Issues

• AI Connector report timeout can leave subsequent pipe requests unable to connect while Skyline UI remains usable

  ProteoWizard/pwiz#4901 · Filter by author mwfoster opened on Oct 22, 2026
  2

• pwiz: Added monthly pinned releases of Core Windows x86_64 (bt83) and a release archive on the website

  enhancementpwiz
  ProteoWizard/pwiz#4899 · Filter by author chambm opened on Oct 22, 2026
  1

  

• Search .blib RefSpectra lacks the predicted RT and CCS (Osprey and BiblioSpec DIA-NN)

  bugosprey
  ProteoWizard/pwiz#4894 · Filter by author brendanx67 opened on Oct 21, 2026
  

• Detect --resolution (unit vs HRAM) from the data

  enhancementosprey
  ProteoWizard/pwiz#4893 · Filter by author brendanx67 opened on Oct 21, 2026
  

• DIA import fails or can drop points when a spill file's MaxTime equals a demultiplexed scan time

  bugskyline
  ProteoWizard/pwiz#4888 · Filter by author maccoss opened on Oct 21, 2026
  

• Graph precursor and transition areas against precursor parameters (spectrum filter values, m/z, charge)

  enhancementskyline
  ProteoWizard/pwiz#4884 · Filter by author bspratt opened on Oct 20, 2026

• Split chromatogram graph shows blank panes when there are too many precursors to fit

  bugskyline
  ProteoWizard/pwiz#4883 · Filter by author bspratt opened on Oct 20, 2026

• View > Libraries: Ion Types / Fragments visibility ignores UI mode, and Ion Types vanishes on hover in 26.1

  bugskyline
  ProteoWizard/pwiz#4880 · Filter by author bspratt opened on Oct 20, 2026
  

• Revert manual integration for individual peaks

  enhancementskyline
  ProteoWizard/pwiz#4873 · Filter by author bspratt opened on Oct 19, 2026
  1

• Per-molecule calibration: regression fit override, more fit types, and per-molecule calibration level concentrations

  enhancementskyline
  ProteoWizard/pwiz#4872 · Filter by author bspratt opened on Oct 19, 2026

• Bring BiblioSpec.IO to Skyline's string standard: resources and localization inspection, column and type constants, file-content errors as I/O errors

  pwiztech-debt
  ProteoWizard/pwiz#4871 · Filter by author brendanx67 opened on Oct 19, 2026

• Fill the global q-value and PEP columns of a .blib from every BlibBuild reader whose format carries them

  enhancementpwiz
  ProteoWizard/pwiz#4870 · Filter by author brendanx67 opened on Oct 19, 2026

• Remove NHibernate from Skyline: iRT, optimization, ion mobility, chromatogram library, background proteome and MIDAS onto hand-written SQLite readers and writers

  skylinetech-debt
  ProteoWizard/pwiz#4869 · Filter by author brendanx67 opened on Oct 19, 2026
  

• Polarity handling: accept unsigned values for negative-mode data where polarity is otherwise clear, and fix places that drop or mangle polarity

  bugskyline
  ProteoWizard/pwiz#4861 · Filter by author bspratt opened on Oct 17, 2026
  

• pwiz: Demultiplexer performance: profile-guided speed-ups that trade exact intensities, and SCIEX ZT Scan

  performancepwiz
  ProteoWizard/pwiz#4822 · Filter by author brendanx67 opened on Oct 11, 2026
  

• osprey: First-pass training on a 300k subsample is underpowered; seed and near-ties move IDs 6-11%

  ospreyperformance
  ProteoWizard/pwiz#4812 · Filter by author brendanx67 opened on Oct 10, 2026
  1

• Percolator q-values lost for dotted Tide file names and Comet data folders at a drive root

  bugskyline
  ProteoWizard/pwiz#4791 · Filter by author bspratt opened on Oct 7, 2026

• Skyline: Add explicit regression parameters

  ProteoWizard/pwiz#4788 · Filter by author saskema opened on Oct 7, 2026

• Support mixed peptide + small-molecule transition lists

  enhancementskyline
  ProteoWizard/pwiz#4785 · Filter by author bspratt opened on Oct 6, 2026
  

• Import Transition List detects a small-molecule list as peptides, and switching to Molecules doesn't redetect columns

  bugskyline
  ProteoWizard/pwiz#4784 · Filter by author bspratt opened on Oct 6, 2026
  1

  

• Support mixed peptide + small molecule transition lists

  enhancementskyline
  ProteoWizard/pwiz#4775 · Filter by author bspratt opened on Oct 6, 2026
  

• Transition list with small-molecule headers is detected as peptides when the first data row is a valid peptide (e.g. MRFA)

  bugskyline
  ProteoWizard/pwiz#4774 · Filter by author bspratt opened on Oct 6, 2026
  

• osprey: Task validity sidecars record a build version that nothing reads, so a resume adopts another build's artifacts

  bugosprey
  ProteoWizard/pwiz#4764 · Filter by author brendanx67 opened on Oct 3, 2026
  

• osprey: DIA-NN TSV loader truncates modified sequences with 2+ bracketed mass mods, silently dropping 18% of library entries

  ProteoWizard/pwiz#4761 · Filter by author mwfoster opened on Oct 2, 2026

• Carafe library RTs plateau at the end of the gradient, so Osprey loses late eluters

  bugosprey
  ProteoWizard/pwiz#4759 · Filter by author maccoss opened on Oct 1, 2026
  2