| | | | | | | | |
| 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 | Matt Chambers | 3 | open | 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 | |
| 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 | |