| 457 | Shared project files not visible | new | gregory | defect | blocker | Proteios 2.4 |
| 423 | No permissions are checked when updating the remaining quantity of a BioMaterial | new | gregory | defect | critical | Proteios 2.4 |
| 302 | Upgrade to Java 6 | reopened | gregory | enhancement | major | Proteios Future Release |
| 327 | Remove all compilation warnings | assigned | gregory | defect | major | Proteios Future Release |
| 365 | Fraction collection from LC-MS runs | new | fredrik | enhancement | major | Proteios Future Release |
| 366 | External file support | assigned | gregory | enhancement | major | Proteios Future Release |
| 392 | import of non-gel search results to hits report | assigned | olle | enhancement | major | Proteios 2.4 |
| 393 | Import of 1D-gel results to hits report | new | gregory | enhancement | major | Proteios Future Release |
| 402 | Proteios FTP server should be upgraded to new version of Xerver | new | olle | enhancement | major | Proteios Future Release |
| 413 | html code possible in user names | new | gregory | defect | major | Proteios Future Release |
| 435 | X!Tandem GUI should obtain standard alternatives for search parameter values from the used GPM site | assigned | olle | enhancement | major | Proteios 2.4 |
| 447 | Sessions should be logged out after each request but are not when exceptions occur | assigned | gregory | defect | major | Proteios 2.4 |
| 448 | User preferences storage and editing | assigned | olle | enhancement | major | Proteios 2.4 |
| 449 | Compilation errors on mac with java 1.5.0_13 | assigned | gregory | defect | major | Proteios 2.4 |
| 453 | Plug-in listing is strange | new | olle | defect | major | Proteios 2.4 |
| 456 | Retrieval of Mascot XML results from Mascot server | new | gregory | enhancement | major | Proteios Future Release |
| 47 | AnnotationType recognition by value | new | olle | enhancement | minor | Proteios Future Release |
| 85 | FTP service control through gui | new | gregory | enhancement | minor | Proteios Future Release |
| 149 | Add "Run plugin" button to PeakListSet list | new | gregory | enhancement | minor | Proteios Future Release |
| 164 | Sorting of columns | new | olle | enhancement | minor | Proteios Future Release |
| 179 | Merging of hits result with spectrum plot | new | fredrik | enhancement | minor | Proteios Future Release |
| 223 | Allow linking of pick list to gel | new | fredrik | enhancement | minor | Proteios Future Release |
| 231 | Rewrite the QuickImport plugin as an extension | new | gregory | enhancement | minor | Proteios Future Release |
| 237 | Java installer | assigned | gregory | enhancement | minor | Proteios Future Release |
| 239 | Go-to spot number in hits report | new | gregory | enhancement | minor | Proteios Future Release |
| 246 | Clear/hide jobs from the log | new | gregory | enhancement | minor | Proteios Future Release |
| 247 | Jump to page # on "Jobs"-page | new | olle | enhancement | minor | Proteios Future Release |
| 256 | Enable users to work within Experiments | new | gregory | enhancement | minor | Proteios Future Release |
| 257 | Email notification of job completion | assigned | olle | enhancement | minor | Proteios 2.4 |
| 266 | Used quantity is negative for extracts | new | gregory | defect | minor | Proteios Future Release |
| 276 | Filter value in TableFactory should be checked against variable type | new | olle | enhancement | minor | Proteios Future Release |
| 320 | Fix placement of tab buttons for different browser settings | new | gregory | enhancement | minor | Proteios Future Release |
| 323 | Add columns for common annotations | new | fredrik | enhancement | minor | Proteios Future Release |
| 324 | Batch gel generation | new | gregory | enhancement | minor | Proteios Future Release |
| 344 | Hits import wizard potentially confusing phrasing | new | gregory | defect | minor | Proteios Future Release |
| 345 | Output directory when running conversion plugin | new | gregory | enhancement | minor | Proteios Future Release |
| 346 | Batch move file and individually delete file | new | gregory | enhancement | minor | Proteios Future Release |
| 357 | Enable filtering of Extracts | new | gregory | enhancement | minor | Proteios Future Release |
| 358 | Enable filtering of Labeled Extracts | new | gregory | enhancement | minor | Proteios Future Release |
| 364 | Allow selection of grouping annotation for DIGE Analyzer | assigned | olle | enhancement | minor | Proteios 2.4 |
| 377 | User-defined order of column sorting | new | gregory | enhancement | minor | Proteios Future Release |
| 382 | Viewing trashcan is broken | new | gregory | defect | minor | Proteios Future Release |
| 387 | Better warning/error message when running extensions and not having an active project | new | gregory | enhancement | minor | Proteios Future Release |
| 395 | Hits import wizard null stacktrace | new | gregory | defect | minor | Proteios Future Release |
| 397 | Use ConfigureTableFactory2 to filter News | new | gregory | enhancement | minor | Proteios Future Release |
| 401 | Document SSL configuration of apache/tomcat in conjunction with proteios | assigned | olle | enhancement | minor | Proteios 2.4 |
| 403 | ant doc generates a lot of warnings | new | gregory | defect | minor | Proteios Future Release |
| 405 | Support export for publication | new | fredrik | defect | minor | Proteios 2.5 |
| 409 | Update ImplementAction page with new contexts | new | gregory | task | minor | Proteios Future Release |
| 414 | Use TableFactory2 to display 'My Projects' | assigned | olle | enhancement | minor | Proteios 2.4 |
| 420 | Wizzards for input guidance | assigned | gregory | enhancement | minor | Proteios 2.4 |
| 424 | Share plugins to groups | new | gregory | enhancement | minor | Proteios Future Release |
| 426 | Check db schema at startup | new | gregory | enhancement | minor | Proteios Future Release |
| 427 | Howering description of extensions | new | gregory | enhancement | minor | Proteios 2.5 |
| 428 | Group extensions by their functionality | new | gregory | enhancement | minor | Proteios 2.5 |
| 429 | Remove unused plugins | new | gregory | task | minor | Proteios Future Release |
| 430 | Support compressed mzML | assigned | olle | defect | minor | Proteios 2.4 |
| 433 | Proteios extension wiki information | assigned | olle | defect | minor | Proteios 2.4 |
| 434 | Proteios extension subversion directory layout information needed | assigned | olle | task | minor | Proteios 2.4 |
| 436 | General Proteios Wiki Update | assigned | olle | enhancement | minor | Proteios 2.4 |
| 437 | Creating new items, a general workflow | assigned | gregory | enhancement | minor | Proteios Future Release |
| 438 | Titles missing or not standardized | new | gregory | defect | minor | Proteios Future Release |
| 439 | Fieldset legends should be replaced with titles | assigned | olle | enhancement | minor | Proteios 2.4 |
| 440 | Redesign FormFactory | new | gregory | enhancement | minor | Proteios Future Release |
| 441 | Use In Project button should be shaded if no project is active | new | gregory | defect | minor | Proteios Future Release |
| 442 | Menu changes related to Project navigation | assigned | olle | enhancement | minor | Proteios 2.4 |
| 443 | Implement POST method in webservice | assigned | gregory | enhancement | minor | Proteios 2.4 |
| 444 | Enable uploading of files through webservice PUT method | assigned | gregory | enhancement | minor | Proteios Future Release |
| 450 | mzML reader should support referencable param groups | assigned | olle | defect | minor | Proteios 2.4 |
| 451 | Proteios FTP Server double-clickable start and stop scripts for MS-Windows | assigned | olle | enhancement | minor | Proteios 2.4 |
| 452 | Database schema version number should be updated before release | new | gregory | task | minor | Proteios 2.4 |
| 454 | mzML reader should use accession number properties instead of name properties in cvParam tags | assigned | olle | enhancement | minor | Proteios 2.4 |