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Skyline Peptide Search cannot read result files with unusual characters in file/directory names

bugSomething isn't workingSomething isn't working

Status: Open.

#4142 In ProteoWizard/pwiz;

· tolot27 opened on Apr 8, 2026

Peak boundary import fails silently for small molecules with numeric charge column

bugSomething isn't workingSomething isn't working

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

Status: Open.

#4138 In ProteoWizard/pwiz;

· bspratt opened on Apr 7, 2026

Add "mobilogram" display to Full Scan graph for ion mobility data

enhancementNew feature or requestNew feature or request

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

Status: Open.

#4132 In ProteoWizard/pwiz;

· bspratt opened on Apr 2, 2026

Require ExceptionReporter to be set before using CommonActionUtil.RunAsync

enhancementNew feature or requestNew feature or request

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

Status: Open.

#4128 In ProteoWizard/pwiz;

· brendanx67 opened on Mar 31, 2026

Add functional test coverage for graph NodeTips (tooltips)

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4117 In ProteoWizard/pwiz;

· brendanx67 opened on Mar 30, 2026

Using Consensus Library RT for Alignment and Imputation

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4109 In ProteoWizard/pwiz;

· maccoss opened on Mar 26, 2026

Transition > Peptide and Peptide > Protein Median Polish

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4097 In ProteoWizard/pwiz;

· maccoss opened on Mar 24, 2026

DIA-NN Sum Coelution Score

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4096 In ProteoWizard/pwiz;

· maccoss opened on Mar 23, 2026

Median-Continuous Wavelet Transform (CWT)

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4095 In ProteoWizard/pwiz;

· maccoss opened on Mar 23, 2026

RT Loess Normalization

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4094 In ProteoWizard/pwiz;

· maccoss opened on Mar 23, 2026

Skyline MCP Phase 3: Generic UI Interaction Framework

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4089 In ProteoWizard/pwiz;

· brendanx67 opened on Mar 22, 2026

Refactor context menus from SkylineWindow into separate SkylineControl classes

enhancementNew feature or requestNew feature or request

skylineSkyline application changes - create Skyline/work branchSkyline application changes - create Skyline/work branch

todoTracked via ai/todos systemTracked via ai/todos system

Status: Open.

#4073 In ProteoWizard/pwiz;

· nickshulman opened on Mar 11, 2026