The following table contains known defects in the software, categorized by software section, with a brief abstract and information related to each defect’s severity and risk. The Item ID is the internal number assigned to each issue. Product management assesses risk, which can differ significantly from the reported severity.
Software section | Severity | Abstract | Risk | Item ID |
|---|---|---|---|---|
Statistics Insights node | Low | The Stats Configuration contents should be shown under the Statistics Insights node for the Result Summaries page. | Low | 817550 |
Predicted library export | Medium | Tribrid instrument, Eclipse, Spectrum Library shown FT as Mass Analyzer. | Low | 823209 |
Protein FDR | Medium | Protein FDR validation cannot be complete when PEP scores are zero. | Med | 828198 |
Predicted library | Low | When predicting the MS library using a peptide list exported from the Proteome Discoverer application, the Normalized Collision Energy parameter of the Spectrum Library Prediction dialog box is not automatically filled with the value retrieved from the CSV file. | Low | 830121 |
Scripting node | Low | When exporting tables with the Scripting node, if there are two columns with the same display name and purpose, only one is exported. | Low | 830428 |
Transition list editor, Minora Targeted Detector | Medium | Before starting the analysis, validate the transition list when the modification is out of range. | Low | 832141 |
Spectrum view | Medium | Mass error does not accurately reflect when the mass tolerance is increased. | Med | 832632 |
Spectrum view | Medium | Annotated peaks are incorrect. | Med | 832635 |
SureQuant nodes | Low | Reading the boundaries file created from Proteome Discoverer by Skyline failed because the peptide contained unrecognized modifications, for example, xxx[Carbbamidoethyl]xxx. | Low | 834323 |
TMT | Low | It is better to show the Scan Type (such as Full or Zoom) in the result tables of TMTpro. | Low | 799432 |
Predicted library | Medium | Add the spectrum library filter information in the Comment column. | Low | 814963 |
Isolation interference | Medium | Quan Spectrum isolation interference should account for when HR scan window is different (0.7mz) compared to the ID MS2 spectrum (1.2 mz). | Med | 844042 |
ProSightPD | Medium | The proteins in the top-down results cannot be exported in the mzIdentML format or the mzML format. | Med | 846212 |
Modifications | Medium | The Modifications (All Possible Sites) of some peptide groups does not stay the same when repeating a workflow multiple times. | Low | 847212 |
Study | Low | When editing names in the Input Files column, duplicate names should not be allowed. | Low | 854066 |
Help | Low | When pressing CTRL+F1 on the keyboard to display the Help information for results tables, the target page is not displayed. Rather, the Interpreting Search Results with the Results File is displayed. | Low | 855517 |
Ardia | Medium | The MSF file downloaded from an Ardia server cannot be used as results for a consensus analysis. | Med | 856927 |
Minora Targeted Detector | Medium | The Minora Targeted Detector node does not allow for partial reprocessing with CHIMERYS. | Low | 857300 |
Transition list editor, Minora Targeted Detector | Low | When loading a transition list that includes peptide sequence annotation (for example, (light), (heavy)), there is no dialog that allows the correct peptide sequences. | Low | 868506 |
Result Filter/View | Medium | Editing Tags does not immediately carry over to the filter view. | Low | 746930 |
Ardia | Low | Cancelling an upload to Ardia leads to an upload failed message. | Low | 791045 |
Targeted peptide quantifier | Low | There is no ability to view the processing log when invalid lines are found while loading the transition list with the peptide fragment filters in the Targeted Peptide Quantifier node of the consensus workflow. | Low | 867622 |
Spectrum selector | Low | The Acquisition Type parameter in the Spectrum Selector node shows a very technical error message. | Low | 815428 |
Library prediction | Medium | Library predictions from a peptide list contain more peptides (same sequence, same modifications, different charge state) than requested. | Low | 848258 |
Sever settings | Low | Need more information for the Max. Number of Processing Workflows in Parallel Execution. | Low | 851958 |
Mascot | Low | The job should be aborted after the Mascot analysis failed. | Low | 842791 |
DIA results | Medium | In DIA experiments, the normalization of DIA precursors, sequences, and isoforms should take the normalization factors calculated for the peptide groups. | Low | 861908 |
Library prediction | Medium | The invalid INFERYS peptides should be filtered out when you save a CSV peptide list from a .raw file generated from a transition list. | Low | 862120 |
Transition list editor | Medium | When loading a transition list with fragment ion information and peptides where the precursor m/z are close (delta m/z is less than 0.01), the fragment ions listed will be the union of all peptides within that range. | Low | 855715 |
CHIMERYS on Ardia | Medium | When the search space for the CHIMERYS on Ardia sever exceeds the limit, there is no hint information to reduce the search space, only an exit code. | Low | 754229 |
CHIMERYS | Medium | The Proteome Discoverer application allows the combination of CHIMERYS results with different quan values, and in the DIA Precursors tables, the values for Area and Intensity are not reported in separate columns. | Med | 713421 |
Ardia | Medium | Multiconsensus results generated in Proteome Discoverer 3.3 from remote MSF files from Proteome Discoverer 3.2 provide no quan ratios in the result. There is workaround to use the Proteome Discoverer 3.2 application to produce multiconsensus results or use remote .raw files to create new MSF files. | Med | 827042 |
Reporter ion quantification | Medium | The Minimum Channel Occupancy parameter does not filter as expected. | Med | 869823 |
PTM annotation | Low | The modification string for a protein might be different when multiple search engines are used. | Med | 870723 |
Spectral annotation | Medium | The PSM Details dialog box does not show the predicted spectrum when the peptide has a met-loss modification. | Low | 866816 |
Export | Medium | When exporting the library in a FASTA format, there are only peptide sequences in the exported file, but no mass list, which is unexpected. | Med | 784270 |
Targeted peptide chromatograms | Low | The plot of Chromatogram Traces View cannot be toggled among a sequence at the Targeted Precursor Groups, its Targeted Precursors, and its Targeted Fragment Peak. | Low | 845542 |
PSM table | Low | The PSMs orders are different in the PSMs table when repeating the analysis. | Low | 869748 |