | 22.1 |
862 | Defect | Skyline | "Importing Results..." window should resize its multi-file progress control when there's a vertical scrollbar in use (currently cuts off the "Cancel" buttons and looks funny) | Guest | 3 | closed | 22.1 |
861 | Todo | Skyline | Implement better peptide to protein assignment strategies for target selection | Matt Chambers | 2 | open | 22.1 |
860 | Defect | Skyline | Support more than one fragment specification per line in transition list column picker, for small molecules at least | Brian Pratt | 3 | open | |
859 | Defect | Skyline | Add peak apex CCS to Transition Result | Nick Shulman | 3 | open | 22.1 |
858 | Defect | Skyline | make "ImportPeptideSearch with the IMS filtering visible" a form view that can be shown in the SkylineTester Forms tab | Guest | 3 | closed | 22.1 |
857 | Defect | Skyline | ImportTransitionListColumnSelectDlg lags a bit when associate proteins checked | Brendan MacLean | 3 | resolved | 21.2 |
856 | Defect | Skyline | When training a "Default" peak scoring model, the model should be able to use feature scores that are present for some but not all peptides | Guest | 3 | closed | 22.1 |
855 | Defect | Skyline | Log scale with median normalization does not mention the normalization in the y-axis label | Brendan MacLean | 3 | resolved | 22.2 |
854 | Defect | Skyline | Peak Areas - Replicate Comparison - Normalize to strangely chooses poorly | Brendan MacLean | 2 | resolved | 21.2 |
853 | Defect | Skyline | Remove peak should make dotp annotations and line missing | Guest | 1 | closed | 21.2 |
852 | Defect | Skyline | Full-Scan graph no longer auto-scales the y-axis when clicking arrow buttons | Brendan MacLean | 2 | resolved | 21.2 |
851 | Todo | Skyline | Rename auto trained peak scoring models | Kaipo Tamura | 3 | open | 22.1 |
850 | Defect | Skyline | Fix performance issue with ion moblity filtering in library viewer | Brian Pratt | 3 | open | 22.1 |
849 | Defect | Skyline | Failure opening .sky file saying audit log entry has been modified | Brendan MacLean | 2 | resolved | 21.2 |
848 | Defect | Skyline | Show a better error message if check for Panorama server fails | Vagisha Sharma | 1 | open | 23.1 |
847 | Defect | Skyline | Add option to use explicit RT instead of measured for exporting scheduled methods | Kaipo Tamura | 3 | open | |
846 | Defect | Skyline | Trouble exporting polarity-switching QQQ method from Skyline to Agilent-6495C | Kaipo Tamura | 3 | open | |
845 | Defect | Skyline | User says Agilent 6495C can go down to a dwell time of 0.5ms, but we insist on integer dwell times in UI | Kaipo Tamura | 3 | open | |
844 | Defect | Skyline | Libraries should load without error even if the directory that the library is in is not writeable. | Guest | 2 | closed | 21.2 |
843 | Defect | Skyline | Update "_elementMasses" in MaxQuantReader.cpp | Guest | 2 | closed | 21.2 |
842 | Todo | Skyline | Add a setting for RT annotation display to Chromatogram graph right-click > properties form | Guest | 2 | closed | |
841 | Defect | Skyline | Insert Transition List with heavy precursors results in document that cannot be opened. | Guest | 2 | closed | |
840 | Defect | Skyline | is M+Na precursor being handled properly in display of split graphs and heat maps, and is it being used properly in SONAR extraction? | Guest | 3 | closed | |
839 | Defect | Skyline | Inconsistent representation of "squared" in IM peak display on chromatogram graphs | Guest | 3 | closed | |
838 | Defect | Skyline | initial zoom on ion mobility heat map should not default to zero as lower range | Guest | 3 | closed | 21.1 |
837 | Defect | Skyline | Import Peptide wizard "Configure Full-Scan Settings" IMS stuff should have its own page/step | Guest | 3 | closed | 21.1 |
836 | Defect | Skyline | Certain TransitionSettings>Library tab controls dealing with product ion filtering should be declared as proteomic | Guest | 3 | closed | 21.2 |
835 | Defect | Skyline | Audit verification error after minimizing and sharing Skyline document | Rita Chupalov | 3 | open | |
834 | Defect | Skyline | Precursors for the same peptide with same precursor m/z get lost in the .skyd file | Guest | 2 | closed | |
833 | Todo | Skyline | Show rdotp in Peak Areas > Replicate Comparison plot when Normalize To > Heavy is chosen | Guest | 3 | closed | 21.2 |
832 | Defect | Skyline | Improve ZedGraph handing of clipboard exceptions | Guest | 3 | closed | 21.2 |
831 | Defect | Skyline | Change or add an option for MS/MS spectrum graph dotp value in mirror plot with Prosit | Rita Chupalov | 2 | open | 22.1 |
830 | Todo | Skyline | Add a "High resolution" check box to Transition Settings - Library - Ion match tolerance | Rita Chupalov | 2 | open | 22.1 |
829 | Todo | Skyline | Change reports to report 1-based AA positions | Guest | 3 | closed | 21.2 |
828 | Todo | Skyline | Make it possible to see RT with more precision in chromatogram graphs | Brian Pratt | 3 | closed | 22.1 |
827 | Defect | BiblioSpec | X! Tandem point mutations not understood by BlibBuild | Matt Chambers | 2 | open | 23.1 |
826 | Defect | Skyline | Choosing an existing standard during Assay Library import fails to add library spectrum to BLIB | Kaipo Tamura | 3 | open | 21.2 |
825 | Todo | Skyline | SDRF Reports | Nick Shulman | 3 | open | 23.1 |
824 | Todo | Skyline | Implement command-line option --import-peak-boundaries | Guest | 3 | closed | 22.1 |
823 | Todo | Skyline | Make it easier to export FASTA file of the proteins in the targets window | Brian Pratt | 3 | open | |
822 | Defect | Skyline | Show Prosit spectrum always when Mirror is on | Rita Chupalov | 3 | open | 22.1 |
821 | Todo | Skyline | Expand multiple selection handling in chromatogram graphs to handle precursors | Kaipo Tamura | 3 | open | |
820 | Defect | Skyline | Ion Mobility Library editor should offer to wipe CCS value when IM value is altered | Brian Pratt | 3 | open | |
819 | Todo | Skyline | Implement new option to synchronize integration | Brendan MacLean | 2 | resolved | 21.2 |
818 | Todo | Skyline | BlibBuild needs to write more information to .blib files | Guest | 2 | closed | |
817 | Todo | Skyline | Small molecule support for Import > Transition > List column picker | Guest | 1 | closed | 21.2 |
816 | Todo | Skyline | File>Share should offer to include a selection of raw files | Brian Pratt | 3 | open | |
815 | Todo | Skyline | Settings UI should offer choices when a change is made that would break consistency | Brendan MacLean | 3 | open | 22.1 |
814 | Todo | Skyline | Need a way to more easily run all tests that produce audit logs | Guest | 3 | closed | 21.2 |
813 | Defect | Skyline | tidy up user-facing notation for mass-only fragments, and adjust sense of "[M-]", "[M+2]" etc to means "inherently charged, m/z to mass conversion is simple multiplication, no particles lost/gained" | Brian Pratt | 3 | open | |
812 | Todo | Skyline | Calculate and store peak skewness/asymmetry value | Guest | 2 | closed | 23.1 |
811 | Defect | Skyline | deal with the TODO from commit "When adding small molecule library values to a document, just ignore any fragment peaks with absurdly small or large m/z values" | Brian Pratt | 3 | open | |
810 | Defect | Skyline | Manage Reports - Copy button still has "Open View Editor" menu item | Guest | 3 | closed | 21.2 |
809 | Todo | Skyline | Implement better searching in Library Explorer for small molecules | Guest | 3 | closed | |
808 | Todo | Skyline | Change Targeted to PRM and add a SureQuant option to Acquisition method list | Guest | 3 | closed | 21.2 |
807 | Defect | Skyline | Fix/Improve File > Export > Spectral Library | Brendan MacLean | 3 | resolved | 21.2 |
806 | Defect | Skyline | "Column1", "Column2" etc generated headers in the column picker should be localized. | Guest | 3 | closed | |
805 | Defect | Skyline | Stopping SkylineTester does not abort the second run of SkylineNightly | Guest | 3 | closed | |
804 | Todo | Skyline | Implement simple filtering for MSP file import | Brian Pratt | 3 | open | |
803 | Todo | Skyline | Retain previous iRT values in iRT databases | Guest | 2 | closed | 22.1 |
802 | Todo | Skyline | Add "Synchronize Integration" option | Guest | 3 | closed | 21.2 |
801 | Defect | Skyline | BiblioSpec MaxQuant reader should look for all necessary raw data files and issue a block error about any that are missing | Guest | 3 | closed | 21.2 |
800 | Defect | Skyline | BiblioSpec MaxQuant reader should look in parent folders for raw data files | Guest | 3 | closed | 21.2 |
799 | Todo | Skyline | Improve Library Match behavior when precursor not selected | Brendan MacLean | 3 | resolved | 22.1 |
798 | Todo | Skyline | When missing chromatograms but we have a RT prediction, we should graph that | Nick Shulman | 3 | open | 22.2 |
797 | Todo | Skyline | Transitions Split Graph confusing for multiple precursor charges | Nick Shulman | 3 | open | 22.1 |
796 | Defect | Skyline | Import Transition List column picker is too sticky | Guest | 3 | closed | 21.1 |
795 | Defect | Skyline | Import Peptide Search library build with Automatic iRT leaves standard peptides hidden | Guest | 3 | closed | 21.1 |
794 | Defect | Skyline | Unable to deselect (or remove) the Prosit library for library matching in Molecule UI | Guest | 3 | closed | |
793 | Todo | Skyline | Create a way to limit the set of replicates immediately under analysis without removing replicates | Nick Shulman | 3 | open | |
792 | Defect | Skyline | trying to type an adduct description into the Modify... popup is maddening, cursor location keeps jumping back to start of line | Guest | 3 | closed | |
791 | Defect | Skyline | Inconsistencies in Small Molecule UI mode make it difficult to reopen a closed Targets window | Guest | 3 | closed | |
790 | Todo | Skyline | Edit > Insert > Peptides lacks the ability to add specific precursors | Nick Shulman | 3 | open | |
789 | Defect | Skyline | No longer able to reset settings in Tools > Options > Misc tab | Guest | 2 | closed | 21.1 |
788 | Defect | Skyline | Need better handling for IO problems in library load | Guest | 3 | closed | |
787 | Todo | Skyline | Custom graph background colors - or maybe just Dark Mode - for Skyline | Brian Pratt | 3 | open | |
786 | Defect | Skyline | Ion mobility library "use results" algorithm improvements | Brian Pratt | 3 | open | |
785 | Defect | Skyline | Transition Settings - Ion Mobility - Fixed width value not saved when it is all that changes | Guest | 2 | closed | 22.1 |
784 | Defect | Skyline | Improvements to associating raw files with .sky.zip files (for support, Panorama, ???) | Brendan MacLean | 3 | open | |
783 | Defect | Skyline | small molecule transition list reader should be more tolerant of missing values for InChIKey etc, and should explain properly when it rejects a mismatch | Brian Pratt | 3 | open | 22.1 |
782 | Defect | Skyline | allow small molecule precursors to support the full range of retention time matching options found in the isotope modification form | Brian Pratt | 3 | open | |
781 | Defect | Skyline | allow user to select which files are used in ion mobility library "Use Results" | Brian Pratt | 3 | open | |
780 | Defect | Skyline | show m/z value in Ion Mobility Library editor window | Brian Pratt | 3 | open | |
779 | Defect | Skyline | Adapt ion mobility library editor "Use Results" to work with FAIMS data | Guest | 3 | closed | |
778 | Defect | Skyline | Pasting into the Target window should be on a LongWaitDialog | Guest | 3 | closed | |
777 | Defect | Skyline | Training IMSDB hangs when raw data files are not present | Guest | 3 | closed | 20.2 |
776 | Defect | Skyline | Standard industry teminology for CCS has landed on "Collision Cross Section", we call it "Collisional Cross Section" and should change that | Brian Pratt | 3 | open | |
775 | Defect | Skyline | follow up on possible improper parenting of MessageDlg | Brian Pratt | 3 | open | |
774 | Defect | Skyline | add an error sense to ion mobility filtering in chromatogram extraction, akin to what we do in the RT dimension | Brian Pratt | 3 | open | |
773 | Defect | Skyline | ImportTransitionListColumnSelectDlg needs a better code page for text | Brian Pratt | 3 | open | |
772 | Defect | Skyline | ImportTransitionListColumnSelectDlg.CheckForErrors() needs to use a LongWaitDlg | Guest | 1 | closed | 21.1 |
771 | Defect | Skyline | MSP reader should be aware same peptide mods as the rest of Skyline | Brian Pratt | 3 | open | |
770 | Todo | Skyline | Allow user to select RT display units - currently fixed at minutes, seconds is desirable too | Rita Chupalov | 3 | open | |
769 | Todo | Skyline | Support parent ion scanning for Sciex (and Thermo?) | Brian Pratt | 3 | open | |
768 | Todo | Skyline | Update audit log to use SHA-256 or better | Rita Chupalov | 4 | open | |
767 | Defect | Skyline | Phase 2 work item for hierarchical clustering | Guest | 3 | closed | |
766 | Todo | Skyline | further enhancements to the Import Transition List column picker | Guest | 3 | closed | |
765 | Defect | Skyline | Refactor AuditLog hash calculation | Guest | 3 | closed | 20.2 |
764 | Defect | Skyline | the list of pre-made iRT standards should be filtered based on UI mode - don't present peptide standards for small molecules mode and vice versa | Brian Pratt | 3 | open | |
763 | Defect | Skyline | Editing iRT standard in Edit iRT Calculator form no longer sets standard to None | Guest | 3 | closed | 20.2 |
762 | Defect | Skyline | enforce or infer setting ion mobilty units for explicit ion mobility values | Guest | 3 | closed | |
761 | Defect | Skyline | User would like to force integration of areas that don't have identifiable peaks | Brendan MacLean | 3 | open | |
760 | Defect | Skyline | Skyline should probably offer to reimport raw data after user creates or alters an ion mobility library | Brian Pratt | 3 | open | |
759 | Defect | Skyline | "Use Results" button on the Edit Ion Mobility Library dialog does not fail promptly when raw data is not present | Brian Pratt | 3 | open | |
758 | Defect | Skyline | Chromatogram peaks should show IM information as well as RT | Guest | 3 | closed | |
757 | Todo | Skyline | add a display for ion mobility spectrum | Rita Chupalov | 3 | open | |
756 | Todo | Skyline | add support for Thermo mzVault small molecule spectral libraries | Guest | 3 | closed | |
755 | Defect | Skyline | Improved handling of ambiguous entries when importing spectral libraries that are .MSP format database dumps | Brian Pratt | 3 | open | |
754 | Todo | Skyline | Make Import Peptide Search wizard smarter about isolation schemes | Kaipo Tamura | 3 | open | 22.1 |
753 | Defect | Skyline | Value list annotations should not allow empty lists | Nick Shulman | 3 | open | 22.1 |
752 | Todo | Skyline | Add option to use 1-based amino acid position numbering | Brendan MacLean | 3 | resolved | |
751 | Defect | Skyline | When creating IM library from results, don't create high energy offsets that are impossible for the equipment (e.g. positive drift time offset - that should only decrease) | Brian Pratt | 3 | open | |
750 | Defect | Skyline | small molecule accession numbers in Document Grid should be made editable | Brian Pratt | 3 | open | |
749 | Defect | Skyline | Reimport after adding new transitions causes new transitions to have #N/A peak areas | Guest | 3 | closed | 20.2 |
748 | Defect | Skyline | Edit>Insert>TransitionList should issue a warning when ignoring an input line because it duplicates or conflicts with an existing transition | Brian Pratt | 3 | open | |
747 | Todo | Skyline | Import > Assay Library should automatically recognize Water and Ammonia losses | Kaipo Tamura | 2 | open | 22.1 |
746 | Defect | Skyline | Retention time alignment makes mouse act out of phase on aligned replicate graphs | Guest | 3 | closed | 20.2 |
745 | Defect | Skyline | qualification in skyline | Guest | 3 | closed | |
744 | Defect | Skyline | qualification 偶发 | Guest | 3 | closed | |
743 | Documentation | BiblioSpec | Create Bibliospec library (.blib) using Tabular text input (.tsv) | Guest | 1 | closed | |
740 | Todo | Skyline | Change the scale of the peptide intensity | Brendan MacLean | 3 | open | |
739 | Defect | Skyline | setup.exe fails on Windows Server 12 and 16 | Guest | 3 | closed | |
738 | Defect | Skyline | issue to download Skyline 64bit | Guest | 3 | closed | |
737 | Defect | Skyline | Webinar #19: Ion Mobility Spectrum Filtering with Skyline some problem encounter | Guest | 3 | closed | |
736 | Defect | Skyline | Webinar #19: Ion Mobility Spectrum Filtering with Skyline some problem encounter | Guest | 3 | closed | |
735 | Todo | Skyline | Skyline should attempt BlibBuild conversion when confronted with a spectral library whose format is not natively supported | Brian Pratt | 3 | open | |
734 | Defect | Skyline | Enable joining partial .skyd files when the filenames do not have a hash | Vagisha Sharma | 3 | open | |
733 | Todo | Skyline | Can Skyline export the protein intensities? | Guest | 3 | closed | 20.2 |
732 | Defect | Skyline | Exporting user-defined reports from command line | Guest | 3 | closed | |
731 | Defect | Skyline | Varying small molecule implementations of .MSP format aren't handled well by Skyline | Brian Pratt | 3 | open | |
730 | Defect | Skyline | Peak MS1 integration with FAIMS | Matt Chambers | 2 | open | |
729 | Defect | Skyline | Confusing progress indicator behavior on SRM import when targeted transitions are less intense than other unmatched transitions - it just shows grey | Brian Pratt | 3 | open | |
728 | Defect | Skyline | AutoQC: retry upload to Panorama if upload fails due to network error | Guest | 3 | closed | |
727 | Defect | Skyline | Panorama upload issues | Vagisha Sharma | 3 | open | 22.1 |
726 | Defect | BiblioSpec | Skyline nonredundant blib format to MS2 conversion | Guest | 3 | closed | |
725 | Defect | Skyline | Need to improve inference of ionization type when reading small molecule .MSP files | Guest | 3 | closed | |
724 | Defect | Skyline | Import multiple files as a single run for iRT calibration | Kaipo Tamura | 3 | open | |
723 | Defect | Skyline | Precursors per sample injection think's it is transitions per sample injection | Brendan MacLean | 3 | open | |
722 | Todo | Skyline | How can I put z+1 ions in the fragments list for ETD? | Rita Chupalov | 2 | open | 22.1 |
721 | Defect | Skyline | Skyline cannot properly analyze Agilent QQQ with waste diverter in the beginning of the run | Brendan MacLean | 3 | open | |
720 | Defect | Skyline | Upload to Panorama fails when There are custom annotations for the Transitions | Guest | 3 | closed | |
719 | Defect | Skyline | Calibration curve of Sodiated Adduct not appearing | Guest | 3 | closed | |
718 | Todo | Skyline | Allow overlay of QC traces on chromatograms | Brendan MacLean | 3 | open | |
717 | Defect | Skyline | Improve handling of unknown adducts in small molecule transition reader (exception on seeing adduct "[+]" not caught gracefully) | Brian Pratt | 3 | open | |
716 | Defect | Skyline | When light and heavy precursors have different sets of transitions, all quantifiable transitions should be summed when calculating Light:Heavy ratios | Guest | 3 | closed | 21.1 |
715 | Defect | Skyline | Prosit not available | Brendan MacLean | 3 | open | |
714 | Defect | Skyline | Question about Data upload to panorama | Guest | 3 | closed | |
713 | Defect | Skyline | Unable to view or explore spectral libraries in Skyline Daily | Guest | 3 | closed | |
712 | Defect | Skyline | Acetyl 2H(3) K modification disappears on heavy en medium peptides, when library is created from Maxquant | Guest | 2 | closed | |
711 | Defect | Skyline | Troubles with skyline document file upload to LabKey Server | Guest | 3 | closed | |
710 | Defect | Skyline | Skyline Unistall problems | Guest | 3 | closed | |
709 | Defect | Skyline | Potentially possible to do a better job at routing external tool support requests to tool-specific support boards | Brendan MacLean | 4 | open | |
708 | Defect | Skyline | Renaming a molecule in Targets tree causes Skyline to miscalculate mass of transition with heavy label adduct | Guest | 3 | closed | 19.2 |
707 | Defect | Skyline | Default report names stuck in installation language | Nick Shulman | 3 | open | 22.1 |
706 | Defect | Skyline | Peptide data not imported for a few peptides | Brendan MacLean | 3 | open | |
705 | Defect | Skyline | Too much audit logging for Refine > Accept Peptides | Rita Chupalov | 3 | open | |
704 | Defect | Skyline | Skyline silently fails reading FASTA files with sequences in lowercase | Brian Pratt | 3 | open | |
703 | Defect | Skyline | Nightly tutorial tests should not always re-download data sets - makes us too vulnerable to temporary outages | Guest | 3 | closed | |
702 | Defect | Skyline | Illegal character is phosphopeptide sequence | Guest | 3 | closed | |
701 | Defect | Skyline | Malfunctioning of the reintegration tool | Guest | 3 | closed | |
700 | Defect | Skyline | Malfunctioning of the reintegration tool | Guest | 3 | closed | |
699 | Defect | Skyline | Malfunctioning of the reintegration tool | Guest | 3 | closed | |
698 | Todo | Skyline | Add Mass Errors to Spectrum Match graph | Guest | 3 | closed | |
697 | Defect | Skyline | import wizard should not ask about ion mobility handling if the files to be imported don't contain any IM info | Guest | 3 | closed | |
696 | Defect | Skyline | library filename extensions are case sensitive (e.g. Skyline recognizes "foo.msp" but not "foo.MSP") | Guest | 3 | closed | 19.2 |
695 | Defect | Skyline | Failed importing results DIA | Guest | 3 | closed | |
694 | Defect | Skyline | Audit Log records a failed operation and does not roll it back | Guest | 3 | closed | |
693 | Todo | Skyline | Improve "Apply Peak to All" peak matching | Kaipo Tamura | 4 | open | |
692 | Todo | Skyline | Change some default settings | Brendan MacLean | 3 | open | 22.1 |
691 | Defect | Skyline | Limiting Transition Settings - Instrument - Max m/z has unintended consequences on spectral library transition picking | Kaipo Tamura | 2 | open | 19.2 |
690 | Defect | Skyline | Before starting a new Import > Results we need to check that Decoys are representative of the Targets | Guest | 2 | closed | 19.2 |
689 | Defect | Skyline | File > Export > Spectral Library losing information from small molecule documents | Brian Pratt | 2 | open | |
688 | Todo | Skyline | Add Product Loss Formula column to Edit > Insert > Transitions for small molecules | Guest | 2 | closed | 19.2 |
687 | Todo | Skyline | Implement support for charged losses where Skyline currently has only neutral losses | Guest | 2 | closed | 19.2 |
686 | Todo | Skyline | Implement a better system for assigning a version which is not web installed | Guest | 2 | closed | 19.2 |
685 | Defect | Skyline | Show progress in LongWaitDlg for Skyline document import on Panorama | Guest | 3 | closed | 19.2 |
684 | Defect | Skyline | Do not use getContainers to determine if a URL is for a LabKey Server | Guest | 3 | closed | 19.2 |
683 | Todo | Skyline | Add support for opening .skyp files in Skyline | Guest | 3 | closed | 19.2 |
682 | Defect | Skyline | Import peptide search from Start page differs from File > Import > Peptide Search | Guest | 2 | closed | 19.1 |
681 | Todo | Skyline | Export method sorted by m/z | Kaipo Tamura | 3 | resolved | |
680 | Todo | Skyline | Add access to some of the explicit values added for small molecules to peptide transition list import | Brendan MacLean | 3 | open | |
679 | Todo | Skyline | Make ion mobility library creation available for use from command-line | Brian Pratt | 3 | open | 22.2 |
678 | Defect | Skyline | Unhandled error when importing peak boundaries for document with no result files | Guest | 4 | closed | |
677 | Todo | Skyline | Add PEP (localFDR) as another score beside q values for mProphet picked peaks | Kaipo Tamura | 3 | open | |
675 | Todo | Skyline | View > Proteins and View > Peptides menu items added and remove View > Targets | Guest | 2 | closed | 19.2 |
674 | Todo | Skyline | Work out a way for an interactive tool to know Skyline is closing or has closed | Brendan MacLean | 3 | open | |
673 | Defect | Skyline | Order By > Annotation in summary plots got broken | Guest | 2 | closed | 19.1 |
672 | Defect | Skyline | Querying UniProt for SGD Yeast FASTA information having problems | Guest | 1 | closed | 19.2 |
671 | Todo | Skyline | Improve small molecule peak boundaries import | Guest | 3 | closed | 22.1 |
670 | Defect | Skyline | SkylineTester's tutorial demo mode should roll forever, and slow down a bit | Guest | 3 | closed | |
669 | Todo | Skyline | Consider adding explicit window size for CCS and/or IM for transition list import | Brian Pratt | 3 | open | |
668 | Defect | Skyline | UI mode selection capability should be available in the menu system | Guest | 3 | closed | 19.2 |
667 | Defect | Skyline | Include fragment ion annotation when "Copy Data" from Library Match tab | Brendan MacLean | 3 | open | |
666 | Defect | Skyline | The "Add small molecule test nodes" checkbox on SkylineTester is obsolete and confusing, should be removed | Guest | 3 | closed | |
665 | Defect | Skyline | Replicate Label Fonts on Graph Axis too small | Guest | 3 | closed | |
664 | Todo | Skyline | Add "Only max precursor peak" checkbox below "Max peptide peak rank" field in Refine > Advanced - Results tab | Guest | 3 | closed | 19.2 |
662 | Todo | Skyline | Add View > Peptides > By menu items | Guest | 3 | closed | 19.2 |
661 | Todo | Skyline | Update unimod.xml which is now about 2 years old | Matt Chambers | 3 | open | 22.1 |
660 | Todo | Skyline | revisit changes around ReSharper 2019.1 issues with false null check warnings | Brian Pratt | 3 | open | |
659 | Defect | Skyline | need better handling of typing mistakes (or partially completed typing) when user is renaming a peptide | Brian Pratt | 3 | open | |
658 | Defect | Skyline | nonstandard (or at least non-intuitive) keystroke handling causes exception | Brian Pratt | 3 | open | |
657 | Defect | Skyline | Record BlibBuild command-line arguments in LibInfo table | Matt Chambers | 3 | open | 22.1 |
656 | Todo | Skyline | add diaPASEF support | Guest | 3 | closed | 19.2 |
655 | Defect | Skyline | adjust behavior of "Explicit Retention Time" to match user expectations | Guest | 3 | closed | 19.2 |
654 | Todo | Skyline | Add support for PEFF extended FASTA format (http://www.psidev.info/peff) | Brian Pratt | 3 | open | |
653 | Todo | Skyline | Implement arbitrary peptide proportion grouping | Guest | 2 | closed | 19.2 |
652 | Todo | Skyline | Controlling the (#) suffix added to replicate filenames from a .wiff Import | Guest | 3 | closed | 4.3 |
651 | Todo | Skyline | Document Settings - Reports should have buttons to manage the list or add a new report | Guest | 3 | closed | |
650 | Todo | Skyline | Add a menuitem to turn off MIDAS triggered spectra annotations | Brendan MacLean | 3 | open | |
649 | Todo | Skyline | Need a way for external tools to produce annotations that get imported into the current document | Nick Shulman | 3 | open | 22.1 |
648 | Defect | Skyline | Error when building a library from MetaMorpheus results (*.mzID) | Guest | 3 | closed | 4.3 |
647 | Defect | Skyline | Problems with annotations in reports | Guest | 2 | closed | 19.2 |
646 | Defect | Skyline | Problem to build library from MaxQuant | Guest | 3 | closed | 4.3 |
645 | Defect | Skyline | MaxQuant mod parser will fail when first two letters are shared between 2 different mods | Matt Chambers | 3 | open | |
644 | Todo | Skyline | Add ability to set a minimum and maximum when generating optimization values | Brendan MacLean | 3 | open | |
643 | Defect | Skyline | Problem interpreting modification format found in NIST phospho libraries | Brian Pratt | 3 | open | |
642 | Defect | Skyline | BiblioSpec unicode filepath support | Guest | 3 | closed | 4.3 |
641 | Documentation | Skyline | How to assign report template name in Command-line argument | Guest | 3 | closed | 4.3 |
640 | Defect | Skyline | Unable to process chromatograms for the molecule | Guest | 3 | closed | 4.3 |
633 | Defect | Skyline | Usability idea: when we fail to open a Skyline document, check to see if it actually IS a Skyline document | Guest | 3 | closed | |
632 | Defect | Skyline | Failure importing SRM runs | Guest | 3 | closed | |
631 | Todo | Skyline | Finding *.dat files from the spectral library | Guest | 4 | closed | 4.3 |
630 | Defect | Skyline | rdotp uses Statistics.Angle() when it should be using NormalizedContrastAngleSqrt() | Guest | 2 | closed | 21.2 |
629 | Defect | Skyline | No import due to overlapping chromatogram start times? | Nick Shulman | 2 | open | |
628 | Todo | Skyline | Thermo RAW attribute access | Guest | 3 | closed | 4.3 |
627 | Todo | Skyline | Import results from multi-injection wiff files that have the same sample/injection names | Guest | 3 | closed | 19.2 |
626 | Todo | Skyline | Add command-line arguments to select samples to import from multi-injection wiff files | Guest | 3 | closed | 19.2 |
625 | Todo | Skyline | Lipid quant using Skyline and LipidSearch | Matt Chambers | 3 | open | |
624 | Todo | Skyline | Audit log format changes | Guest | 3 | closed | |
623 | Todo | Skyline | Add command-line arguments to support background proteome creation and adding | Brendan MacLean | 4 | open | |
622 | Defect | Skyline | Building CCS containing library | Brian Pratt | 2 | open | 22.1 |
621 | Todo | Skyline | Change default centroiding value to summed intensity from trapezoidal area | Guest | 2 | closed | 4.3 |
620 | Todo | Skyline | Expose refinement options through command-line interface | Guest | 2 | closed | 19.2 |
619 | Todo | Skyline | Control of extraction range in MS1 is desirable | Matt Chambers | 3 | open | |
618 | Todo | Skyline | Problem accessing MS/MS in method with multiple fragmentation modes | Guest | 3 | closed | |
617 | Todo | Skyline | Decoy generation should only maintain C-terminus when it matches the enzyme cleavage pattern | Brendan MacLean | 3 | open | |
616 | Todo | Skyline | Request for instrument serial numbers as data file attribute in Skyline reports | Brendan MacLean | 3 | open | |
615 | Todo | Skyline | Add more information to multi-peptide chromatogram labels | Rita Chupalov | 4 | open | |
614 | Todo | Skyline | Include CSRF token when SkylineNightly posts to LabKey Server | Guest | 3 | closed | 4.2 |
613 | Todo | | Add clarifier "(in min.)" to axis legends of Skyline graphs showing duration through time | Brendan MacLean | 4 | open | |
612 | Todo | Skyline | Support Pressure Traces in Skyline .skyd files | Guest | 2 | closed | 4.2 |
611 | Defect | Skyline | IndexOutOfRangeException switching spectrum type between MS1 and MS/MS in DDA mode file | Guest | 2 | closed | 4.2 |
610 | Todo | Skyline | Fix MaxQuant library builder to extract original spectra from source data files | Guest | 2 | closed | 4.3 |
609 | Todo | Skyline | Implement a way to remove peaks from a set of PrecursorResults selected in the Document Grid | Guest | 3 | closed | 4.3 |
608 | Defect | Skyline | Conflict with transition Ion exception when two precursors have the same charge state, and transitions with the same mass. | Guest | 3 | closed | 4.3 |
607 | Defect | Skyline | Peak area graph Group By should allow Analyte Concentration | Guest | 3 | closed | 4.3 |
606 | Defect | Skyline | Lists need better audit logging | Brendan MacLean | 1 | resolved | 4.2 |
605 | Todo | Skyline | Resize Previous Files Bar on Start Page | Brendan MacLean | 3 | open | 22.1 |
604 | Defect | Skyline | .NET 4.7.2 install on Wwindows 10 1803 | Guest | 4 | closed | 4.2 |
603 | Defect | Skyline | Prompt user about removing unused chromatograms when uploading document to Panorama | Nick Shulman | 3 | open | |
602 | Defect | Skyline | Enable using the Document Grid to filter and sort Replicate Comparison and Peptide Comparison graphs | Guest | 3 | closed | 4.3 |
601 | Documentation | Skyline | Number of data points per LC peak vs cycle time in scheduled MRM | Guest | 3 | closed | 4.2 |
600 | Defect | Skyline | Skyline-Daily Small molecules: Filter to screen out false positives based on number and proportion of transitions. | Guest | 3 | closed | |
599 | Defect | Skyline | Failing importing Agilent GC-MS/MS SRM data after upgrade to 18257 | Guest | 3 | closed | 4.2 |
597 | Todo | Skyline | Users would like to be able to tile all chromatograms in a scrollable pane for ease of inspection | Guest | 3 | closed | 4.2 |
596 | Todo | Skyline | When using a spectral library with ion mobility info, we should direct user's attention to the "Use Spectral Library Ion Mobility Values" setting | Guest | 3 | closed | 19.2 |
595 | Defect | Skyline | Loss of adjusted peak boundaries after copy paste | Nick Shulman | 3 | open | |
594 | Defect | Skyline | The MS1 "precursor [M-1]" ion should have Quantitative property off by default | Guest | 3 | closed | 4.1 |
593 | Defect | Skyline | cannot find spectal library | Guest | 3 | closed | 4.1 |
592 | Defect | Skyline | small molecule targets don't connect with spectral libraries unless created from spectral libraries | Brian Pratt | 3 | open | |
591 | Todo | Skyline | Move AutoQC code into Skyline.CommandLine to allow running its functionality without the UI | Vagisha Sharma | 3 | open | |
590 | Defect | Skyline | SpectrumMill mzXMLs not loading "no scans match current filter settings" | Guest | 3 | closed | 4.1 |
589 | Defect | Skyline | Modify Skyline output for data analysis using MSstats | Guest | 3 | closed | 4.1 |
588 | Defect | Skyline | Duplicate vs repeated peptides | Guest | 4 | closed | 4.1 |
587 | Defect | Skyline | SkylineRunner Instant Crash | Guest | 3 | closed | 4.1 |
586 | Defect | Skyline | Pivot Editor causes SkylineWindow deactivation | Guest | 3 | closed | 4.2 |
585 | Defect | Skyline | 1 raw file used with 2 skyline template issue | Guest | 3 | closed | 4.1 |
584 | Todo | Skyline | Audit log improvements | Guest | 3 | closed | 4.2 |
583 | Todo | Skyline | Library Match view should show the same metadata (RT, IM , ?) seen in Library Explorer | Brendan MacLean | 3 | open | |
582 | Defect | Skyline | Usability idea: use Library Match window even when document wasn't populated from a library | Brian Pratt | 3 | open | |
581 | Todo | Skyline | Usability idea: empty document should have getting-started hint text in the Targets window | Brian Pratt | 3 | open | |
580 | Defect | Skyline | a couple more adduct description syntax variations seen in the wild | Guest | 3 | closed | 4.2 |
579 | Todo | Skyline | use "Natural Sort Order" for filenames | Brian Pratt | 3 | open | |
578 | Defect | Skyline | Background proteome file not loading shows error message with OK button | Guest | 3 | closed | 4.3 |
577 | Defect | Skyline | Failed to import MassLynx (centered) Q-TOF raw data | Guest | 3 | closed | 4.1 |
576 | Defect | Skyline | Creating Reports: atomic composition (formula) does not contain stable isotope info | Guest | 3 | closed | 4.1 |
575 | Defect | Skyline | Error opening file in skyline-daily | Guest | 3 | closed | 4.1 |
574 | Defect | Skyline | Error downloading small molecule tutorial file | Guest | 3 | closed | 4.1 |
573 | Todo | Skyline | Add -> refine window missing OK / Cancel buttons | Guest | 0 | closed | |
572 | Todo | Skyline | Add View > Peak Areas > Regression plots | Rita Chupalov | 3 | open | |
571 | Defect | Skyline | issue with normalization ratio | Guest | 1 | closed | 4.1 |
570 | Todo | Skyline | Chromatogram extraction should respect Explicit Retention Time Window and not just Explicit Retention Time | Guest | 3 | closed | 19.2 |
569 | Defect | Skyline | Trouble in importing Altis SRM data in skyline daily | Guest | 1 | closed | 4.1 |
568 | Todo | Skyline | For Import of columnar text where we currently guess the column meanings show a grid to choose instead | Brendan MacLean | 2 | open | |
567 | Todo | Skyline | Add Expand All menu item to Targets View right-click menu when at least 1 parent node is selected | Brendan MacLean | 3 | open | |
566 | Todo | Skyline | 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 Pratt | 3 | open | |
565 | Todo | Skyline | Accept defined annotation types as valid column headers for small molecule transition lists (and peptide transition lists, while we're at it) | Brian Pratt | 3 | open | 22.1 |
564 | Todo | Skyline | Add checkboxes to invert meaning of Edit > Refine > Accept Proteins/Peptides | Brendan MacLean | 3 | open | |
563 | Todo | Skyline | Not all document grid columns have descriptions in help | Guest | 3 | closed | 4.2 |
562 | Todo | Skyline | Implement Audit Log for Skyline | Guest | 2 | closed | 4.2 |
561 | Defect | Skyline | Skyline-daily loosing peak integrations | Guest | 3 | closed | 4.1 |
560 | Todo | Skyline | Implement group by graph panes for summary graphs | Brendan MacLean | 3 | open | |
559 | Todo | Skyline | Cannot load msf result file (PD) when building a library | Matt Chambers | 3 | open | |
558 | Todo | Skyline | Add results search paths to Document Settings | Kaipo Tamura | 3 | open | |
557 | Defect | Skyline | ChooseFormatDlg needs a documentation link | Guest | 3 | closed | 4.3 |
556 | Defect | Skyline | Issues with Waters schedule MRM data. Can't load. | Guest | 3 | closed | 3.7 |
555 | Defect | Skyline | Skyline assumes /labkey context path when pinging Panorama | Guest | 3 | closed | 4.1 |
554 | Defect | Skyline | Assigning a wrong peak and not following the spectral library retention time | Guest | 3 | closed | 4.1 |
553 | Defect | Skyline | Support Contains filter for report column that looks like text | Guest | 3 | closed | 4.1 |
552 | Todo | Skyline | Support multiple replicate selection in summary graph panes and Remove Peak | Kaipo Tamura | 3 | open | |
551 | Defect | Skyline | Skyline file not opening | Guest | 3 | closed | 4.1 |
550 | Defect | Skyline | Only iRT traces are imported | Guest | 3 | closed | |
547 | Defect | Skyline | XML Error -- Reading mz values; small molecule transition list | Guest | 3 | closed | 4.1 |
546 | Defect | Skyline | Unable to build spectral library | Guest | 3 | closed | 4.1 |
545 | Todo | Skyline | Add Include charge state checkbox to Edit > Insert > Peptides | Brendan MacLean | 3 | open | |
544 | Defect | Skyline | Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges | Guest | 3 | closed | 4.1 |
539 | Defect | Skyline | Heavy/Light Peptide Chromatogram Import Range Discrepancies | Guest | 3 | closed | 4.1 |
538 | Todo | Skyline | Multi-peptide calibration curves would be nice | Guest | 3 | closed | 4.3 |
537 | Defect | Skyline | How to add a column to the documents or results grid that contains the heavy or ISTD areas? | Nick Shulman | 3 | open | |
536 | Defect | Skyline | Points across peak count should scale with chromatogram graph font settings | Guest | 4 | closed | 4.1 |
535 | Defect | Skyline | MS1 chromatograms in scheduled PRM data should get limited to times of matching MS/MS scans | Guest | 2 | closed | 4.1 |
534 | Todo | Skyline | Multi-peptide graph fixes / enhancements | Rita Chupalov | 3 | open | |
533 | Defect | Skyline | Reporter ion masses must be less than or equal to 5000 | Guest | 2 | closed | 4.1 |
532 | Todo | Skyline | X!Tandem in Skyline | Brendan MacLean | 3 | open | |
531 | Todo | Skyline | Include Replicate Name as column in exported chromatograms | Guest | 3 | closed | 4.1 |
530 | Defect | Skyline | NIST .msp reader ignores peptide entries with n- or c-terminal modifications | Kaipo Tamura | 3 | open | |
529 | Todo | Skyline | Consider imposing spectrum filtering based on Full-Scan settings | Brendan MacLean | 3 | open | |
528 | Defect | Skyline | Column header sort messes up peak scoring model training grid | Guest | 3 | closed | 4.1 |
527 | Defect | Skyline | Double-clicking .sky file does not seem to work for Administrator Installation | Guest | 3 | closed | 21.1 |
526 | Todo | Skyline | Enhancements to AutoCopyUSB | Guest | 4 | closed | 4.1 |
525 | Defect | Skyline | Results Grid or calibration curve | Guest | 3 | closed | 4.1 |
524 | Todo | Skyline | Make it possible to rename replicates through the Document Grid | Guest | 3 | closed | 4.1 |
523 | Todo | Skyline | Make it easy to connect raw data file sample information to annotations in Skyline | Guest | 2 | closed | 4.3 |
522 | Todo | Skyline | Add a way to add annotations to a document from the command-line | Guest | 2 | closed | 4.1 |
521 | Todo | Skyline | Add CE recognition to transition list import | Kaipo Tamura | 4 | open | |
520 | Todo | Skyline | Make ctrl-Page Up ctrl-Page Down retreat or advance all document panes at once | Brendan MacLean | 3 | open | |
519 | Todo | Skyline | Synchronize zooming for RT and Area plots | Guest | 3 | closed | 4.1 |
518 | Defect | Skyline | Resolve issue of hard-coding Waters CE equations | Kaipo Tamura | 4 | open | |
517 | Todo | Skyline | Add Remove Peak and Apply Peak to All menus to retention time graph | Guest | 3 | closed | |
516 | Defect | Skyline | Manual peak integrations are reset after import of new results file | Guest | 0 | closed | 3.7 |
515 | Todo | Skyline | Add some way to produce summary statistics to reports by grouping replicate annotations | Guest | 1 | closed | 4.1 |
514 | Todo | Skyline | Expand neutral loss support to allow for charged losses from the precursor | Brendan MacLean | 3 | open | |
513 | Defect | Skyline | Fix ExclusionUseDIAWindow setting to consider IsolationWindow.MethodStart and MethodEnd | Guest | 3 | closed | |
512 | Todo | Skyline | Add summary statistics for q values | Guest | 3 | closed | 20.2 |
511 | Todo | Skyline | Request for customizable bulk peak removal | Guest | 2 | closed | 4.1 |
510 | Todo | Skyline | Updates to iRT standards necessary | Guest | 3 | closed | 3.7 |
509 | Todo | Skyline | remoove limit of 200aa or increase this number for analysis top-down or middle-down data | Guest | 3 | closed | 3.7 |
508 | Defect | Skyline | Make SkylineCmd.exe return non-zero when a line starting with "Error:" is output | Guest | 2 | closed | 4.1 |
507 | Documentation | Skyline | Skyline Menu for all terminology. | Guest | 3 | closed | 3.7 |
506 | Todo | Skyline | Add Cone Voltage optimization support for Waters triple quadrupoles | Guest | 3 | closed | 3.7 |
505 | Todo | Skyline | Add RF Lens optimization for Thermo triple quadrupole | Kaipo Tamura | 3 | open | |
504 | Todo | Skyline | Add support for CE optimization for PRM on Waters Xevo QTOF | Kaipo Tamura | 2 | open | |
503 | Todo | Skyline | Improve document minimizing and command-line support | Brendan MacLean | 2 | open | |
502 | Todo | Skyline | Improve UnimodCompiler to preserve modification more than one decimal place for modifications that require more to disambiguate | Guest | 2 | closed | 4.1 |
501 | Defect | Skyline | Improve BlibBuild handling of multiple searches on the same raw data files | Guest | 3 | closed | 3.7 |
500 | Defect | Skyline | Instrument tab not limiting time for extraction based on RT prediction | Guest | 3 | closed | 4.3 |
499 | Todo | Skyline | Mass error replicate comparison does not support split graph | Guest | 3 | closed | 4.3 |
498 | Defect | Skyline | Theoretical peptide z ion does not match | Guest | 3 | closed | 3.7 |
497 | Defect | Skyline | Ignore full-scan settings for retention time prediction when importing SRM data | Brendan MacLean | 3 | resolved | 21.1 |
496 | Defect | Skyline | Cannot publish data to Panorama. | Guest | 3 | closed | 3.6 |
495 | Todo | Skyline | More flexibility in View > Arrange Graphs > Grouped | Brendan MacLean | 4 | open | |
494 | Defect | Skyline | Can Skyline Support Waters UNIFI data format .UEP file | Guest | 2 | closed | 3.7 |
493 | Defect | Skyline | iRT standard peptides added to document can gain extra precursors | Guest | 3 | closed | 3.6 |
492 | Defect | Skyline | Another library building error | Guest | 2 | closed | |
491 | Defect | Skyline | Issue with building spectral library | Guest | 3 | closed | 3.6 |
490 | Defect | Skyline | ID line | Guest | 3 | closed | 3.6 |
489 | Defect | Skyline | Importing negative ion transitions from Masshunter (small molecules) | Guest | 2 | closed | 3.6 |
488 | Defect | Skyline | Peptide uniqueness change should probably ignore automanage states, or at least offer to | Brian Pratt | 3 | open | |
487 | Defect | Skyline | make automanage status of each node knowable (ideally changeable) in DocumentGrid | Guest | 3 | closed | 4.3 |
486 | Todo | Skyline | Come up with clearer way of informing a user that iRT regression was not good enough | Guest | 2 | closed | |
485 | Todo | Skyline | Add Help > Check for Updates | Guest | 3 | closed | 3.6 |
484 | Todo | Skyline | Add confidence intervals for slope and intercept in calibration regressions | Nick Shulman | 3 | open | 22.1 |
483 | Defect | Skyline | Precursor isotope peaks (M+1, M+2) not automatically shown for small molecules | Guest | 3 | closed | 3.6 |
482 | Todo | Skyline | set negative ion mode for peptides | Guest | 3 | closed | 3.6 |
481 | Defect | Skyline | Error trying to access Tool Store in Skyline Daily | Guest | 3 | closed | 3.6 |
480 | Defect | Skyline | Skyline Daily does not support Agilent Automation Tool | Guest | 3 | closed | 3.6 |
479 | Defect | Skyline | Skyline Daily shows no data when there is data - Agilent QQQ | Guest | 2 | closed | 3.6 |
478 | Defect | Skyline | Peak Boundary List File Fails to Load | Guest | 3 | closed | 3.5 |
477 | Todo | Skyline | Request for occupancy proportion report value | Guest | 3 | closed | |
476 | Defect | Skyline | Issues with QuaSAR | Guest | 3 | closed | 3.6 |
475 | Defect | Skyline | Need to close and reopen Document Grid after adding new annotations | Guest | 2 | closed | 4.3 |
474 | Defect | Skyline | Ask user about Library settings if changing peptide Filter settings | Brendan MacLean | 3 | open | |
473 | Defect | Skyline | Missing 2nd transition for some samples_small molecules | Guest | 3 | closed | 3.6 |
472 | Defect | Skyline | method export for Quantiva failed | Guest | 3 | closed | 3.6 |
471 | Defect | Skyline | MaxQuant library builder fails to understand T(2) modification | Guest | 2 | closed | 3.6 |
470 | Todo | Skyline | Add TotalAreaMS1Adjusted column to reports | Guest | 3 | closed | 4.3 |
469 | Todo | Skyline | document grid TransitionResult should show extraction width, as well as drift time and window | Brian Pratt | 3 | open | |
468 | Defect | Skyline | S-lens value isn't written to Exported transition list when checked | Guest | 3 | closed | 3.6 |
467 | Defect | Skyline | Skyline-daily (3.5.1.9673, 64-bit) locks up when uploading .raw files. | Guest | 3 | closed | 3.6 |
466 | Defect | Skyline | SkylineRunner scriptability improvements: version number and help info from commandline, and non-zero exit code on error | Guest | 2 | closed | 19.2 |
465 | Defect | Skyline | Generating DIA Isolation Schemes with Optimize window placement does not work correctly for odd m/z (or fractional m/z) Window widths | Guest | 1 | closed | 3.6 |
464 | Todo | Skyline | Support exporting isolation list from command line | Guest | 3 | closed | 3.6 |
463 | Defect | Skyline | Automating Skyline for HT Proteomics with Skyline Runner | Guest | 3 | closed | 3.6 |
462 | Defect | Skyline | Add "Thermo TSQ Quantiva" to transition settings | Guest | 2 | closed | 3.6 |
461 | Defect | Skyline | Unable to change transition settings | Guest | 3 | closed | 3.6 |
460 | Defect | Skyline | provide a means of updating protein metadata to current Uniprot level for document and background proteome | Brian Pratt | 3 | open | |
459 | Defect | Skyline | Only one chromatogram type in Full-Scan graph for chromatogram clicked in split graph mode | Guest | 3 | closed | 21.1 |
458 | Defect | Skyline | MRM Chromatogram not Processed | Guest | 3 | closed | |
457 | Todo | Skyline | Add access to SpectraST retention times to library implementation | Guest | 3 | closed | 3.6 |
456 | Defect | Skyline | reimport after changing full scan settings to "Centroided" doesn't actually perform centroiding | Brian Pratt | 3 | open | |
455 | Todo | Skyline | Add option to allow exporting mass errors with File > Export > Chromatograms | Brendan MacLean | 3 | open | |
454 | Todo | Skyline | Remove asymetric isolation scheme support and add ability to specify a margin | Guest | 3 | closed | 3.6 |
453 | Todo | Skyline | Add check box to Digestion tab to allow removal of protein N-terminal Methionine | Brian Pratt | 3 | open | |
452 | Defect | Skyline | Copy-paste fails to recognize equivalent modifications with different names | Brendan MacLean | 3 | resolved | |
451 | Todo | Skyline | Add redundant library access to Library Explorer | Kaipo Tamura | 3 | open | |
450 | Defect | Skyline | Skyline should warn when importing a transition list with values that exceed the current instrument m/z range | Brian Pratt | 3 | open | |
449 | Defect | Skyline | LIBRARY BUILD ERROR | Guest | 2 | closed | 3.6 |
448 | Defect | Skyline | Add optimization step to compound names in Quantiva method/transition list export | Guest | 3 | closed | 3.6 |
447 | Defect | Skyline | Change of e-mail address | Guest | 3 | closed | 3.6 |
446 | Defect | Skyline | idopt not shown when log view activated | Nick Shulman | 3 | open | 22.1 |
445 | Defect | Skyline | DIA-MS on Fusion | Guest | 3 | closed | 3.2 |
444 | Todo | Skyline | Add errors and warnings for documents where Full-Scan settings do not match Filter ion types | Guest | 3 | closed | 3.2 |
443 | Todo | Skyline | Improve behavior of Cancel for a re-import or re-score operation | Brendan MacLean | 3 | open | |
442 | Todo | Skyline | Skyline should prefer heavy spectra in many cases | Brendan MacLean | 2 | open | |
441 | Todo | Skyline | Reevaluate Edit > Refine > Advanced for new filtering opportunities | Brendan MacLean | 3 | open | |
440 | Defect | BiblioSpec | Graceful failure during MaxQuantReader constructor | Guest | 3 | closed | |
439 | Defect | Skyline | MS1 Full-Scan import = match with mascot search, ppm values missing | Guest | 3 | closed | 3.2 |
438 | Defect | Skyline | Make "Insert Transition List" for small molecules tolerant of empty product ion columns | Guest | 3 | closed | 3.2 |
437 | Todo | BiblioSpec | Improve performance of BlibBuild spectral library building from pepXML/mzXML | Guest | 2 | closed | 3.2 |
436 | Todo | Skyline | Add TraML as a transition list import format | Guest | 3 | closed | |
435 | Defect | Skyline | Problem handling 'Optimize CE' data | Guest | 3 | closed | 3.2 |
434 | Todo | Skyline | Add chromatogram export support to command-line interface | Guest | 3 | closed | 3.2 |
433 | Defect | Skyline | Allow Remove Peak and Apply to All from peptide view with multiple precursors | Guest | 2 | closed | 3.2 |
432 | Todo | Skyline | Make it possible to view instrument-specific scan information from the full-scan view | Brendan MacLean | 3 | open | |
431 | Todo | Skyline | Allow clicking on totals chromatograms to show Full-Scan graph | Brendan MacLean | 3 | open | |
430 | Defect | Skyline | Cancelling report export leaves a truncated report on disk | Guest | 3 | closed | 3.2 |
429 | Todo | Skyline | Extend the Insert Transition List dialog to be as flexible for peptides as it is for small molecules | Guest | 3 | closed | 22.1 |
428 | Defect | Skyline | Mulriple injection import error when no scans match document peptides or current filter settings | Guest | 3 | closed | |
427 | Todo | Skyline | Create Thermo TraceFinder export tool | Guest | 2 | closed | 3.6 |
426 | Todo | Skyline | Add peak area shading to show the area integrated in Skyline | Guest | 2 | closed | 3.2 |
425 | Defect | Skyline | Hard to figure out how to filter on true/false columns in Document Grid | Guest | 2 | closed | 3.2 |
424 | Defect | Skyline | Colored summary chromatogram disappeared with latest Skyline-daily update | Guest | 3 | closed | 3.2 |
423 | Defect | BiblioSpec | Handle multiple modifications on the same residue | Guest | 4 | closed | |
422 | Todo | Skyline | Attempt to make Skyline ignore spectra from incorrect mass analyzer type | Brian Pratt | 3 | open | |
421 | Defect | Skyline | Implement cursor changes for the start-up form | Guest | 4 | closed | 3.2 |
420 | Todo | Skyline | Add refinement option for DDA data based on peak IDs | Brendan MacLean | 4 | open | |
419 | Todo | Skyline | Add SkylineRunner support for Edit > Refine > Reintegrate | Guest | 3 | closed | 3.2 |
418 | Todo | Skyline | Improve peak removal UI | Guest | 3 | closed | 3.2 |
417 | Todo | Skyline | Add explicit property support for peptides | Guest | 3 | closed | 3.2 |
416 | Defect | Skyline | Having many disconnected network drives causes the Import Results form to hang for a long time | Guest | 3 | closed | 3.2 |
415 | Defect | Skyline | Transition list import should pick modified sequence column over bare sequence column | Guest | 3 | closed | 3.2 |
414 | Todo | Skyline | Add the ability to show the center of mass and possibly the target mass for an extraction region in the full-scan graph | Brendan MacLean | 3 | open | |
413 | Defect | Skyline | Keep optimization values from being negative | Kaipo Tamura | 2 | open | |
412 | Todo | Skyline | Need ways to see isolation windows on full-scan graphs | Rita Chupalov | 3 | open | 22.1 |
411 | Defect | Skyline | Column filters do not apply to Export and Copy All | Guest | 1 | closed | 3.1 |
410 | Defect | Skyline | Multiple selection color is too faint | Guest | 3 | closed | 3.2 |
409 | Defect | Skyline | Skyline guesses poorly when it encounters AQUA/SILAC labeling | Kaipo Tamura | 3 | open | |
408 | Defect | Skyline | Group comparison grid and graph can become disconnected | Guest | 1 | closed | 3.2 |
407 | Defect | Skyline | Opening a .sky file in a .zip file can be confusing | Guest | 2 | closed | 4.3 |
406 | Defect | Skyline | Need better error message for Waters instruments when multiple RT windows are required | Guest | 3 | closed | 3.2 |
405 | Todo | Skyline | Add View > Group Comparisons > Edit List... item | Guest | 3 | closed | 3.2 |
404 | Todo | Skyline | Increased versioning requested for validated environments | Brendan MacLean | 3 | open | |
403 | Todo | Skyline | Make it possible to choose top N transitions for quantification | Guest | 1 | closed | 20.2 |
402 | Todo | Skyline | Make it possible to do group comparison normalization by a replicate annotation value | Guest | 3 | closed | 3.2 |
401 | Defect | Skyline | AssumptionException SummaryPeptidePeakData.GetMzFilters | Guest | 3 | closed | 4.3 |
400 | Todo | Skyline | Add option to export chromatograms to SkylineRunner | Guest | 2 | closed | 3.6 |
399 | Defect | Skyline | Instrument info not imported from RAW file | Guest | 3 | closed | 3.1 |
398 | Todo | BiblioSpec | Investigate Mascot score threshold | Guest | 3 | closed | 3.1 |
397 | Todo | Skyline | Support mzid and pride xml from PeptideShaker | Guest | 3 | closed | 3.1 |
396 | Todo | Skyline | Naming convention for peptides in Thermo Quantiva transition list export | Guest | 3 | closed | 3.1 |
395 | Defect | Skyline | Exception thrown trying to sort Results Grid | Guest | 3 | closed | 3.1 |
394 | Defect | Skyline | Skyline not in Alt-Tab list when Customize View is showing | Guest | 3 | closed | 3.1 |
393 | Defect | Skyline | Use different strategy when we detect slow loading of Thermo files over the network | Guest | 4 | closed | 3.1 |
392 | Defect | Skyline | Problems importing spectral libraries from DDA to iRT libraries | Guest | 3 | closed | 3.1 |
391 | Defect | Topograph | Discrepancies in point count | Guest | 1 | closed | 3.1 |
390 | Defect | Topograph | Cannot access individual protein half-lives within Topograph | Guest | 0 | closed | 3.1 |
389 | Todo | | Finalize AutoQC | Guest | 3 | closed | 3.1 |
388 | Todo | | Test Results | Guest | 3 | closed | 3.1 |
387 | Todo | Skyline | L10N for VS2013/RS9 & team city fail builds | Guest | 3 | closed | 3.1 |
386 | Todo | | Skyline slider | Guest | 3 | closed | 3.1 |
385 | Todo | Skyline | Web args collector documentation | Nick Shulman | 3 | open | |
384 | Todo | | Sign Up module | Guest | 3 | closed | 3.1 |
383 | Todo | Skyline | Monitoring charged losses could be made easier | Brendan MacLean | 3 | open | |
382 | Todo | Skyline | Improve modifications for glycans | Brendan MacLean | 3 | open | |
381 | Defect | Topograph | Protein Key is not displaying the correct information | Guest | 0 | closed | 3.1 |
380 | Todo | Skyline | Add support for PRM and DIA-with-DDA workflows to Import Peptide Search wizard | Guest | 2 | closed | 3.1 |
379 | Defect | Skyline | Small molecules: Annotations and user-set peaks don't serialize properly for custom molecules | Guest | 1 | closed | 3.1 |
378 | Todo | Skyline | Add support for IDPicker 3 .idpDB as an a search result format for BlibBuild | Guest | 3 | closed | 3.1 |
377 | Todo | Topograph | Need to limit the peptides used in calculating PP enrichment to those from short-lived proteins | Guest | 1 | closed | 3.1 |
376 | Defect | Skyline | Background Proteome Problems -“Resolving protein details for background proteome not working” | Brian Pratt | 3 | open | |
375 | Defect | Skyline | Small molecules: need negative ion capability | Guest | 3 | closed | 3.1 |
374 | Defect | Skyline | Small molecules: users want to import m/z values, not masses | Guest | 3 | closed | 3.1 |
373 | Defect | Skyline | Small molecules: Insert Transition list doesn't construct the tree properly | Guest | 3 | closed | 3.1 |
372 | Defect | Skyline | Small Molecule issues with transition settings | Guest | 3 | closed | 3.1 |
371 | Defect | Skyline | Small molecules: need to be able to import and/or set CE, RT and DT for individual precursors and products | Guest | 3 | closed | 3.1 |
370 | Defect | Skyline | Small Molecule CE Output not working | Guest | 3 | closed | 4.1 |
369 | Defect | Skyline | "An item with the same key has already been added" when adding peptides from a library | Guest | 2 | closed | 3.1 |
368 | Todo | Skyline | Tool Require Multiple R Versions | Guest | 3 | closed | |
367 | Defect | Topograph | Results by Cohort feature produces no output | Guest | 1 | closed | 3.1 |
366 | Defect | Topograph | Mass accuracy cannot be changed for an individual protein/peptide | Guest | 3 | closed | 3.1 |
365 | Defect | Skyline | Make peptide matching to background proteome more flexible | Guest | 3 | closed | 3.7 |
364 | Todo | Skyline | Add PeptideTotalArea and ProteinTotalArea values to reports and graphs | Guest | 3 | closed | 20.2 |
363 | Todo | Skyline | Handle Mascot Distiller settings which are problematic for Skyline | Guest | 3 | closed | 3.1 |
362 | Todo | Skyline | Add support to Skyline for querying a Mascot Server directly for search results | Matt Chambers | 3 | open | |
361 | Defect | Skyline | Shrink font before hiding dtop or idotp values on the Peak Areas graph | Guest | 3 | closed | 3.1 |
360 | Defect | Skyline | Review all forms with tips and extend AutoPopDelay to 60000 (1 minute) | Guest | 3 | closed | 3.6 |
359 | Defect | Skyline | Double-click to zoom out on chromatogram graphs not reflected in synchronized zooming | Rita Chupalov | 4 | open | |
358 | Defect | Skyline | Tool Framework Python package installation bug | Guest | 3 | closed | |
357 | Todo | Skyline | Add support for Thermo Fusion method export to Skyline | Guest | 2 | closed | 3.1 |
356 | Todo | Skyline | Implement export isolation list for Waters Q-TOF | Guest | 1 | closed | 3.1 |
355 | Todo | Skyline | Add support for RT column to BiblioSpec SSL spectrum matching format | Guest | 3 | closed | 3.1 |
354 | Defect | Skyline | CE optimization library populated with data for labeled peptides does not work for analyte peptides | Guest | 3 | closed | 3.1 |
353 | Defect | Topograph | Custom view info lost with upgrade; cannot use Customize View | Guest | 2 | closed | 3.1 |
352 | Todo | Skyline | Annotate reporter ions in Library Match graph | Rita Chupalov | 2 | open | 22.1 |
351 | Defect | Topograph | Reject/Accept setting does not work from Half-Life tab for a protein | Guest | 2 | closed | 3.1 |
350 | Defect | Topograph | Cannot click through on peptide names from Half-Life view of protein | Guest | 3 | closed | 3.1 |
349 | Defect | Skyline | Acquired time attribute lost for files on Chorus | Guest | 2 | closed | |
348 | Todo | Skyline | Implement intensity threshold for Edit > Refine > Advanced | Guest | 3 | closed | 4.1 |
347 | Todo | Skyline | More work on full-scan graph for ion labels in unzoomed mode | Rita Chupalov | 2 | open | |
346 | Todo | Skyline | Make multi-peptide graphs clickable | Guest | 2 | closed | 3.1 |
345 | Defect | Skyline | Import Peptide Search wizard should show full-scan settings no matter what | Guest | 2 | closed | 3.1 |
344 | Defect | Skyline | Exclude spectrum source files checkbox present in ImportResultsControl but not functional | Guest | 2 | closed | 3.1 |
343 | Todo | Skyline | Tool store display order | Kaipo Tamura | 4 | resolved | |
342 | Defect | Skyline | Spectral Library Explorer and MS1 Analysis | Brendan MacLean | 3 | open | |
341 | Defect | Skyline | Centroided spectra show up with profile lines in full-scan graph | Guest | 3 | closed | 2.6 |
340 | Todo | Skyline | Support pasting a list of protein accession numbers directly into Skyline when the document has a background proteome | Guest | 3 | closed | |
339 | Todo | Skyline | Support charged loss from precursor ions | Brendan MacLean | 3 | open | |
338 | Todo | Skyline | Support Thermo Crystal library format | Guest | 3 | closed | 3.1 |
337 | Defect | Skyline | mascot v2.4 MS1 import raw data | Guest | 2 | closed | 2.6 |
335 | Todo | Skyline | Improve access to optimization values in Skyline UI | Nick Shulman | 3 | open | 22.1 |
334 | Defect | Skyline | RT prediction not working for all decoy types | Guest | 3 | closed | 2.6 |
333 | Todo | Skyline | Add "Exclude precursor isolation window" checkbox to Transition Settings - Filter | Guest | 3 | closed | 2.6 |
332 | Defect | Skyline | Skyline crashes while uploading document to a Panorama server with no disk space | Guest | 3 | closed | 2.6 |
331 | Todo | Skyline | Improve Import Results form | Matt Chambers | 3 | open | |
330 | Todo | Topograph | Group fly peptides by CG number | Guest | 3 | closed | 2.6 |
329 | Defect | Topograph | Workaround for replicates with 100% turnover to prevent ValueOutOfRange error | Guest | 3 | closed | 2.6 |
328 | Todo | Skyline | Implement support for associating protein FASTA after a document exists as a set of peptide lists | Guest | 3 | closed | |
327 | Defect | Skyline | File | Import | TransitionList... always gives charge state 1 if there is a peptide mass column to the left of the actual m/z column | Guest | 3 | closed | 19.2 |
326 | Defect | Skyline | Group by peak area graphs should not stack when showing all transitions | Brendan MacLean | 3 | resolved | 4.3 |
325 | Todo | BiblioSpec | Add support for .idXML as an a search result format for BlibBuild | Guest | 3 | closed | |
324 | Todo | Skyline | Improve unexpected error UI to solicit more information | Guest | 3 | closed | 3.1 |
323 | Defect | Skyline | Fix PeptideDocNode.CalcBestResult() to use current peak scoring algorithm | Brendan MacLean | 3 | open | |
322 | Defect | Skyline | Changing selected file in GraphChromatogram does not update Targets view | Brendan MacLean | 3 | open | |
321 | Todo | Skyline | Add relative ion abundance columns to reports | Nick Shulman | 3 | open | |
320 | Todo | Skyline | Add support for .sptxt as an a search result format for BlibBuild | Guest | 3 | closed | 2.6 |
319 | Todo | Skyline | Add support for SpectraST retention times to Skyline | Guest | 3 | closed | 3.1 |
318 | Todo | Skyline | Add multi-peptide RT graph | Guest | 3 | closed | |
317 | Todo | Skyline | Add UI to Accept Peptides form to allow specifying a list of proteins | Guest | 2 | closed | 3.2 |
316 | Defect | Skyline | Saving a minimized skyline doc which uses an XHunter library doesn't work if peptide ranking is turned on | Brian Pratt | 3 | open | |
315 | Todo | Skyline | Improve support for library scores in Skyline | Kaipo Tamura | 3 | open | |
314 | Defect | Skyline | Support modifications not associated with an amino acid in SSL format for spectral library building | Guest | 2 | closed | 3.1 |
313 | Todo | Skyline | Add separate groups for Live Report views | Guest | 3 | closed | 3.1 |
312 | Todo | Skyline | Add Tools > Options - Language tab to v2.5 branch | Guest | 0 | closed | 2.5 |
311 | Defect | Skyline | IndexOutOfRangeException UniquePrefixGenerator.GetUniquePrefix | Guest | 3 | closed | 2.5 |
310 | Defect | Skyline | IndexOutOfRangeException in GraphChromatogram.DisplayPeptides | Guest | 3 | closed | 2.5 |
309 | Defect | Skyline | Problems running R for MSstats on computers that report successful installation | Guest | 2 | closed | 2.5 |
308 | Defect | Skyline | Missing R.exe after MSstats installation | Guest | 3 | closed | 3.1 |
307 | Todo | Skyline | Get Skyline window on screen faster | Guest | 2 | closed | 3.1 |
306 | Defect | Skyline | Message box timeout code should be disabled when pausing a test | Guest | 1 | closed | 2.6 |
305 | Defect | Skyline | Columns appear multiple times in PrescursorResults view | Guest | 1 | closed | 2.5 |
304 | Defect | Skyline | Proteins added to an existing protDB don't get digested | Brian Pratt | 3 | open | |
303 | Localization | Skyline | LOCALIZATION: Create build tool that scans the source for strings without "Not L10N" | Guest | 3 | closed | 2.6 |
302 | Localization | Skyline | LOCALIZATION: Make SkylineRunner command-line interface localizable | Guest | 3 | closed | 2.6 |
301 | Localization | Skyline | LOCALIZATION: Several strings have been added since .resx files were given to Language Scientific | Guest | 3 | closed | 2.5 |
300 | Defect | Skyline | Change encoding of filepaths in .skyd files from Default to UTF-8 | Guest | 3 | closed | 2.6 |
299 | Defect | Skyline | chromatogram extraction with .wiff data in TestMS1Tutorial is about 2x slower when run in French or Japanese | Guest | 3 | closed | 2.6 |
298 | Todo | Skyline | Add accession number and human readable protein name to proteins | Guest | 2 | closed | 2.6 |
297 | Localization | Skyline | LOCALIZATION: Live reports toolbar not localized | Guest | 3 | closed | 2.5 |
296 | Defect | Skyline | IrtDb can prevent document from being saveable. | Guest | 2 | closed | 2.5 |
295 | Defect | Skyline | InvalidOperationException in TransitionGroupDocNode.CalcMatchingPeak | Guest | 2 | closed | 2.5 |
294 | Defect | Skyline | peak splitting | Guest | 3 | closed | 2.6 |
293 | Defect | Skyline | Unhandled exception | Guest | 3 | closed | 2.6 |
292 | Todo | Skyline | Add Replicate Comparison order for View > Arrange Graphs > Grouped | Guest | 3 | closed | 3.6 |
291 | Defect | Skyline | Results grid last selected customized view needs to be remembered | Guest | 3 | closed | 2.5 |
290 | Todo | Skyline | Add in-place filtering to Live Reports | Guest | 3 | closed | 3.1 |
289 | Localization | Skyline | LOCALIZATION: Report headers cannot be translated | Guest | 3 | closed | 2.6 |
288 | Defect | Skyline | InvalidOperationException in AdlerChecksum.MakeForString if type filename into Import Results File Open Dialog | Guest | 2 | closed | 2.5 |
287 | Defect | Skyline | ArgumentOutOfRangeException in ChromDataSet.SetBestPeak | Guest | 2 | closed | 2.5 |
286 | Defect | Skyline | NRE in TransitionPeakPairData<TData>.GetMatchingReferencePairs | Guest | 2 | closed | 2.5 |
285 | Defect | Skyline | "An item with the same key has already been added" exception in TargetDecoyGenerator.PopulateDictionary | Guest | 2 | closed | 2.5 |
284 | Defect | Skyline | Fix sluggish update of multiple peptides graph after "Select All" on a large document | Guest | 1 | closed | 3.2 |
283 | Defect | Skyline | Synchronized zooming should work for tabbed graphs | Guest | 4 | closed | |
282 | Todo | Skyline | Add new TotalArea values to reports | Guest | 3 | closed | 2.6 |
281 | Defect | Skyline | MSStats (Skyline External Tool) installation is noisy and full of scary warnings | Guest | 3 | closed | |
280 | Defect | Skyline | "External Tools | Add" UI is mildly confusing - presents a picklist where it should be a simple textbox | Guest | 4 | closed | |
279 | Documentation | Skyline | Merge QuaSAR GenePattern documentation with Tool Store version | Guest | 3 | closed | 2.2 |
278 | Defect | Skyline | BiblioSpec bug parsing pep.xml from Prospector | Guest | 3 | closed | 2.5 |
277 | Defect | Skyline | Add ByOnic support to BiblioSpec | Guest | 3 | closed | 2.5 |
276 | Defect | Skyline | MaxQuant no matching mod error in BiblioSpec | Guest | 3 | closed | 2.5 |
275 | Documentation | Skyline | Create External Tools examples for Web Sites and Java Tools | Nick Shulman | 4 | open | |
274 | Defect | Skyline | Refactor new Live Reports class names to stop using the product name Skyline | Guest | 3 | closed | 3.1 |
273 | Defect | Skyline | Dot-product labels clipped in peak area graphs | Guest | 3 | closed | 3.1 |
272 | Defect | Skyline | NRE in MS1Probe external tool | Guest | 3 | closed | 2.1 |
271 | Todo | Skyline | Add group-by queries to exported reports | Guest | 1 | closed | 4.1 |
270 | Todo | Skyline | Save window layouts in a way that allows them to be used across documents | Brendan MacLean | 4 | open | |
269 | Todo | Skyline | Allow m/z or ppm tolerance for chromatogram extraction | Guest | 3 | closed | 3.1 |
268 | Todo | Skyline | Create UI to allow hiding/showing replicates | Nick Shulman | 3 | open | |
267 | Todo | Skyline | Change Skyline File > Share file extension to .sky.zip | Guest | 3 | closed | 2.2 |
266 | Defect | Skyline | Fail to create peptide library by using .mzid file from MSGF+ searching result! | Guest | 2 | closed | 2.5 |
265 | Defect | Skyline | Skyline won't recognize precursor transitions in certain RAW files | Guest | 3 | closed | 2.1 |
264 | Todo | BiblioSpec | Clarify limitation on BlibBuild reading vendor raw files and consider lifting it | Guest | 3 | closed | |
263 | Defect | Skyline | Too strict about choosing only one precursor for every MS/MS scan in Targeted MS/MS | Guest | 3 | closed | 2.1 |
262 | Todo | Skyline | Add way to specify charge state when pasting peptide lists | Brendan MacLean | 3 | open | |
261 | Todo | Skyline | Add a raw intensity filter for peaks to Edit > Refine > Advanced | Guest | 3 | closed | |
260 | Defect | Skyline | ArgumentOutOfRangeException pasting into calibrate window | Guest | 2 | closed | 2.1 |
259 | Defect | Skyline | Near isobars in spectral library building getting merged | Guest | 2 | closed | 4.1 |
258 | Defect | Skyline | InvalidOperationException clicking on column to sort rows in EditIrtCalcDlg.Calibrate | Guest | 2 | closed | 2.1 |
257 | Defect | Skyline | DIA isolation scheme editor needs an instrument method mode | Guest | 3 | closed | 2.6 |
256 | Defect | Skyline | Fix normalized CE column for Q Exactive isolation list export | Guest | 2 | closed | 2.1 |
255 | Todo | Skyline | Create ToolReportCache class to make repeated analysis faster | Guest | 2 | closed | 2.1 |
254 | Todo | Skyline | Peak Areas > Peptide Comparison graph should have stacked all transitions display | Nick Shulman | 3 | open | |
253 | Todo | Skyline | Create Document Settings form and implement fold-change statistics | Guest | 2 | closed | |
252 | Defect | Skyline | Light and heavy transitions can be different for several cases | Guest | 3 | closed | 3.1 |
251 | Defect | BiblioSpec | BlibFilter crashes, if it cannot find :redundant: in the library LSID | Guest | 3 | closed | 2.1 |
250 | Todo | Skyline | Method and transition list export for Waters Xevo uses a constant cone voltage of 35 | Kaipo Tamura | 4 | open | |
249 | Todo | Skyline | Add support for storing optimized CE values in a database file like iRT | Guest | 3 | closed | 2.6 |
248 | Todo | Skyline | Add light to heavy dot-products | Guest | 3 | closed | 2.2 |
247 | Todo | Skyline | Add modification sites field to Skyline custom reports | Nick Shulman | 4 | open | |
246 | Todo | Skyline | Enable scheduled targeted-MS/MS method export on Orbitrap Elite, etc. | Guest | 4 | closed | |
245 | Todo | Skyline | Support MSGF+ pepXML in BlibBuild | Guest | 2 | closed | 2.1 |
244 | Todo | Skyline | Add Thermo Quantiva to Export > Transition List options | Guest | 3 | closed | 2.1 |
243 | Todo | Skyline | Add tool tips to some of the graphs | Rita Chupalov | 4 | open | |
242 | Todo | Skyline | Add option to show only chromatograms for transitions that contribute to total peak area | Guest | 4 | closed | 4.2 |
241 | Defect | Skyline | Improve BlibFilter best spectrum picking for targeted MS/MS data | Guest | 2 | closed | 2.1 |
240 | Todo | Skyline | Add Row and Column to View > Arrange menu | Guest | 4 | closed | 3.1 |
239 | Defect | Skyline | Raw data for certain transitions not being imported from Xevo into Skyline | Guest | 3 | closed | 2.1 |
238 | Todo | Skyline | Add ability to import peptide search to SkylineRunner | Guest | 3 | closed | 3.2 |
237 | Defect | Skyline | Popup pick lists can end up inserting nodes that are out of sync with the settings | Brendan MacLean | 3 | open | |
236 | Defect | Skyline | error in building spectral library | Guest | 3 | closed | 2.1 |
235 | Todo | Skyline | Auto-check HTTPS for Panorama server configuration when HTTP is specified and fails | Guest | 3 | closed | 2.1 |
234 | Todo | Skyline | Preserve tree expansion in PublishDocumentDlg | Guest | 3 | closed | 2.1 |
233 | Defect | Skyline | Move from dictionary to array in pwiz.Skyline.Model.Results.ChromDataCollectorSet.ProcessExtractedSpectrum(Double, ExtractedSpectrum) | Guest | 3 | closed | 2.5 |
232 | Defect | Skyline | Improve chromatogram read performance for large full-scan files | Guest | 3 | closed | 3.1 |
231 | Defect | Skyline | Fix MSGraph to include annotation boundaries in graph scaling | Guest | 3 | closed | 2.1 |
230 | Todo | Skyline | Add Filter By... menu item with Group By and Order By | Guest | 3 | closed | 3.1 |
229 | Todo | Skyline | Add ability to specify a list of peptide sequences to BlibBuild | Guest | 2 | closed | 2.1 |
228 | Defect | Skyline | When re-importing, peak boundaries that have been manually set should recompute integration | Guest | 2 | closed | 21.2 |
227 | Todo | Skyline | Show more complete list of error transitions on paste of transition list | Guest | 3 | closed | |
226 | Defect | Skyline | Need better error message when isolation windows conflict | Guest | 3 | closed | 2.6 |
225 | Todo | Skyline | Streamline File > Publish to Panorama first use | Guest | 3 | closed | 2.1 |
224 | Defect | Skyline | Fix SkylineRunner to support multiple instances running at the same time | Guest | 3 | closed | 2.1 |
223 | Todo | Skyline | Add PPM and resolution options to Transition Settings - Library - Ion match tolerance | Rita Chupalov | 3 | resolved | |
222 | Todo | Skyline | Prediction versus confidence intervals in peak area plots | Nick Shulman | 3 | open | |
221 | Todo | Skyline | Add retention time prediction indicators to retention time summary graphs | Rita Chupalov | 3 | open | |
220 | Todo | Skyline | Enable sorting by annotation value in Replicate Comparison | Guest | 3 | closed | 2.1 |
219 | Defect | Skyline | Import results with folder selected does not work as expected | Guest | 3 | closed | 2.1 |
218 | Todo | Skyline | Add checkbox to Transition Settings - Filter to add neutral loss ions | Guest | 3 | closed | |
217 | Defect | Skyline | Importing a Document with the DIA analysis of same files, different peptides | Brendan MacLean | 3 | open | |
216 | Todo | Skyline | Add ragged end flag to the Peptide class and expose this value in reports | Brendan MacLean | 4 | open | |
215 | Todo | Skyline | Add graph properties to allow user control of axis label font size and orientation | Guest | 3 | closed | 3.1 |
214 | Todo | Skyline | Ambiguous peptide spectrum matches are removed during library building without any notification | Guest | 3 | closed | 3.1 |
213 | Defect | Skyline | Unhandled InvalidOperationException | Guest | 3 | closed | |
212 | Todo | Skyline | Add filter exclusion for peptide duplication | Guest | 3 | closed | 3.1 |
211 | Defect | Skyline | Unhandled System.NullReferenceException in pwiz.Skyline.Model.Find.BookmarkEnumerator.set_Current | Guest | 2 | closed | 1.4 |
210 | Defect | Skyline | Unhandled exception in RecordNavBar.UpdateAll() | Guest | 2 | closed | 2.1 |
209 | Todo | Skyline | Add Peptides.StructuralModifiedSequence to custom report fields in Skyline | Guest | 1 | closed | 1.4 |
208 | Todo | Skyline | Allow R scripts to act as external tools in Skyline | Guest | 3 | closed | 2.1 |
207 | Todo | Skyline | Add a Prompt for arguments check box to the External tools form in Skyline | Guest | 2 | closed | 2.1 |
206 | Todo | Skyline | Skyline should show progress in the status bar when a report is being generated for an external tool | Guest | 2 | closed | 2.1 |
205 | Todo | Skyline | Add Auto-zoom Y-axis sub-menu which includes Best Peak | Rita Chupalov | 3 | open | |
204 | Todo | Skyline | Add Min intensity value to Chromatogram Graph Properties form | Guest | 4 | closed | |
203 | Todo | Skyline | TargetedMSMS-BSA_Protea | Guest | 3 | closed | 2.1 |
202 | Defect | Skyline | Improve multiplexing detector to reject multi-precursor isolations that are not really multiplexed | Guest | 3 | closed | 2.1 |
201 | Defect | Skyline | Neutral loss ions lost in pivoted report when same non-neutral loss ions are present | Guest | 3 | closed | 1.4 |
200 | Todo | Skyline | Add File > Import > Replicate Annotations... menu item | Guest | 3 | closed | 2.1 |
199 | Defect | Skyline | Editing annotation values in Results Grid with protein selected has strange grid selection behavior | Guest | 2 | closed | 1.4 |
198 | Todo | Skyline | Add the ability to incorporate spectral library retention times into scheduling RT prediction | Guest | 3 | closed | 2.1 |
197 | Todo | Skyline | Add ability to annotate replicates | Guest | 3 | closed | 1.4 |
196 | Documentation | Skyline | Create a new instructional video on working with full-scan data | Guest | 3 | closed | |
195 | Documentation | Skyline | Write a Data Independent Acquisition tutorial | Guest | 3 | closed | |
194 | Documentation | Skyline | Write an Integration with External Tools tutorial | Guest | 3 | closed | |
193 | Documentation | Skyline | Write a Command-Line Automation tutorial | Brendan MacLean | 3 | open | |
192 | Documentation | Skyline | Write a Chromatogram Peak Integration tutorial | Guest | 3 | closed | |
191 | Documentation | Skyline | Write an Advanced Peptide Modifications tutorial | Guest | 3 | closed | |
190 | Todo | BiblioSpec | Add library building support for Proteome Discoverer native .msf files | Guest | 3 | closed | |
189 | Todo | BiblioSpec | Add library building support for PRIDE XML | Guest | 3 | closed | 2.1 |
188 | Documentation | Skyline | Tutorials using Thermo RAW data should mention need for English (US) number format settings | Guest | 4 | closed | 2.1 |
187 | Todo | Skyline | Plot Base Peak and TIC chromatograms | Guest | 3 | closed | 2.1 |
186 | Defect | Skyline | Fix multi-line error messages for Agilent method export | Guest | 2 | closed | 1.2 |
185 | Todo | Skyline | N- and C-terminal protease combinations | Guest | 4 | closed | 2.1 |
184 | Todo | Skyline | Levey-Jennings Chart for QC | Guest | 3 | closed | |
183 | Todo | Skyline | Save internal pane state in .sky.view | Guest | 3 | closed | |
182 | Defect | Skyline | Spiky chromatograms from MSFileReader when two targets have the same Q1 and Q3 but different scheduling windows | Guest | 3 | closed | 2.5 |
181 | Todo | Skyline | Add Edit > Refine > Rename Proteins form | Guest | 3 | closed | |
180 | Todo | Skyline | Add refinement support for merging repeated proteins | Brendan MacLean | 2 | open | |
179 | Defect | Skyline | local copy work-around error when importing thermo TSQ raw files | Guest | 3 | closed | 1.2 |
178 | Documentation | Skyline | Background | Guest | 3 | closed | 1.2 |
177 | Defect | Skyline | How to import WIFF files for SWATH data? | Guest | 3 | closed | 1.2 |
176 | Todo | BiblioSpec | Implement BiblioSpec library building support for MaxQuant Andromeda | Guest | 3 | closed | 2.1 |
175 | Todo | Skyline | Allow exporting multiple DIA methods to cover larger mass ranges, using smaller windows | Kaipo Tamura | 3 | open | |
174 | Todo | Skyline | Add protein terminal modification support to Skyline | Guest | 3 | closed | |
173 | Todo | BiblioSpec | Support peak list files for ProteinProspector (UCSF) | Guest | 4 | closed | |
172 | Todo | Skyline | What time does the Skyline version 1.3 release? | Guest | 3 | closed | 1.2 |
171 | Defect | Skyline | Edit > Insert > Proteins should ignore white space on paste | Brian Pratt | 4 | open | |
170 | Todo | Skyline | Correct peptide start and end indices to use 1-based indexing instead of 0-base indexing | Brendan MacLean | 3 | open | |
169 | Defect | BiblioSpec | BlibBuild status for ProteinPilot (.group.xml) is broken | Guest | 3 | closed | |
168 | Todo | Skyline | Copy Data on retention time copies time of end of peak, instead of peak apex | Guest | 3 | closed | 1.2 |
167 | Todo | Skyline | Add orthogonal peak ranking for MS1 and MS/MS filtering | Guest | 3 | closed | 3.5 |
166 | Defect | Skyline | Declustering potential abbreviated CE under the transition settings | Guest | 3 | closed | 1.2 |
165 | Defect | Topograph | Unhandled exception error message on half-lives results page | Guest | 3 | closed | 1.2 |
164 | Todo | Skyline | Add Max peptide rank field to Refine form | Guest | 3 | closed | 2.1 |
163 | Defect | Skyline | will/is SkyLine MS1 filtering be capable of peak picking in MS-only data? | Guest | 3 | closed | 1.2 |
162 | Todo | Skyline | Add new data file fields to Skyline reports | Guest | 3 | closed | 3.1 |
161 | Todo | Skyline | Store Spectral Library Explorer sort order in the library cache files | Guest | 3 | closed | |
160 | Todo | Skyline | Add customizable Tools menu | Guest | 3 | closed | 2.1 |
159 | Todo | Skyline | Spectral Library Explorer displays duplicate entries | Guest | 3 | closed | 1.2 |
158 | Defect | Skyline | When building a library from IdentityE (PLGS) search results the individual transitions are not listed | Guest | 3 | closed | 1.2 |
157 | Defect | Skyline | applying transition filter settings (precursor only) to peptides | Guest | 3 | closed | 1.1 |
156 | Defect | Skyline | DocNode missing results | Guest | 3 | closed | 1.2 |
155 | Todo | Topograph | Depersonalize "Evvie's Filter" | Guest | 4 | closed | 1.2 |
154 | Defect | Skyline | cannot import/merge documents in skyline 1.2 | Guest | 3 | closed | 1.2 |
153 | Defect | Topograph | Error message during generation of Results by Cohort output | Guest | 2 | closed | 1.2 |
152 | Defect | Topograph | Manual "reject" is not working | Guest | 4 | closed | 1.2 |
151 | Defect | Skyline | Problem with MANAGE RESULTS > UP/DOWN function | Guest | 3 | closed | 1.2 |
150 | Defect | Skyline | exporting scheduled method using results for peptides with and without previous retention times | Kaipo Tamura | 3 | open | 22.1 |
149 | Defect | Topograph | Peptides with only one Leu have average turnover scores lower than 1 when out of range | Guest | 4 | closed | 1.2 |
148 | Defect | Topograph | Please correct Y-axis label of half-life graphs to read "ln" rather than "log" | Guest | 3 | closed | 1.2 |
147 | Todo | Skyline | Replace isolation width on full-scan settings tab with isolation scheme | Guest | 2 | closed | 2.1 |
146 | Defect | Skyline | cannot install skyline software | Guest | 3 | closed | 1.2 |
145 | Defect | Skyline | Write automated test for iRT tutorial | Guest | 2 | closed | 1.2 |
144 | Todo | Skyline | Write automated test for MS1 Filtering tutorial | Guest | 2 | closed | 1.2 |
143 | Todo | Skyline | Write automated test for Absolute Quantification tutorial | Guest | 2 | closed | 1.2 |
142 | Defect | Skyline | Q-Exactive data acquired using Xcalibur 2.2 | Guest | 3 | closed | 1.2 |
141 | Defect | Topograph | Serious apparent discrepancies in half-life values | Guest | 1 | closed | 1.2 |
140 | Todo | Skyline | Add support to Edit > Insert > Peptides for not fully cleaved peptides, if protein name is given | Guest | 3 | closed | |
139 | Defect | Skyline | Regarding building spectral library which Skyline can recognise using Mascot(Proteome Discoverer 1.3) | Guest | 3 | closed | 1.2 |
138 | Todo | Skyline | Add report value for spectral library retention time | Nick Shulman | 3 | open | 22.1 |
137 | Defect | Skyline | export of scheduled methods to waters xevo | Guest | 3 | closed | 1.2 |
136 | Todo | Topograph | Add Average Turnover Score cutoff to Half-Lives and Results by Cohort forms | Guest | 2 | closed | 1.2 |
135 | Todo | Topograph | Implement "decrease in old protein" method of calculating half-life | Guest | 2 | closed | 1.2 |
134 | Defect | Topograph | Topograph fails to generate Results by Cohort output | Guest | 1 | closed | 1.2 |
133 | Defect | Topograph | Topograph tries to load peptide analysis when I click on Status drop-down | Guest | 3 | closed | 1.2 |
132 | Defect | Skyline | peak integration and annotation missing after document merging | Guest | 3 | closed | 1.2 |
131 | Defect | Skyline | absolute quantification of mTRAQ-modified peptides | Guest | 3 | closed | 1.2 |
130 | Defect | Topograph | Topograph stops in the middle of generating replicates w/o MS2 IDs, with no error message | Guest | 1 | closed | 1.2 |
129 | Defect | Skyline | Clipboard failure in DataGridView | Guest | 2 | closed | 2.1 |
128 | Defect | Topograph | Topograph throws exceptions during search for replicates w/o MS2 IDs, and those replicates are not accessible | Guest | 2 | closed | 1.2 |
127 | Defect | Skyline | Expecting only one period | Guest | 4 | closed | 1.2 |
126 | Defect | Skyline | Annotations | Guest | 3 | closed | 1.2 |
125 | Defect | Topograph | Topograph threw exception and crashed during recalculation of results | Guest | 3 | closed | 1.2 |
124 | Defect | Skyline | Skyline saved file won't open probably because replicates rearranged | Guest | 3 | closed | 1.2 |
123 | Todo | Skyline | CE,DP optimizing: step number and increment value | Guest | 3 | closed | 1.2 |
122 | Todo | Skyline | Collision Cell Exit Potential (CXP) optimization | Brendan MacLean | 3 | open | |
121 | Todo | Skyline | enzyme combinations (N and C terminal) | Guest | 3 | closed | 1.4 |
120 | Todo | Skyline | Add original measurement times to .skyd file | Guest | 3 | closed | |
119 | Todo | Skyline | Chromatograms display suggestion | Guest | 3 | closed | 1.2 |
118 | Todo | Skyline | Make Skyline graph colors customizable | Guest | 3 | closed | 3.7 |
117 | Todo | Skyline | Add a SkylineRunner command-line parameter to import QC data from a directory | Guest | 2 | closed | 1.2 |
116 | Defect | Topograph | Topograph failed and gave "contact manufacturer" message on home computer | Guest | 2 | closed | 1.2 |
115 | Todo | Skyline | Add feature to make multiple selection graph multiple precursor or transition chromatogram together | Brendan MacLean | 3 | open | |
114 | Todo | Skyline | Add ability to overlay all heavy and light transitions | Guest | 4 | closed | 1.2 |
113 | Todo | Skyline | Strict scientific notation for y-axis intensity scale | Guest | 3 | closed | 3.1 |
112 | Defect | Skyline | Add PrecursorResults.MaxHeight value to reports | Guest | 3 | closed | 1.2 |
111 | Todo | Skyline | Implement Edit / Refine / Reintegrate | Guest | 2 | closed | 2.1 |
110 | Defect | Skyline | Building spectral libraries from Mascot results slower than before? | Guest | 3 | closed | 1.2 |
109 | Defect | Topograph | AUC cutoff value set on the HalfLivesForm is not transmitted to individual half-life tabs | Guest | 3 | closed | 1.2 |
108 | Defect | Skyline | Inserting a medium-large transition list with a background proteome can appear to hang Skyline | Guest | 4 | closed | |
107 | Todo | Skyline | Add gene name property to proteins and UI to support it | Guest | 3 | closed | 2.6 |
106 | Todo | Skyline | Support new columns in Thermo TSQ transition list user interface | Guest | 3 | closed | 1.2 |
105 | Todo | Topograph | Create ultra-simple outlier filter (>2 SD) | Guest | 2 | closed | 1.2 |
104 | Todo | Skyline | Add flexible custom naming for Analyst transition lists | Guest | 3 | closed | |
103 | Todo | Skyline | Implement support for MS3 full-scan filtering for neutral losses | Guest | 3 | closed | |
102 | Todo | Skyline | Add Minimize... button to Edit / Manage Results form | Guest | 2 | closed | 2.1 |
101 | Todo | Topograph | Add "minimum area under curve" cutoff to Acceptance Criteria dialog | Guest | 3 | closed | 1.2 |
100 | Defect | Skyline | Attempted row add in Results Grid without any columns | Guest | 2 | closed | 2.1 |
99 | Defect | Skyline | InvalidOperationException in PreviewReportDlg.SetResults | Guest | 3 | closed | 2.1 |
98 | Defect | Skyline | NullReferenceException in ResultsGrid.UpdateGridNotReplicate | Guest | 3 | closed | 1.2 |
97 | Todo | Topograph | Incorporate protein identification/localization info from spreadsheet into Topograph | Guest | 3 | closed | 1.2 |
96 | Defect | Topograph | Percent turnover in Results by Cohort does not match value from Half-Life tab | Guest | 1 | closed | 1.2 |
95 | Defect | Topograph | Half-Lives view sometimes comes up "blank" (all zero/NaN values) | Guest | 2 | closed | 1.2 |
94 | Defect | Skyline | export image in .emf format can not be read by Adobe Illustrator | Guest | 3 | closed | |
93 | Todo | Skyline | Add custom finder to find transitions that overlap | Brendan MacLean | 3 | open | |
92 | Todo | Topograph | Create a feature to view % newly synthesized on the protein level | Guest | 2 | closed | 1.2 |
91 | Todo | Topograph | Modify the "Evvie's Filter" algorithm to exclude extreme outliers first | Guest | 2 | closed | 1.2 |
90 | Defect | Topograph | Duplicate entries in drop-down when using the Find box in the Half-Lives tab | Guest | 4 | closed | 1.2 |
89 | Defect | Skyline | File / Share minimal needs to be aware of retention time information | Guest | 3 | closed | 1.2 |
88 | Defect | Skyline | Add peptide ID flag to results peak attributes | Guest | 3 | closed | 1.2 |
87 | Defect | Skyline | Zoom stops responding during analysis of multiple peptides and replicates | Guest | 3 | closed | 2.6 |
86 | Defect | Skyline | Unhandled exception in DataGridViewRowCollection.RowComparer.CompareObjects | Guest | 2 | closed | 1.2 |
85 | Defect | Skyline | Results grid hangs trying to set annotations | Guest | 1 | closed | 1.2 |
84 | Defect | Skyline | Cant export MRM transition list to Analyst method file | Guest | 3 | closed | 1.2 |
83 | Defect | Skyline | Can't export .exp method file for Xevo MassLynx | Guest | 3 | closed | 1.2 |
82 | Defect | Skyline | global setting for synchronizing isotope types | Guest | 3 | closed | 1.2 |
81 | Defect | Skyline | MethodEdit.zip | Guest | 3 | closed | 1.2 |
80 | Todo | Skyline | Add support for opening File / Share ZIP files directly | Guest | 3 | closed | 1.2 |
79 | Defect | Skyline | Find of an annotation name should find all items with the annotation set | Guest | 2 | closed | 1.2 |
78 | Todo | Skyline | Add Advanced button to Find dialog with checkbox list of things to find | Guest | 2 | closed | 1.2 |
77 | Defect | Skyline | NullReferenceException in Results Grid | Guest | 2 | closed | 1.2 |
76 | Todo | BiblioSpec | BlibBuild needs to store file names with same basename as original instrument data files | Guest | 2 | closed | 1.2 |
75 | Todo | Skyline | Skyline should have document-wide grid view (live report) | Guest | 3 | closed | |
74 | Defect | Skyline | Improvements to exception posting | Guest | 3 | closed | 1.2 |
73 | Defect | Skyline | Add error message when incompatible isotope modifications are chosen | Brendan MacLean | 4 | open | |
72 | Todo | Skyline | Implement MS1 isotope values in reports | Guest | 3 | closed | 1.2 |
71 | Todo | Skyline | Implement File / Print Graphs | Guest | 3 | closed | |
70 | Defect | Skyline | Overlapping transitions causes unpredictable results during CE optimization | Brendan MacLean | 3 | open | |
69 | Defect | Skyline | "Pick Children" causes exception when there is only a peptide list (no proteins) | Guest | 3 | closed | 1.2 |
68 | Defect | Skyline | PasteTest does not test intended automanage case | Guest | 4 | closed | 1.2 |
67 | Defect | Skyline | Before shrinking font in replicate plots truncate names when possible | Guest | 3 | closed | 1.2 |
66 | Todo | Skyline | Find View for Skyline | Guest | 2 | closed | 1.2 |
65 | Todo | Skyline | Allow multiple note flags per node attached to specific users | Guest | 3 | closed | |
64 | Defect | Skyline | Summary plots should not reset zooming on selection change | Guest | 3 | closed | 3.1 |
63 | Todo | Skyline | Add quick menu access to custom annotations | Guest | 3 | closed | |
62 | Defect | Skyline | Document must be fully loaded before it can be saved | Guest | 2 | closed | 1.2 |
61 | Todo | Skyline | Should be possible to view a list of files from which a library was created | Guest | 4 | closed | 1.2 |
60 | Defect | Skyline | Import transition list can pick unlikely ions when more likely ions are with m/z match tolerance | Guest | 4 | closed | 1.2 |
59 | Defect | Skyline | Synchronized zooming can make it hard to Undo All Zoom/Pan | Guest | 3 | closed | |
58 | Todo | Skyline | Implement Experiment Templates in Skyline | Brendan MacLean | 3 | open | |
57 | Defect | Skyline | Peptide highlighting in tips problems with variable modifications | Brendan MacLean | 3 | open | |
56 | Defect | Skyline | Paste with missing library message strange | Guest | 3 | closed | 1.2 |
55 | Todo | Skyline | Add option to show both heavy and light transitions as split graph in same view | Guest | 3 | closed | |
54 | Defect | Skyline | Force matching boundaries between light-heavy precursors with Matching modifications | Guest | 2 | closed | 2.1 |
53 | Defect | Skyline | Library spectrum chart does not always rank ions correctly | Guest | 3 | closed | 1.2 |
52 | Defect | Skyline | Copy data in multi-paned graph only copies first pane | Guest | 3 | closed | |
51 | Defect | Skyline | CE Optimization mass shifts limited to m/z match tolerance | Guest | 4 | closed | |
50 | Todo | Skyline | Consider allowing separate scheduling of peptide precursors for CE optimization | Guest | 4 | closed | |
49 | Defect | Skyline | background database with two enzymes doesn't work for first enzyme | Guest | 3 | closed | 2.6 |
48 | Todo | Skyline | Add Audit algorithm for detecting transition interference | Nick Shulman | 3 | open | |
47 | Todo | Skyline | Add isoelectric point as peptide filter | Brendan MacLean | 4 | open | |
46 | Defect | Skyline | move transition selection box so it doesn't cover transition rankings in tree view (please) | Guest | 4 | closed | 1.2 |
45 | Todo | Skyline | Support unlabeled internal standards | Guest | 3 | closed | |
44 | Todo | Skyline | Add "Show All" right-click menu to tree view | Brendan MacLean | 3 | open | |
43 | Todo | Skyline | Need an easier way to review transitions not integrated | Guest | 3 | closed | 1.2 |
42 | Todo | Skyline | Add ability to assign meaning and structure to the replicates in a Skyline document | Brendan MacLean | 3 | open | |
41 | Defect | Skyline | Editing protein names for "fully backed" fasta proteins. | Guest | 3 | closed | 1.2 |
40 | Todo | Skyline | Allow user to specify new location for missing result files | Guest | 3 | closed | |
39 | Todo | Skyline | Richer Graph Properties | Guest | 4 | closed | 3.1 |
38 | Todo | Skyline | Make skyline support case-control experiment analysis | Guest | 3 | closed | |
37 | Defect | Skyline | Multi-select drag-drop does not work as expected | Guest | 3 | closed | 1.2 |
36 | Todo | BiblioSpec | Import spectral libraries in .csv format (e.g. created from SRM atlas) | Guest | 3 | closed | 2.6 |
35 | Todo | Skyline | Make it possible to find note/annotation text from Find dialog | Guest | 3 | closed | 1.2 |
34 | Todo | Skyline | Add new support for ion highlighting options in spectral library graph | Rita Chupalov | 2 | open | 22.1 |
33 | Defect | Skyline | Chemical formula ordering should not effect warning about existing Unimod modification | Guest | 3 | closed | 1.2 |
32 | Todo | Skyline | Delete results for invidiual peptides | Guest | 3 | closed | |
31 | Todo | Skyline | Export inclusion lists for Skyline documents with only MS1 full--scan filtering | Guest | 3 | closed | 1.2 |
30 | Todo | Skyline | Use retention time regression to better predict peptide peaks over multiple replicates | Guest | 3 | closed | 1.2 |
29 | Todo | Skyline | Implement support for overlapping light-heavy isotope envelopes in MS1 filtering | Nick Shulman | 3 | open | |
28 | Todo | Skyline | Use MS/MS with peptide IDs in MS1-only full-scan filtering | Guest | 3 | closed | 1.2 |
27 | Todo | Skyline | Implement full-scan method export for QSTAR and Triple-TOF 5600 | Guest | 3 | closed | 1.2 |
26 | Todo | Skyline | Implement full-scan method export for Waters Q-TOF instruments | Guest | 2 | closed | 3.1 |
25 | Todo | Skyline | Make Thermo EZ Method transition list format the default even for unscheduled runs | Guest | 3 | closed | |
24 | Todo | Skyline | Implement targeted MS/MS methods for Agilent Q-TOF | Guest | 3 | closed | 1.2 |
23 | Todo | Skyline | Interesting scenarios for Thermo tools require precursor mass shifts | Guest | 3 | closed | |
22 | Todo | Skyline | Make fragment ion labeling in spectral library not limited to two labels. | Guest | 3 | closed | |
21 | Todo | Skyline | Add refinement option to add missing product ions with matching data | Brendan MacLean | 3 | open | |
20 | Todo | Skyline | Implement command-line interface for Skyline | Guest | 2 | closed | 1.2 |
19 | Todo | Skyline | Add a tip somewhere that shows the ion table for the library spectrum | Brendan MacLean | 4 | open | |
18 | Defect | Skyline | Chosing the number of unscheduled methods | Guest | 3 | closed | 1.2 |
17 | Todo | Skyline | Dynamically size position/count indicators based on transition counts | Guest | 4 | closed | 3.1 |
16 | Defect | Skyline | Data import dialog scans drives unnecessarily | Guest | 3 | closed | 1.2 |
15 | Defect | Skyline | Export modification assignemt | Guest | 3 | closed | 1.2 |
14 | Defect | Skyline | Export method error Xevo TQ-S | Guest | 3 | closed | 2.1 |
13 | Defect | Skyline | Missing filtered ion types can have surprising effect on the dot-product | Brendan MacLean | 3 | open | 22.1 |
12 | Todo | Skyline | Add signal-to-noise value in reports | Brendan MacLean | 4 | open | |
11 | Defect | Skyline | Background proteome build fails with large FASTA file | Guest | 4 | closed | |
10 | Todo | Skyline | Add reporter ion type for measuring constant mass ions like ITRAQ | Guest | 3 | closed | 2.6 |
9 | Todo | Skyline | Library spectrum graph should offer UI to choose manually specturm matches | Brendan MacLean | 3 | open | |
8 | Todo | Skyline | Add an Apply To All action to the chromatogram graphs | Guest | 3 | closed | |
7 | Todo | Skyline | Make all Results Grid columns available in column picking UI always | Guest | 3 | closed | 2.2 |
6 | Defect | Skyline | Results columns should get #N/A when no results available | Guest | 2 | closed | 2.1 |
5 | Todo | Skyline | Implement full-scan method export for Agilent QTOF instruments | Guest | 3 | closed | |
4 | Todo | Skyline | Implement custom neutral losses | Guest | 3 | closed | |
3 | Todo | Skyline | Add a way to specificy document level information | Guest | 3 | closed | 1.2 |
2 | Todo | Skyline | Support second round CE optimization | Kaipo Tamura | 4 | open | |
1 | Todo | Skyline | Implement custom ion support | Guest | 2 | closed | 3.1 |