891 Defect Skyline Adjusting peak boundaries with non-quantitative transitions is confusing Nick Shulman 3 open 22.1 890 Defect Skyline Audit log Skyline Version upgrade Kaipo 3 open 22.1 889 Todo Skyline Make more instrument parameters available on Files in the Document Grid matt.chambers42@gmail.com 3 open 22.1 888 Defect Skyline File > Import > Peptide Search with existing library reports the build settings in the Audit Log Nick Shulman 3 open 22.1 887 Defect Skyline Smooth handling of .skyp file for server lacking credentials Kaipo 3 open 22.1 886 Defect Skyline AutoQC Loader stops scrolling log text area after a wrapped line Vagisha Sharma 3 open 22.1 885 Defect Skyline Dotp line graph points should be clickable for changing the active replicate ritach 3 open 22.1 884 Defect Skyline Some user are really unhappy that they can't type transition lists into Skyline like they used to do Brian Pratt 3 open 883 Documentation Skyline Update tutorials with new library building interface Guest 2 closed 882 Todo Skyline Clean out apparent IMS related cruft in Full Scan tab Guest 3 closed 881 Defect Skyline Move Bruker timsTOF method export into BuildMethod Kaipo 3 open 880 Todo Skyline SSL format changes for Feature Detection Brian Pratt 3 open 22.1 879 Defect Skyline Need some way to show user FAIMS information in raw scan view, to demystify jagged chromatograms before IM filters are applied Brian Pratt 3 open 878 Defect Skyline Need to handle retention time shifts for deuterated internal standards Brian Pratt 3 open 877 Defect Skyline "How Skyline Calculates Peak Areas and Heights" tip could use updating Brendan MacLean 3 open 876 Defect Skyline Typo in "Skyline Small Molecule Method Development and CE Optimization" tutorial Nat Brace 3 open 875 Defect Skyline The adduct pick list (as used in Modify... in Targets tree) should include [M+] and [M-] Guest 3 closed 874 Defect Skyline Default Win32 MAX_PATH value of 260 is too small for some users Brian Pratt 3 open 873 Defect Skyline Feature request: single molecule/peptide re-integration Brendan MacLean 3 open 872 Defect Skyline Document created by an m/z-only transition list should not depend on list order Guest 3 closed 22.1 871 Defect Skyline Clean up the interaction of small molecule transition list imports and Transition Settings that affect precursor isotope ([M+1], [M+2] etc) creation Brian Pratt 1 open 22.1 870 Todo Skyline Implement special peak statistics for DDA MS/MS Nick Shulman 1 open 22.1 869 Todo Skyline Add a Prosit RT calculator parallel to SSRCalc Kaipo 3 open 868 Todo Skyline Consider generating a dictionary of less common isotopes instead of hardcoding them piecemeal in response to user requests Brian Pratt 3 open 867 Todo Skyline Possible Improvements to Edit>Insert>TransitionList Brian Pratt 3 open 22.1 866 Defect Skyline Provide option in Skyline to upload a minimized library to Panorama Guest 3 closed 22.1 865 Defect Skyline Adding heavy mods in Peptide Settings does not add "Ratio to Heavy" normalization to Quantification tab Guest 1 closed 21.2 864 Defect Skyline Various issues reading this small molecule transition list with heavy label formulas Guest 3 closed 22.1 863 Defect Skyline Problem loading a small mol document with isotope labels - Skyline complains that they aren't known modifications (which should not matter) Guest 3 closed 22.1 862 Defect Skyline "Importing Results..." window should resize its multi-file progress control when there's a vertical scrollbar in use (currently cuts off the "Cancel" buttons and looks funny) Guest 3 closed 22.1 861 Todo Skyline Implement better peptide to protein assignment strategies for target selection matt.chambers42@gmail.com 2 open 22.1 860 Defect Skyline Support more than one fragment specification per line in transition list column picker, for small molecules at least Brian Pratt 3 open 859 Defect Skyline Add peak apex CCS to Transition Result Nick Shulman 3 open 22.1 858 Defect Skyline make "ImportPeptideSearch with the IMS filtering visible" a form view that can be shown in the SkylineTester Forms tab Guest 3 closed 22.1 857 Defect Skyline ImportTransitionListColumnSelectDlg lags a bit when associate proteins checked Brendan MacLean 3 resolved 21.2 856 Defect Skyline When training a "Default" peak scoring model, the model should be able to use feature scores that are present for some but not all peptides Guest 3 closed 22.1 855 Defect Skyline Log scale with median normalization does not mention the normalization in the y-axis label Nick Shulman 3 open 21.2 854 Defect Skyline Peak Areas - Replicate Comparison - Normalize to strangely chooses poorly Brendan MacLean 2 resolved 21.2 853 Defect Skyline Remove peak should make dotp annotations and line missing Guest 1 closed 21.2 852 Defect Skyline Full-Scan graph no longer auto-scales the y-axis when clicking arrow buttons Brendan MacLean 2 resolved 21.2 851 Todo Skyline Rename auto trained peak scoring models Kaipo 3 open 22.1 850 Defect Skyline Fix performance issue with ion moblity filtering in library viewer Brian Pratt 3 open 22.1 849 Defect Skyline Failure opening .sky file saying audit log entry has been modified Brendan MacLean 2 resolved 21.2 848 Defect Skyline Show a better error message if check for Panorama server fails Vagisha Sharma 3 open 22.1 847 Defect Skyline Add option to use explicit RT instead of measured for exporting scheduled methods Kaipo 3 open 846 Defect Skyline Trouble exporting polarity-switching QQQ method from Skyline to Agilent-6495C Kaipo 3 open 845 Defect Skyline User says Agilent 6495C can go down to a dwell time of 0.5ms, but we insist on integer dwell times in UI Kaipo 3 open 844 Defect Skyline Libraries should load without error even if the directory that the library is in is not writeable. Guest 2 closed 21.2 843 Defect Skyline Update "_elementMasses" in MaxQuantReader.cpp Guest 2 closed 21.2 842 Todo Skyline Add a setting for RT annotation display to Chromatogram graph right-click > properties form Guest 2 closed 841 Defect Skyline Insert Transition List with heavy precursors results in document that cannot be opened. Guest 2 closed 840 Defect Skyline is M+Na precursor being handled properly in display of split graphs and heat maps, and is it being used properly in SONAR extraction? Guest 3 closed 839 Defect Skyline Inconsistent representation of "squared" in IM peak display on chromatogram graphs Guest 3 closed 838 Defect Skyline initial zoom on ion mobility heat map should not default to zero as lower range Guest 3 closed 21.1 837 Defect Skyline Import Peptide wizard "Configure Full-Scan Settings" IMS stuff should have its own page/step Guest 3 closed 21.1 836 Defect Skyline Certain TransitionSettings>Library tab controls dealing with product ion filtering should be declared as proteomic Guest 3 closed 21.2 835 Defect Skyline Audit verification error after minimizing and sharing Skyline document ritach 3 open 834 Defect Skyline Precursors for the same peptide with same precursor m/z get lost in the .skyd file Guest 2 closed 833 Todo Skyline Show rdotp in Peak Areas > Replicate Comparison plot when Normalize To > Heavy is chosen Guest 3 closed 21.2 832 Defect Skyline Improve ZedGraph handing of clipboard exceptions Guest 3 closed 21.2 831 Defect Skyline Change or add an option for MS/MS spectrum graph dotp value in mirror plot with Prosit ritach 2 open 22.1 830 Todo Skyline Add a "High resolution" check box to Transition Settings - Library - Ion match tolerance ritach 3 open 22.1 829 Todo Skyline Change reports to report 1-based AA positions Guest 3 closed 21.2 828 Todo Skyline Make it possible to see RT with more precision in chromatogram graphs Brian Pratt 3 closed 22.1 827 Defect BiblioSpec X! Tandem point mutations not understood by BlibBuild Kaipo 2 open 22.1 826 Defect Skyline Choosing an existing standard during Assay Library import fails to add library spectrum to BLIB Kaipo 3 open 21.2 825 Todo Skyline SDRF Reports Nick Shulman 3 open 22.1 824 Todo Skyline Implement command-line option --import-peak-boundaries Guest 3 closed 22.1 823 Todo Skyline Make it easier to export FASTA file of the proteins in the targets window Brian Pratt 3 open 822 Defect Skyline Show Prosit spectrum always when Mirror is on ritach 3 open 22.1 821 Todo Skyline Expand multiple selection handling in chromatogram graphs to handle precursors Kaipo 3 open 820 Defect Skyline Ion Mobility Library editor should offer to wipe CCS value when IM value is altered Brian Pratt 3 open 819 Todo Skyline Implement new option to synchronize integration Brendan MacLean 2 resolved 21.2 818 Todo Skyline BlibBuild needs to write more information to .blib files Guest 2 closed 817 Todo Skyline Small molecule support for Import > Transition > List column picker Guest 1 closed 21.2 816 Todo Skyline File>Share should offer to include a selection of raw files Brian Pratt 3 open 815 Todo Skyline Settings UI should offer choices when a change is made that would break consistency Brendan MacLean 3 open 22.1 814 Todo Skyline Need a way to more easily run all tests that produce audit logs Guest 3 closed 21.2 813 Defect Skyline tidy up user-facing notation for mass-only fragments, and adjust sense of "[M-]", "[M+2]" etc to means "inherently charged, m/z to mass conversion is simple multiplication, no particles lost/gained" Brian Pratt 3 open 812 Todo Skyline Calculate and store peak skewness/asymmetry value Nick Shulman 2 open 22.1 811 Defect Skyline deal with the TODO from commit "When adding small molecule library values to a document, just ignore any fragment peaks with absurdly small or large m/z values" Brian Pratt 3 open 810 Defect Skyline Manage Reports - Copy button still has "Open View Editor" menu item Guest 3 closed 21.2 809 Todo Skyline Implement better searching in Library Explorer for small molecules Guest 3 closed 808 Todo Skyline Change Targeted to PRM and add a SureQuant option to Acquisition method list Guest 3 closed 21.2 807 Defect Skyline Fix/Improve File > Export > Spectral Library Brendan MacLean 3 resolved 21.2 806 Defect Skyline "Column1", "Column2" etc generated headers in the column picker should be localized. Guest 3 closed 805 Defect Skyline Stopping SkylineTester does not abort the second run of SkylineNightly Guest 3 closed 804 Todo Skyline Implement simple filtering for MSP file import Brian Pratt 3 open 803 Todo Skyline Retain previous iRT values in iRT databases Guest 2 closed 22.1 802 Todo Skyline Add "Synchronize Integration" option Guest 3 closed 21.2 801 Defect Skyline BiblioSpec MaxQuant reader should look for all necessary raw data files and issue a block error about any that are missing Guest 3 closed 21.2 800 Defect Skyline BiblioSpec MaxQuant reader should look in parent folders for raw data files Guest 3 closed 21.2 799 Todo Skyline Improve Library Match behavior when precursor not selected Brendan MacLean 3 resolved 22.1 798 Todo Skyline When missing chromatograms but we have a RT prediction, we should graph that Nick Shulman 3 open 22.1 797 Todo Skyline Transitions Split Graph confusing for multiple precursor charges Nick Shulman 3 open 22.1 796 Defect Skyline Import Transition List column picker is too sticky Guest 3 closed 21.1 795 Defect Skyline Import Peptide Search library build with Automatic iRT leaves standard peptides hidden Guest 3 closed 21.1 794 Defect Skyline Unable to deselect (or remove) the Prosit library for library matching in Molecule UI Guest 3 closed 793 Todo Skyline Create a way to limit the set of replicates immediately under analysis without removing replicates Nick Shulman 3 open 792 Defect Skyline trying to type an adduct description into the Modify... popup is maddening, cursor location keeps jumping back to start of line Guest 3 closed