| | | | | | | | |
| 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 | Vagisha Sharma | 3 | open | 22.1 |
| 865 | Defect | Skyline | Adding heavy mods in Peptide Settings does not add "Ratio to Heavy" normalization to Quantification tab | Nick Shulman | 1 | open | 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) | Brian Pratt | 3 | open | 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.chambers42@gmail.com | 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 | Brian Pratt | 3 | resolved | 22.1 |
| 857 | Defect | Skyline | ImportTransitionListColumnSelectDlg lags a bit when associate proteins checked | Brian Pratt | 3 | open | 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 | Nick Shulman | 3 | open | 22.1 |
| 855 | Defect | Skyline | Log scale with median normalization does not mention the normalization in the y-axis label | Nick Shulman | 3 | open | 21.2 |
| 854 | Defect | Skyline | Peak Areas - Replicate Comparison - Normalize to strangely chooses poorly | Nick Shulman | 2 | open | 21.2 |
| 853 | Defect | Skyline | Remove peak should make dotp annotations and line missing | ritach | 1 | resolved | 21.2 |
| 852 | Defect | Skyline | Full-Scan graph no longer auto-scales the y-axis when clicking arrow buttons | ritach | 2 | open | 21.2 |
| 851 | Todo | Skyline | Rename auto trained peak scoring models | Kaipo | 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 | 3 | open | 22.1 |
| 847 | Defect | Skyline | Add option to use explicit RT instead of measured for exporting scheduled methods | Kaipo | 3 | open | |
| 846 | Defect | Skyline | Trouble exporting polarity-switching QQQ method from Skyline to Agilent-6495C | Kaipo | 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 | 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 | ritach | 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 | ritach | 3 | resolved | 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 | ritach | 3 | open | 22.1 |
| 830 | Todo | Skyline | Add a "High resolution" check box to Transition Settings - Library - Ion match tolerance | ritach | 3 | 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 | Kaipo | 2 | open | 21.2 |
| 826 | Defect | Skyline | Choosing an existing standard during Assay Library import fails to add library spectrum to BLIB | Kaipo | 3 | open | 21.2 |
| 825 | Todo | Skyline | SDRF Reports | Nick Shulman | 3 | open | 22.1 |
| 824 | Todo | Skyline | Implement command-line option --import-peak-boundaries | Brendan MacLean | 3 | resolved | 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 | ritach | 3 | open | 22.1 |
| 821 | Todo | Skyline | Expand multiple selection handling in chromatogram graphs to handle precursors | Kaipo | 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 | Kaipo | 2 | open | 21.2 |
| 818 | Todo | Skyline | BlibBuild needs to write more information to .blib files | matt.chambers42@gmail.com | 2 | open | |
| 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 | 21.2 |
| 814 | Todo | Skyline | Need a way to more easily run all tests that produce audit logs | Brendan MacLean | 3 | open | 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 | Nick Shulman | 2 | open | 22.1 |
| 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 | Kaipo | 3 | open | 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 | Brian Pratt | 3 | open | |
| 804 | Todo | Skyline | Implement simple filtering for MSP file import | Brian Pratt | 3 | open | |
| 803 | Todo | Skyline | Retain previous iRT values in iRT databases | Kaipo | 2 | open | 21.2 |
| 802 | Todo | Skyline | Add "Synchronize Integration" option | Kaipo | 3 | resolved | 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 | Kaipo | 3 | open | 21.2 |
| 798 | Todo | Skyline | When missing chromatograms but we have a RT prediction, we should graph that | Nick Shulman | 3 | open | 21.2 |
| 797 | Todo | Skyline | Transitions Split Graph confusing for multiple precursor charges | Nick Shulman | 3 | open | 21.2 |
| 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 | Brian Pratt | 3 | open | |
| 791 | Defect | Skyline | Inconsistencies in Small Molecule UI mode make it difficult to reopen a closed Targets window | Brian Pratt | 3 | resolved | |
| 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 | Brian Pratt | 3 | open | |
| 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 | Brian Pratt | 2 | open | 21.1 |
| 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 | ritach | 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 | ritach | 4 | open | |