| | | | | | | | |
| 1016 | Todo | Skyline | Use new "Associate Proteins" dialog in other places proteins are associated | Matt Chambers | 3 | open | |
| 1015 | Defect | Skyline | Glycan idotp values incorrect until close and re-open document | Brendan MacLean | 3 | resolved | 23.2 |
| 1014 | Defect | Skyline | Immediate Window does not support ESC to focus the Targets View | Brendan MacLean | 3 | open | 23.2 |
| 1013 | Todo | Skyline | Consider adding ability to filter MS/MS during DDA import peptide search | Matt Chambers | 3 | open | 23.2 |
| 1012 | Defect | Skyline | Ratio to Heavy not available in small molecule mode until heavy precursors added | Brian Pratt | 3 | open | 23.2 |
| 1011 | Defect | Skyline | Out of Memory Error for Yeast.hlf in MethodEdit tutorial on Polish system | Brendan MacLean | 2 | open | 23.2 |
| 1010 | Todo | Skyline | Add shortcuts for Peptide Settings and Transition Settings | Brendan MacLean | 2 | open | 23.2 |
| 1009 | Defect | Skyline | bottleneck in spectral library viewer when attempting to access ion mobility values | Brian Pratt | 3 | open | |
| 1008 | Defect | Skyline | include more .D metadata in Skyline replicates | Matt Chambers | 3 | open | |
| 1007 | Defect | Skyline | ModificationMatcher over guesses with Acetyl modifications | Nick Shulman | 2 | open | 23.2 |
| 1006 | Defect | Skyline | ImportTransitionListColumnSelectDlg too trusting of column header names | Brian Pratt | 3 | open | 23.2 |
| 1005 | Todo | Skyline | Add support for setting Settings > Integrate All from the command-line | Matt Chambers | 2 | open | 23.2 |
| 1004 | Todo | Skyline | Add support for adding modifications from the command-line | Brendan MacLean | 2 | open | 23.2 |
| 1003 | Defect | Skyline | Fix TransitionGroup.GetTransitions() for small molecules to use library information when available | Brendan MacLean | 3 | open | 23.2 |
| 1002 | Defect | Skyline | trouble with transition list created with our own document grid export | Brian Pratt | 3 | open | |
| 1001 | Defect | Skyline | need exceptiion handling for bad MoleculeMassOffset.SplitFormulaAndMasses input | Brian Pratt | 3 | open | |
| 1000 | Defect | Skyline | When reading peptide transition lists we should offer to apply document settings - adding reporter ions, other precursor charges etc. | Brendan MacLean | 3 | open | |
| 999 | Defect | Skyline | Investigate using ExcludeFromAssay field from DIA-NN | Brendan MacLean | 3 | open | |
| 998 | Defect | Skyline | Fix issues with matching DIANN speclib to report TSV | Matt Chambers | 3 | open | |
| 997 | Defect | Skyline | We should allow adducts with formulaic losses on mass-only molecule description (e.g. don't complain that Adduct "[M-CO2]-" calls for removing more C atoms than are found in the molecule [+331.977251]) | Brian Pratt | 3 | open | |
| 996 | Todo | Skyline | Feature detection could be reworked to parallelize tasks | Brian Pratt | 3 | open | |
| 995 | Todo | Skyline | Import Peptide Search should default to no decoys when Library.UseExplicitPeakBounds will be used | Matt Chambers | 3 | open | 23.2 |
| 994 | Todo | Skyline | File > Import > Peptide Search - FASTA page should have Peptide Settings - Filter options | Matt Chambers | 3 | open | 23.2 |
| 993 | Defect | Skyline | Weirdness in the raw data view when switching from IM-containing replicate to non-IM replicate | Rita Chupalov | 3 | open | 23.2 |
| 992 | Defect | Skyline | DIA-NN Speclib handling in BlibBuild mishandles n-terminal mods | Guest | 2 | closed | 23.2 |
| 991 | Defect | Skyline | We should add a "Run" submenu to Skyline's File menu, and move Feature Detection, Encyclopedia, and peptide search engines there from the "Import" menu | Brian Pratt | 3 | open | |
| 990 | Todo | Skyline | Clean up Transition Settings and IMS arguments in command-line documentation | Brian Pratt | 3 | open | 23.2 |
| 989 | Todo | Skyline | Need to add new coverage for Peptide Settings changes by command-line | Guest | 1 | closed | 23.2 |
| 988 | Defect | Skyline | Need to normalize Transition Settings change command-line output | Guest | 3 | closed | 23.2 |
| 987 | Defect | Skyline | Displaying tooltip for protein sometimes takes a really long time when "Enforce Uniqueness" is enabled | Brian Pratt | 3 | open | |
| 986 | Defect | Skyline | Make ion mobility library editor searchable | Brian Pratt | 3 | open | |
| 985 | Defect | Skyline | Target tree's Find function results window says "Peptide" where it should say "Molecule" | Brian Pratt | 3 | open | |
| 984 | Defect | Skyline | "zombie chromatograms" complicate merging of Skyline files | Nick Shulman | 3 | open | |
| 983 | Defect | Skyline | manually modifying molecule mass does not modify the m/z of precursor transitions below | Brian Pratt | 3 | open | |
| 982 | Todo | Skyline | Improved error message when user tries to File>Open a mass spec data file in Skyline | Brian Pratt | 3 | open | |
| 981 | Defect | Skyline | CE optimization does not work for SCIEX QTOF instruments | Matt Chambers | 3 | open | |
| 979 | Defect | Skyline | Support isotope nomenclature like "[13C]3H7[15N]O2" (that's C'3H7N'O2 in Skyline-speak) | Brian Pratt | 3 | open | |
| 978 | Defect | Skyline | Need a way to represent targets that were dimers in the IMS stage but broke into monomers in the MS stage | Brian Pratt | 3 | open | |
| 977 | Defect | Skyline | Need a way to import and display keys other than InChI, SMILES, KEGG etc - e.g. "METLIN ID" | Brian Pratt | 3 | open | |
| 976 | Defect | Skyline | Library Explorer: Allow for searching within peptide/molecule description | Brian Pratt | 3 | open | |
| 975 | Todo | Skyline | feature request: User-editable keyboard shortcuts for menu items | Brendan MacLean | 3 | open | |
| 974 | Defect | Skyline | OpenDataSourceDialog WIFF/WIFF2 data type causes file selection to be painful | Brendan MacLean | 2 | resolved | 23.2 |
| 973 | Todo | Skyline | Add a way to add annotation definitions to a Skyline document from the command-line | henrytsanford | 2 | open | 23.2 |
| 972 | Defect | Skyline | Feature: Export mProphet features from commandline | henrytsanford | 3 | open | |
| 971 | Defect | Skyline | Small molecule transition list reader could be more clever about setting formulas | Brian Pratt | 3 | open | |
| 970 | Todo | Skyline | Feature request: Right click on molecule in the molecule tree to “Add to iRT Database” | Brendan MacLean | 3 | open | |
| 969 | Defect | Skyline | Trouble handling transition lists that declare precursor isotopes | Brian Pratt | 3 | open | |
| 968 | Defect | Skyline | NullReferenceException when uploading to a saved Panorama URI | Vagisha Sharma | 3 | open | |
| 967 | Defect | Skyline | Create matching small molecule versions of all standard peptide reports in Document Grid | Guest | 3 | closed | |
| 966 | Todo | Skyline | "Mobiligram" display for ion mobility filtered chromatograms (alternate view to our ion mobility heatmap) | Rita Chupalov | 3 | open | |
| 965 | Todo | Skyline | Add command arg to SkylineRunner.exe to run any instance of Skyline by path | Brendan MacLean | 3 | open | 23.2 |
| 964 | Defect | Skyline | Feature Request - Surrogate calibration curves | Guest | 3 | closed | |
| 963 | Defect | Skyline | Feature Request - Remove Replicate/Result from Chromatogram or Replicate Right-click menu | Brendan MacLean | 3 | open | |
| 962 | Defect | Skyline | Find CCS values for targets not found in an IMSDB library without changing existing values | Brendan MacLean | 3 | open | |
| 961 | Todo | Skyline | Show units for pressure traces in Skyline chromatograms and enable Panorama to do the same | Matt Chambers | 3 | open | 23.2 |
| 960 | Defect | Skyline | Chinese language update: "Centroided" in the drop down list can be translated as 中心对称的 | Brendan MacLean | 2 | open | 23.1 |
| 959 | Todo | Skyline | Improve error message for BlibBuild failures | Brendan MacLean | 2 | resolved | 23.1 |
| 958 | Defect | Skyline | add the Skyline version to the "More Info" text in alert dialogs | Guest | 3 | closed | |
| 957 | Todo | Skyline | Duplicated collision energy settings for SCIEX instruments | Rita Chupalov | 3 | open | |
| 956 | Defect | Skyline | Support for importing results from the Sage search engine | Brian Pratt | 3 | open | |
| 955 | Defect | Skyline | "Associate Proteins" should not remove unmapped peptides from the document. | Guest | 2 | closed | 23.1 |
| 954 | Defect | Skyline | some interesting small molecule transition list weirdness | Brian Pratt | 3 | open | |
| 953 | Defect | Skyline | add a code inspection test to check that the start page Tutorials tab uses the same links as the Tutorials tests | Brian Pratt | 3 | open | |
| 952 | Todo | Skyline | Strategies for reducing ExceptionWeb reports for already-solved issues | Brian Pratt | 3 | open | |
| 951 | Defect | Skyline | Spectral Library ion mobility values don't work intuitively in document grid and method export | Brendan MacLean | 3 | open | |
| 950 | Todo | Skyline | Investigate more efficient sorting of three-array IMS scans - possibly the locally sorted "sawtooth" nature of the mz could be exploited | Guest | 3 | closed | |
| 949 | Defect | Skyline | Peak Areas > Peptide Comparison view should not show a "heavy" pane with nothing in it | Brendan MacLean | 3 | resolved | 23.1 |
| 948 | Todo | Skyline | Make Import Assay Library work for small molecules | Brian Pratt | 3 | open | |
| 947 | Defect | Skyline | IMS spectrum viewer less reliable than it used to be | Brendan MacLean | 2 | resolved | 22.2 |
| 946 | Todo | Skyline | Renaming a molecule in small molecules breaks associations | Guest | 2 | closed | |
| 945 | Todo | Skyline | Add a splitter to Unique Peptides form | Brendan MacLean | 3 | resolved | |
| 944 | Defect | Skyline | Peak area plotting still deceiving when transforms are applied to the chromatograms | Brendan MacLean | 3 | resolved | |
| 943 | Defect | Skyline | Importing BLIB into IMSDB, we should take mean of multiple IM values instead of creating multiple entries | Brian Pratt | 3 | open | |
| 942 | Todo | Skyline | Add Start Time and End Time to spectrum properties | Rita Chupalov | 3 | open | 23.1 |
| 941 | Defect | Skyline | Red and green dots in Targets tree should be customizable colors, or different shapes | Mark Belanger | 3 | open | |
| 940 | Defect | AutoQC | Add sample file filtering option to AutoQC Loader | Vagisha Sharma | 3 | open | |
| 939 | Defect | Skyline | Off-by-one in Enzyme.GetMatches() dealing with protein C-terminus | Guest | 3 | closed | 23.1 |
| 938 | Todo | Skyline | Add property sheets to spectrum graphs | Brendan MacLean | 2 | resolved | 23.1 |
| 937 | Defect | Skyline | DIA Umpire tests are much slower for languages with a comma decimal separator | Matt Chambers | 2 | open | 23.1 |
| 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 | Guest | 3 | closed | |
| 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 | Brendan MacLean | 2 | resolved | 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 | Brendan MacLean | 3 | resolved | 23.1 |
| 921 | Todo | Skyline | Transition list reader should identify special ions by m/z the same way it does calculated peptide fragment ions | Brendan MacLean | 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 |