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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
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