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 Matt Chambers 2 open 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 Matt Chambers 1 open 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 Matt Chambers 2 open 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 Brian Pratt 3 open 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 Nick Shulman 3 open 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. Matt Chambers 2 open 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 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 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 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 Guest 2 closed 22.2 914 Defect Skyline Proteomics features still showing in small molecule mode Guest 3 closed 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 Guest 3 closed 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 Guest 2 closed 23.1 906 Defect Skyline A few details working with Bruker PASER assay library lists Guest 3 closed 22.2 905 Defect Skyline IndexOutOfRangeException bringing up GraphFullScan immediately after modifying the document Rita Chupalov 3 resolved 22.2 904 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