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790
Todo
Skyline
Edit > Insert > Peptides lacks the ability to add specific precursors
Nick Shulman
3
open
789
Defect
Skyline
No longer able to reset settings in Tools > Options > Misc tab
Nick Shulman
2
open
21.1
788
Defect
Skyline
Need better handling for IO problems in library load
Brian Pratt
3
open
787
Todo
Skyline
Custom graph background colors - or maybe just Dark Mode - for Skyline
Brian Pratt
3
open
786
Defect
Skyline
Ion mobility library "use results" algorithm improvements
Brian Pratt
3
open
785
Defect
Skyline
Transition Settings - Ion Mobility - Fixed width value not saved when it is all that changes
Brian Pratt
2
open
21.1
784
Defect
Skyline
Improvements to associating raw files with .sky.zip files (for support, Panorama, ???)
Brendan MacLean
3
open
783
Defect
Skyline
small molecule transition list reader should be more tolerant of missing values for InChIKey etc, and should explain properly when it rejects a mismatch
Brian Pratt
3
open
782
Defect
Skyline
allow small molecule precursors to support the full range of retention time matching options found in the isotope modification form
Brian Pratt
3
open
781
Defect
Skyline
allow user to select which files are used in ion mobility library "Use Results"
Brian Pratt
3
open
780
Defect
Skyline
show m/z value in Ion Mobility Library editor window
Brian Pratt
3
open
779
Defect
Skyline
Adapt ion mobility library editor "Use Results" to work with FAIMS data
Brian Pratt
3
open
778
Defect
Skyline
Pasting into the Target window should be on a LongWaitDialog
Brian Pratt
3
open
777
Defect
Skyline
Training IMSDB hangs when raw data files are not present
Brian Pratt
3
open
20.2
776
Defect
Skyline
Standard industry teminology for CCS has landed on "Collision Cross Section", we call it "Collisional Cross Section" and should change that
Brian Pratt
3
open
775
Defect
Skyline
follow up on possible improper parenting of MessageDlg
Brian Pratt
3
open
774
Defect
Skyline
add an error sense to ion mobility filtering in chromatogram extraction, akin to what we do in the RT dimension
Brian Pratt
3
open
773
Defect
Skyline
ImportTransitionListColumnSelectDlg needs a better code page for text
Brian Pratt
3
open
772
Defect
Skyline
ImportTransitionListColumnSelectDlg.CheckForErrors() needs to use a LongWaitDlg
Brian Pratt
1
open
21.1
771
Defect
Skyline
MSP reader should be aware same peptide mods as the rest of Skyline
Brian Pratt
3
open
770
Todo
Skyline
Allow user to select RT display units - currently fixed at minutes, seconds is desirable too
ritach
3
open
769
Todo
Skyline
Support parent ion scanning for Sciex (and Thermo?)
Brian Pratt
3
open
768
Todo
Skyline
Update audit log to use SHA-256 or better
ritach
3
open
21.1
767
Defect
Skyline
Phase 2 work item for hierarchical clustering
Nick Shulman
3
open
766
Todo
Skyline
further enhancements to the Import Transition List column picker
Brian Pratt
3
open
765
Defect
Skyline
Refactor AuditLog hash calculation
ritach
3
open
764
Defect
Skyline
the list of pre-made iRT standards should be filtered based on UI mode - don't present peptide standards for small molecules mode and vice versa
Brian Pratt
3
open
763
Defect
Skyline
Editing iRT standard in Edit iRT Calculator form no longer sets standard to None
Brendan MacLean
3
resolved
20.2
762
Defect
Skyline
enforce or infer setting ion mobilty units for explicit ion mobility values
Brian Pratt
3
resolved
761
Defect
Skyline
User would like to force integration of areas that don't have identifiable peaks
Brendan MacLean
3
open
760
Defect
Skyline
Skyline should probably offer to reimport raw data after user creates or alters an ion mobility library
Brian Pratt
3
open
759
Defect
Skyline
"Use Results" button on the Edit Ion Mobility Library dialog does not fail promptly when raw data is not present
Brian Pratt
3
open
758
Defect
Skyline
Chromatogram peaks should show IM information as well as RT
Brian Pratt
3
open
757
Todo
Skyline
add a display for ion mobility spectrum
ritach
3
open
756
Todo
Skyline
add support for Thermo mzVault small molecule spectral libraries
Guest
3
closed
755
Defect
Skyline
Improved handling of ambiguous entries when importing spectral libraries that are .MSP format database dumps
Brian Pratt
3
open
754
Todo
Skyline
Make Import Peptide Search wizard smarter about isolation schemes
Kaipo
3
open
20.2
753
Defect
Skyline
Value list annotations should not allow empty lists
Brendan MacLean
3
resolved
20.2
752
Todo
Skyline
Add option to use 1-based amino acid position numbering
Kaipo
3
open
21.1
751
Defect
Skyline
When creating IM library from results, don't create high energy offsets that are impossible for the equipment (e.g. positive drift time offset - that should only decrease)
Brian Pratt
3
open
750
Defect
Skyline
small molecule accession numbers in Document Grid should be made editable
Brian Pratt
3
open
749
Defect
Skyline
Reimport after adding new transitions causes new transitions to have #N/A peak areas
Guest
3
closed
20.2
748
Defect
Skyline
Edit>Insert>TransitionList should issue a warning when ignoring an input line because it duplicates or conflicts with an existing transition
Brian Pratt
3
open
747
Todo
Skyline
Import > Assay Library should automatically recognize Water and Ammonia losses
Kaipo
2
open
20.2
746
Defect
Skyline
Retention time alignment makes mouse act out of phase on aligned replicate graphs
matt.chambers42@gmail.com
3
resolved
20.2
745
Defect
Skyline
qualification in skyline
Guest
3
closed
744
Defect
Skyline
qualification 偶发
Guest
3
closed
743
Documentation
BiblioSpec
Create Bibliospec library (.blib) using Tabular text input (.tsv)
Guest
1
closed
740
Todo
Skyline
Change the scale of the peptide intensity
Brendan MacLean
3
open
739
Defect
Skyline
setup.exe fails on Windows Server 12 and 16
Guest
3
closed
738
Defect
Skyline
issue to download Skyline 64bit
Guest
3
closed
737
Defect
Skyline
Webinar #19: Ion Mobility Spectrum Filtering with Skyline some problem encounter
Guest
3
closed
736
Defect
Skyline
Webinar #19: Ion Mobility Spectrum Filtering with Skyline some problem encounter
Guest
3
closed
735
Todo
Skyline
Skyline should attempt BlibBuild conversion when confronted with a spectral library whose format is not natively supported
Brian Pratt
3
open
734
Defect
Skyline
Enable joining partial .skyd files when the filenames do not have a hash
Vagisha
3
open
733
Todo
Skyline
Can Skyline export the protein intensities?
Guest
3
closed
20.2
732
Defect
Skyline
Exporting user-defined reports from command line
Brendan MacLean
3
resolved
731
Defect
Skyline
Varying small molecule implementations of .MSP format aren't handled well by Skyline
Brian Pratt
3
open
730
Defect
Skyline
Peak MS1 integration with FAIMS
matt.chambers42@gmail.com
2
open
729
Defect
Skyline
Confusing progress indicator behavior on SRM import when targeted transitions are less intense than other unmatched transitions - it just shows grey
Brian Pratt
3
open
728
Defect
Skyline
AutoQC: retry upload to Panorama if upload fails due to network error
Vagisha
3
open
727
Defect
Skyline
Panorama upload issues
Vagisha
3
open
20.2
726
Defect
BiblioSpec
Skyline nonredundant blib format to MS2 conversion
matt.chambers42@gmail.com
3
resolved
725
Defect
Skyline
Need to improve inference of ionization type when reading small molecule .MSP files
Brian Pratt
3
resolved
724
Defect
Skyline
Import multiple files as a single run for iRT calibration
Kaipo
3
open
20.2
723
Defect
Skyline
Precursors per sample injection think's it is transitions per sample injection
Brendan MacLean
3
open
722
Defect
Skyline
How can I put z+1 ions in the fragments list for ETD?
Brendan MacLean
2
open
21.1
721
Defect
Skyline
Skyline cannot properly analyze Agilent QQQ with waste diverter in the beginning of the run
Brendan MacLean
3
open
720
Defect
Skyline
Upload to Panorama fails when There are custom annotations for the Transitions
Brendan MacLean
3
resolved
719
Defect
Skyline
Calibration curve of Sodiated Adduct not appearing
Brian Pratt
3
resolved
718
Todo
Skyline
Allow overlay of QC traces on chromatograms
Brendan MacLean
3
open
717
Defect
Skyline
Improve handling of unknown adducts in small molecule transition reader (exception on seeing adduct "[+]" not caught gracefully)
Brian Pratt
3
open
716
Defect
Skyline
When light and heavy precursors have different sets of transitions, all quantifiable transitions should be summed when calculating Light:Heavy ratios
Guest
3
closed
21.1
715
Defect
Skyline
Prosit not available
Brendan MacLean
3
open
714
Defect
Skyline
Question about Data upload to panorama
Guest
3
closed
713
Defect
Skyline
Unable to view or explore spectral libraries in Skyline Daily
Guest
3
closed
712
Defect
Skyline
Acetyl 2H(3) K modification disappears on heavy en medium peptides, when library is created from Maxquant
matt.chambers42@gmail.com
2
resolved
711
Defect
Skyline
Troubles with skyline document file upload to LabKey Server
Vagisha
3
open
710
Defect
Skyline
Skyline Unistall problems
Guest
3
closed
709
Defect
Skyline
Potentially possible to do a better job at routing external tool support requests to tool-specific support boards
Brendan MacLean
4
open
708
Defect
Skyline
Renaming a molecule in Targets tree causes Skyline to miscalculate mass of transition with heavy label adduct
Brian Pratt
3
resolved
19.2
707
Defect
Skyline
Default report names stuck in installation language
Nick Shulman
3
open
21.1
706
Defect
Skyline
Peptide data not imported for a few peptides
Brendan MacLean
3
open
705
Defect
Skyline
Too much audit logging for Refine > Accept Peptides
ritach
3
open
704
Defect
Skyline
Skyline silently fails reading FASTA files with sequences in lowercase
Brian Pratt
3
open
703
Defect
Skyline
Nightly tutorial tests should not always re-download data sets - makes us too vulnerable to temporary outages
Guest
3
closed
702
Defect
Skyline
Illegal character is phosphopeptide sequence
Brendan MacLean
3
resolved
701
Defect
Skyline
Malfunctioning of the reintegration tool
Brendan MacLean
3
resolved
700
Defect
Skyline
Malfunctioning of the reintegration tool
Guest
3
closed
699
Defect
Skyline
Malfunctioning of the reintegration tool
Guest
3
closed
698
Todo
Skyline
Add Mass Errors to Spectrum Match graph
ritach
3
open
697
Defect
Skyline
import wizard should not ask about ion mobility handling if the files to be imported don't contain any IM info
Brian Pratt
3
resolved
696
Defect
Skyline
library filename extensions are case sensitive (e.g. Skyline recognizes "foo.msp" but not "foo.MSP")
Brian Pratt
3
resolved
19.2
695
Defect
Skyline
Failed importing results DIA
Guest
3
closed
694
Defect
Skyline
Audit Log records a failed operation and does not roll it back
Tobias Rohde
3
open
693
Todo
Skyline
Improve "Apply Peak to All" peak matching
Kaipo
3
open
692
Todo
Skyline
Change some default settings
Brendan MacLean
3
open
19.2
691
Defect
Skyline
Limiting Transition Settings - Instrument - Max m/z has unintended consequences on spectral library transition picking
Kaipo
2
open
19.2
690
Defect
Skyline
Before starting a new Import > Results we need to check that Decoys are representative of the Targets
Kaipo
2
open
19.2
689
Defect
Skyline
File > Export > Spectral Library losing information from small molecule documents
Brian Pratt
2
open
19.2