All pull requests

Pull requests

• osprey: Added a stamp consistency check to FirstPassFDR's analysis-wide products on load

  osprey
  #4875·brendanx67 opened Oct 19, 2026Member·4 tasks done·

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• skyline: Cherry-pick: Fixed import of mzML from waters_connect - was discarding every spectrum because they were mistaken for lockspray

  skyline
  #4874·bspratt opened Oct 19, 2026Member·4 tasks done·

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  1

• skyline: Added retries for transient network failures in tool downloads

  skyline
  #4851·chambm opened Oct 15, 2026Member·4 tasks done·

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  1

• pwiz: Changed builds to share one x64 pwiz-sharp tree and build Skyline in one session

  pwiz
  #4850·bspratt opened Oct 15, 2026Member·11 of 13 tasks·

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  7

• skyline: Changed AlphaPeptDeep library building to use CarafeSharp in process instead of Python

  skyline
  #4849·nickshulman opened Oct 15, 2026Contributor·9 of 10 tasks·

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  1

• pwiz: Changed build warnings to fail the build after the tests instead of before

  pwiz
  #4844·chambm opened Oct 14, 2026Member·9 of 10 tasks·

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  7

• skyline: Added icon size arguments to the DevTools ImageExtractor

  skyline
  #4839·rita-gwen opened Oct 13, 2026Contributor·5 tasks done·

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  2

• pwiz: Fixed msconvert option parsing and help regeneration issues from code review

  pwiz
  #4836·chambm opened Oct 13, 2026Member·5 tasks done·

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  8

• osprey: Fixed reported protein-group q-values being far below the true error rate

  osprey
  #4823·nickshulman opened Oct 11, 2026Contributor·2 of 3 tasks·

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  5

• skyline: Added observed ion mobility and CCS to chromatogram extraction

  skyline
  #4787·bspratt opened Oct 6, 2026Member·5 of 6 tasks·

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  17

• skyline: Fixed intermittent MSB3021 copy failures in the Skyline build and code inspection

  skyline
  #4769·chambm opened Oct 5, 2026Member·4 of 5 tasks·

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• pwiz: Fixed VendorPinsGenerator compiling concurrently for each Vendor.Common configuration

  pwiz
  #4724·maccoss opened Sep 28, 2026Contributor·4 tasks done·

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• osprey: Added demultiplexing of overlapping-window DIA to Osprey

  osprey
  #4710·maccoss opened Sep 25, 2026Contributor·8 tasks done·

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  8

• skyline: Changed waters_connect CE optimization to read actual CE values

  enhancementskylinevendor
  #4683·rita-gwen opened Sep 18, 2026Contributor·6 tasks done·

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  4

• skyline: Made the .NET build of Skyline system-DPI-aware (issue #4599)

  skyline
  #4602·rita-gwen opened Aug 21, 2026Contributor·7 tasks done·

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  10

• Proteo wizard master

  #4574·kpnovoselov opened Aug 13, 2026·

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  10

• Allow cancelling "Export Report" from JSON Tool Service API

  #4546·nickshulman opened Aug 7, 2026Contributor·

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• Open document directly from .sky.zip without extracting if necessary files are uncompressed

  #4426·nickshulman opened Jul 16, 2026Contributor·4 tasks done·

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  19

• Filter chromatogram extraction on uninterpreted mzML CV/user parameters

  #4422·bspratt opened Jul 15, 2026Member·7 tasks done·

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  47

• Site-determining ion assistant for modification localization

  #4391·rita-gwen opened Jul 8, 2026Contributor·5 tasks done·

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  5

• pwiz: Updated the PSI-MS and UNIMOD CVs and added the Orbitrap Tribrid Apex and Excedion Thermo models

  pwiz
  #4339·chambm opened Jun 29, 2026Member·4 tasks done·

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  4

• pwiz-sharp: added mzPeak format support (read, write, msconvert)

  #4311·chambm opened Jun 17, 2026Member·2 tasks done·

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• skyline: Added Sage DDA search engine to Skyline

  skyline
  #4303·chambm opened Jun 15, 2026Member·2 tasks done·

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  10

• New peak scoring and normalization options

  #4170·nickshulman opened Apr 28, 2026Contributor·

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• Warn when ion mobility filtering is disabled but IM values are available (#4150)

  #4154·bspratt opened Apr 16, 2026Member·1 task done·

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  7