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