The following table lists defects that were resolved between Proteome Discoverer 3.2 and Proteome Discoverer 3.3. The table excludes Help issues and any cosmetic fixes. In some cases, the original abstract has been amended or expanded upon to better describe the reported issue. Both an engineering fix and follow-up testing (verified by our product evaluation department) have resolved each of these issues.
Item ID | Software section | Abstract |
|---|---|---|
207794 | Help | Documentation: A better description for INFERYS and spectral library prediction functionality is needed. |
792818 | Reporter ion quantification | TMT 32plex: Some values in the PSM are duplicated in the quan channel view plot. |
842421 | Reporter ion quantification | When using the precursor detector and reporter quantifier, the quan spectra are used for PSMs with high isolation interference. |
93039 | Normalization | Enable users to normalize only features found in all sample groups in quan analysis. |
851668 | Ardia | When users are not registered on any Ardia server: For studies containing many analysis files, the repeated check of remote files might slow down the performance. |
842518 | PSM filtering | Low-confident PSMs are still present when they belong to a high-confident peptide group. |
824138 | Spectral libraries | Predict from a FASTA file: The Activation Type parameter always shows HCD even when the CID option is selected during library creation. |
838825 | Spectrum selector | The workflow crashes when the Spectrum Selector node tries to store traces for the .raw files. |
794155 | Familiarization documentation | Familiarization Guide: In Chapter 2 for reporter ion quantification with phosphorylation, the Peptide Groups data source needs to be removed from the Volcano Plot steps. |
798301 | Fragment ions quantifier | The numbering index of the parameters is not correct in the Fragment Ions Quantifier node. |
802042 | Spectrum view | The Fragment Chart displays only charge 1 for DIA spectra. |
802419 | Protein Annotation node | When the database version changed, the workflow's annotation node and search engine node do not recognize the new version of the database, and the workflows need to be updated. |
806818 | MSPepSearch | MSPepSearch InforHint displays an incorrect warning about RAM memory limitations. |
277263 | Reporter ion quantification | An incorrect warning that reporter ion quantification cannot rescale abundance columns displays. |
562597 | Dependencies | The application does not use SQLite 118. |
647791 | Magellan server | Local databases (for example, Server DB) are insecure and not encrypted. Users can compromise settings and data integrity is not enforced. |
746695 | Percolator | Update to Percolator 3-07. |
752141 | Study | The word “Hints” does not appear in the the Execute State column in the analysis result table for jobs that completed with hints. |
756957 | CHIMERYS communication tester | Verify Discoverer can get an object from S3 and there are no network misconfigurations on the client side. |
763521 | FASTA file download | A FASTA file with and without subtaxonomies with the same TaxId cannot be downloaded. |
772816 | Protein table | The values of the #Protein Unique Peptides column in the Proteins table are 0. |
777000 | Ardia | If the default browser is not set to Microsoft Edge, then the sign in to Ardia server will not work. |
778296 | Processing | Processing workflow failed: Caller is unauthorized to delete specified resource[0]. |
782322 | CHIMERYS | The CHIMERYS node failed because it cannot process spectra. |
758266 | Export | Astral .raw files exported to .mgf files contain no precursor mass in cases where the precursor detector is used. |
856182 | Reporter ion quantification | TMT quan values might be swapped when no sample grouping is used. |
856230 | Label free quan results | When the Precursor Ions Quantifier node is used, the chromatogram for the DIA Precursors table is missing. |
764341 | Plots | Originally,hidden tables (even after being made visible) cannot be used to plot histograms. |
797992 | CHIMERYS on Ardia | A gateway timeout occurred when submitting a job that resulted in a conflict. |
829338 | INFERYS library prediction, export, and MSPepSearch | Non-target peptides are added to the predicted library as targets when predicting from a protein FASTA file. The results failed MSPepSearch searches using a target/decoy due to insufficient target/decoys needed for FDR. |
799390 | CHIMERYS cloud | CHIMERYS skips the final merge step and downloads results for input files separately, reducing the length of time to finalize the result. |
802042 | Spectrum view | Only singly charged fragments are annotated for DIA spectra. |