Issues

• Set up Jenkins testing

  smith-chem-wisc/ProteoformSuite#524 · Filter by author acesnik opened on Sep 10, 2018

• Fill in gaps in identification code testing

  Testing
  smith-chem-wisc/ProteoformSuite#523 · Filter by author acesnik opened on Sep 7, 2018
  1

• Biological deamidation special cases

  Improve FeatureNew Feature
  smith-chem-wisc/ProteoformSuite#522 · Filter by author acesnik opened on Sep 6, 2018

• Tidying up DLLs ... or make an installer to put the DLLs far away

  GUI EnhancementImprove Feature
  smith-chem-wisc/ProteoformSuite#502 · Filter by author acesnik opened on Apr 11, 2018
  1

• Lollipop fields -> properties

  Code Quality
  smith-chem-wisc/ProteoformSuite#496 · Filter by author acesnik opened on Feb 27, 2018

• Automatically optimizing parameters

  New Feature
  smith-chem-wisc/ProteoformSuite#486 · Filter by author acesnik opened on Feb 6, 2018
  2

• Create a .pdf user manual

  Documentation
  smith-chem-wisc/ProteoformSuite#485 · Filter by author leahvschaffer opened on Jan 31, 2018 · 0.4.0 End-to-end processing
  1

• Modification types to exclude on Theoretical form not in methods/presets because string[]

  Improve Feature
  smith-chem-wisc/ProteoformSuite#460 · Filter by author leahvschaffer opened on Sep 5, 2017 · 0.4.0 End-to-end processing

• Output proteoform IDs in ProForma format

  New Feature
  smith-chem-wisc/ProteoformSuite#423 · Filter by author trishorts opened on Jul 21, 2017 · 1.0.0 Future tasks
  3

• Add "Possible PFR Numbers" from UniProt in theoretical database and Cytoscape display

  Cytoscape ScriptingNew Feature
  smith-chem-wisc/ProteoformSuite#420 · Filter by author trishorts opened on Jul 14, 2017 · 0.4.0 End-to-end processing
  4

• What does ET histogram look like for orphans only?

  Question
  smith-chem-wisc/ProteoformSuite#408 · Filter by author acesnik opened on Jun 6, 2017 · 1.0.0 Future tasks
  1

• Look for SUMOylation and ubiquitylation (with adjusted lysine count)

  New FeatureQuestion
  smith-chem-wisc/ProteoformSuite#407 · Filter by author acesnik opened on Jun 6, 2017 · 1.0.0 Future tasks

• Looking into relations that are ditched because of no-mans-land

  Question
  smith-chem-wisc/ProteoformSuite#403 · Filter by author acesnik opened on May 30, 2017 · 1.0.0 Future tasks
  1

• Extend UnlocalizedModification to represent complicated mods as set of simpler ones

  Improve Feature
  smith-chem-wisc/ProteoformSuite#398 · Filter by author acesnik opened on May 22, 2017 · 0.4.0 End-to-end processing
  1

• Between-proteoform quantification

  New Feature
  smith-chem-wisc/ProteoformSuite#365 · Filter by author acesnik opened on Apr 20, 2017 · 1.0.0 Future tasks
  2

• Commandline ProteoformSuite

  New Feature
  smith-chem-wisc/ProteoformSuite#362 · Filter by author acesnik opened on Apr 19, 2017 · 0.4.0 End-to-end processing
  1

• Can't mass shift first peak in DGV

  Bug
  smith-chem-wisc/ProteoformSuite#346 · Filter by author leahvschaffer opened on Apr 5, 2017 · 1.0.0 Future tasks
  5

• More information in cytoscape node tables

  Cytoscape BugCytoscape Scripting
  smith-chem-wisc/ProteoformSuite#328 · Filter by author acesnik opened on Mar 21, 2017
  2

• Look for contaminant proteoforms with natural abundance masses (not NeuCode)

  Need More Information
  smith-chem-wisc/ProteoformSuite#297 · Filter by author acesnik opened on Mar 4, 2017
  6

• Automating mass shifting

  New Feature
  smith-chem-wisc/ProteoformSuite#235 · Filter by author acesnik opened on Oct 27, 2016 · 1.0.0 Future tasks
  2

• Manual monoisotope shift for EE relations

  New Feature
  smith-chem-wisc/ProteoformSuite#183 · Filter by author trishorts opened on Jul 28, 2016 · 0.4.0 End-to-end processing
  2

• Verify ptmlist and uniprot-xml making the databases

  GUI Stability
  smith-chem-wisc/ProteoformSuite#79 · Filter by author acesnik opened on May 3, 2016 · 1.0.0 Future tasks

• Import/export proteoform IDs from/to outside database, e.g. CTDP

  New Feature
  smith-chem-wisc/ProteoformSuite#59 · Filter by author trishorts opened on Apr 5, 2016 · 0.4.0 End-to-end processing
  1