| Issue ID | Type | Area | Title | Assigned To | Priority | Status | Milestone |
| 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 | Brian Pratt | 1 | open | 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 | 3 | open | 21.2 |
| 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 | Brendan MacLean | 3 | resolved | 21.2 |
| 809 | Todo | Skyline | Implement better searching in Library Explorer for small molecules | Brian Pratt | 3 | open | |
| 808 | Todo | Skyline | Change Targeted to PRM and add a SureQuant option to Acquisition method list | Nick Shulman | 3 | open | 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. | Brian Pratt | 3 | open | |
| 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 | 3 | open | 21.2 |
| 802 | Todo | Skyline | Add "Synchronize Integration" option | Kaipo | 3 | open | 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 | matt.chambers42@gmail.com | 3 | open | 21.2 |
| 800 | Defect | Skyline | BiblioSpec MaxQuant reader should look in parent folders for raw data files | matt.chambers42@gmail.com | 3 | open | 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 | Brian Pratt | 3 | open | 21.1 |
| 795 | Defect | Skyline | Import Peptide Search library build with Automatic iRT leaves standard peptides hidden | Kaipo | 3 | open | 21.1 |
| 794 | Defect | Skyline | Unable to deselect (or remove) the Prosit library for library matching in Molecule UI | Brian Pratt | 3 | open | |
| 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 | Brendan MacLean | 2 | resolved | 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 | |
| 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 | Brian Pratt | 3 | open | |
| 778 | Defect | Skyline | Pasting into the Target window should be on a LongWaitDialog | Brian Pratt | 3 | open | |
| 777 | Defect | Skyline | Training IMSDB hangs when raw data files are not present | Brian Pratt | 3 | open | 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 | Brian Pratt | 1 | open | 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 | 3 | open | 21.1 |
| 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 | Brian Pratt | 3 | open | |
| 765 | Defect | Skyline | Refactor AuditLog hash calculation | ritach | 3 | open | |
| 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 | Brendan MacLean | 3 | resolved | 20.2 |
| 762 | Defect | Skyline | enforce or infer setting ion mobilty units for explicit ion mobility values | Brian Pratt | 3 | resolved | |
| 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 | Brian Pratt | 3 | open | |
| 757 | Todo | Skyline | add a display for ion mobility spectrum | ritach | 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 | 3 | open | 20.2 |
| 753 | Defect | Skyline | Value list annotations should not allow empty lists | Brendan MacLean | 3 | resolved | 20.2 |
| 752 | Todo | Skyline | Add option to use 1-based amino acid position numbering | Kaipo | 3 | open | 21.1 |
| 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 | 2 | open | 20.2 |
| 746 | Defect | Skyline | Retention time alignment makes mouse act out of phase on aligned replicate graphs | matt.chambers42@gmail.com | 3 | resolved | 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 | 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 | Brendan MacLean | 3 | resolved | |
| 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.chambers42@gmail.com | 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 | Vagisha | 3 | open | |
| 727 | Defect | Skyline | Panorama upload issues | Vagisha | 3 | open | 20.2 |
| 726 | Defect | BiblioSpec | Skyline nonredundant blib format to MS2 conversion | matt.chambers42@gmail.com | 3 | resolved | |
| 725 | Defect | Skyline | Need to improve inference of ionization type when reading small molecule .MSP files | Brian Pratt | 3 | resolved | |
| 724 | Defect | Skyline | Import multiple files as a single run for iRT calibration | Kaipo | 3 | open | 20.2 |
| 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? | Brendan MacLean | 2 | open | 21.2 |
| 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 | Brendan MacLean | 3 | resolved | |
| 719 | Defect | Skyline | Calibration curve of Sodiated Adduct not appearing | Brian Pratt | 3 | resolved | |
| 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 | |