1056 Defect Skyline "Copy Data" for IMS heatmap display in Full Scan view is broken Brian Pratt 3 open 1055 Defect Skyline Alert user when importing ion mobility data when there are IM filter values available (explicit, imsdb, blib) but IM filtering is disabled Brian Pratt 3 open 1054 Defect Skyline NIST .msp peptide descriptions with n and c terminal notation (e.g. "… …Name: n[43]ALAVLALLSLSGLEAIQR/5" or "Name: AACDEFGHIKc[17]/3") are being ignored Brian Pratt 3 open 1053 Defect Skyline Target tree allows for manual creation of nonsense molecules e.g. "U-H2O" Brian Pratt 3 open 1052 Defect Skyline AlphaPeptDeep wording suggestions Brendan MacLean 4 open 25.2 1051 Defect Skyline Too many LongWaitDlgs during AlphaPeptDeep library building dshteyn 3 open 25.2 1050 Defect Skyline AlphaPeptDeep output files need to be written somewhere outside the Skyline.exe/Tools folder dshteyn 2 open 25.2 1049 Todo Skyline Users need to be able to tell Skyline that they have GC EI data Guest 3 closed 1048 Defect Skyline Retention Times - Peptide Comparison graph is not UI mode aware Brian Pratt 3 open 1047 Defect Skyline improve SkylineCmd's handling of unrecognized transition list column names Brian Pratt 3 open 1046 Todo Skyline command line needs the ability to remove named replicates from document Brendan MacLean 3 open 1045 Todo Skyline Users would like settable colors for each molecule Brendan MacLean 3 open 1044 Todo Skyline Add .sdf file support for spectral library creation Brendan MacLean 3 open 1043 Defect Skyline Provide for manual adjustmen of IM integration as we do for RT Brian Pratt 3 open 1042 Todo Skyline Library Explorer should show iRT information when it is present in a BLIB file Rita Chupalov 3 open 24.2 1041 Defect Skyline MSGF+ Installation form does not copy text Brendan MacLean 3 resolved 24.2 1040 Todo Skyline Import DIA Peptide Search should suggest using a prespecified isolation scheme based on the data Matt Chambers 3 open 24.2 1039 Defect Skyline Import DDA Peptide Search produces different replicate name sort order than Import DIA Peptide Search Matt Chambers 3 open 24.2 1038 Todo Skyline Import DIA Peptide Search never suggests chromatogram extraction files Matt Chambers 2 open 24.2 1037 Defect Skyline Documents with lots of mods can get very slow for Import > Transition List Brendan MacLean 3 open 24.2 1036 Todo Skyline Mass spec files contain metadata that could usefully be preserved as annotations on replicates in Skyline Brian Pratt 3 open 1035 Todo Skyline Add Mirror and Koina menu options to Full-Scan graph Brendan MacLean 3 open 24.2 1034 Todo Skyline Add mirror plot option to chromatogram graphs Rita Chupalov 3 open 24.2 1033 Defect Skyline Fix Normalize To > Heavy Peak Areas - Replicate plot to show rdotp line graph Brendan MacLean 2 resolved 24.2 1032 Todo Skyline Skyline needs at least one default report that just gives peak areas for all replicates Nick Shulman 3 open 24.2 1031 Defect Skyline Molecule reports show up in Document Settings - Reports when in proteomics mode Brian Pratt 3 open 24.2 1030 Defect Skyline Small molecule improvements are predicted RT Brian Pratt 3 resolved 1029 Todo Skyline Integrate Carafe into Peptide Settings - Library - Build xgwang 2 open 24.2 1028 Todo Skyline Integrate AlphaPeptDeep prediction into Peptide Settings - Library - Build xgwang 2 open 24.2 1027 Todo Skyline Skyline DDA Searches that use Percolator need to calculate all-files-q-values Brendan MacLean 2 resolved 24.2 1026 Defect Skyline Peak Areas - Relative Abundance includes decoys by default Rita Chupalov 2 open 24.2 1025 Defect Skyline Feature finding should provide information in terms of the expected peptides in a document - what's novel in the search result, what's missing Brian Pratt 3 open 1024 Todo Skyline Support transition list "Note" import for all node levels (molecule, precursor, transition) Guest 3 closed 1023 Defect Skyline ArgumentOutOfRangeException scrolling "Ion Types" context menu Rita Chupalov 2 open 24.2 1022 Defect Skyline idFileName column values are not set in minimized libraries. Vagisha Sharma 3 open 1021 Defect Skyline Discourage training mProphet models when explicit peak boundaries are being used from libraries Guest 3 closed 23.2 1020 Defect Skyline Transition Full Scan Settings page should discourage user from using retention time filtering with PRM Guest 3 closed 23.2 1019 Defect Skyline Confusing behavior of ID lines on chromatograms when library has multiple charge states Nick Shulman 3 open 23.2 1018 Defect Skyline Adducts should not attempt formula math when the molecule is described as mass only Guest 3 closed 1017 Defect Skyline Menuitem enabling needs cleanup for Spectrum Match settings Rita Chupalov 3 open 23.2 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 resolved 1008 Defect Skyline include more .D metadata in Skyline replicates Matt Chambers 3 open 1007 Defect Skyline ModificationMatcher over guesses with Acetyl modifications Brendan MacLean 2 resolved 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 Brendan MacLean 2 resolved 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 resolved 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]) Guest 3 closed 996 Todo Skyline Feature detection could be reworked to parallelize tasks Brian Pratt 3 resolved 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 resolved 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 resolved 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 resolved 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