The following table lists defects that were resolved or no longer relevant between the BioPharma Finder 1.0 and BioPharma Finder 5.4 software release, excluding Help issues and cosmetic fixes. In some cases, the description has been amended or extended from the original version to better describe the reported issue. The resolution of each of the listed issues involves both an engineering fix and follow-up testing verified by our product evaluation department.
Item number | Software area | Description |
|---|---|---|
240503 | Ardia Platform | A network error prevents multiple users from opening the same experiment simultaneously. |
397422 | Ardia Platform | After leaving the BioPharma Finder application running overnight, the Ardia homepage appears, instead of the expected login dialog box. |
554126 | Ardia Platform | Ardia Platform version 1.0 is not compatible with BioPharma Finder 5.3. |
639912 605057 | Ardia Platform | Reports saved for Peptide Mapping Analysis experiments in Ardia Platform version 1.1 are not displayed in BioPharma Finder versions 5.1 or 5.2. |
38723 | General | Application updated to integrate the latest version of MongoDB. |
38744 | General | Memory usage is not optimized during various operations, such as loading results or switching from the Process and Review page to the Mapping page. |
(TFS) 40758 | Installer | MsFileReader is not installed when running the installer in repair mode. |
(TFS) 81000 | Installer | On a few Windows 7 machines, when the BioPharma Finder installer is run, the installer might get stuck at the "Initializing" step. |
123001 | Installer | Attempting to upgrade to BioPharma Finder to version 4.0 (or later) will fail if the user has not launched the current version (3.0 or earlier) of the software. |
(TFS) 3388 | Intact Mass Analysis | When a user resets a processing method, the chromatogram parameters are not reset. |
(TFS) 5145 | Intact Mass Analysis | If a user zooms in on a chromatogram, the modification peak labels do not update when selecting another peak. |
(TFS) 23543 | Intact Mass Analysis | When 64-bit ReSpect™ DLL is delivered with BPF 1.0, the data intensity is very different and missing some low-resolution data. |
39286 | Intact Mass Analysis | When BioPharma Finder version 1.0sp1 is upgraded to 2.0, the retention time (RT) range for custom processing methods is set to “0” instead of the correct range. |
39311 | Intact Mass Analysis | On the Parameters > Report page of the processing method editing wizard, all of the reporting parameters are shown as “enabled” for a multiconsensus experiment with all reporting parameters disabled. |
39526 | Intact Mass Analysis | On the Reporting page, the header in the “Source Chromatogram” section displays “F:” for filter, but filters do not apply to chromatograms. |
39534 | Intact Mass Analysis | For an Xtract with Sliding Windows deconvolution experiment, when you save a component as a reference from the Process and Review > Results table, the information displayed for the reference spectrum incorrect. |
39535 | Intact Mass Analysis | On Parameters > Target Sequence Matching page of the processing method editing wizard, the default “Sequence Matching Tolerance” parameter is very large; this parameter has been updated to a reasonable value of 20 ppm. |
39537 | Intact Mass Analysis | On the Process and Review page, after zooming out to full-scale on the source spectrum or deconvoluted spectrum, the scroll bar is still visible. |
39538 | Intact Mass Analysis | When a user exports the top-level results in the Process and Review > Results table, the exported file contains an additional expandable row (blank) after the last component row. |
39540 | Intact Mass Analysis | On the Reporting page, the order of information listed in the “Matching Sequence” column of the “ReSpect/Xtract Masses Table” section is not consistent with the order displayed in the “Deconvolved Spectrum” section or in the Process and Review > Results table. |
39541 | Intact Mass Analysis | When a user selects a component in the Process Review > Results table, the chromatogram displays the zoomed retention time (RT) range from the previously selected component instead of resetting the full-scale chromatogram view. |
39542 | Intact Mass Analysis | In an uncommon scenario involving an Xtract deconvolution, the run queue becomes corrupted and the experiment fails. |
39543 | Intact Mass Analysis | If the user adds a reference spectrum to an Xtract with Sliding Windows deconvolution experiment, the experiment fails. |
39545 | Intact Mass Analysis | During an Xtract deconvolution, experiment processing fails intermittently due to a missing source spectrum. |
39546 | Intact Mass Analysis | The application takes an excessive amount of time to add a large number of jobs to the run queue. |
39558 | Intact Mass Analysis | The extracted ion chromatogram (XIC) is generated incorrectly for experiments with both full-scan and MS/MS data after the ReSpect or Xtract deconvolution. |
39559 | Intact Mass Analysis | A warning message has been implemented to warn users that the ReSpect or Xtract algorithms cannot deconvolve centroid data, only profile data. |
40004 | Intact Mass Analysis | There are several UI style inconsistencies in Protein Deconvolution 4.0. |
40019 | Intact Mass Analysis | On the Parameters > Chromatogram page of the processing method editing wizard, if invalid values are entered for the “Chromatogram m/z Range” parameter, the expected red error message on the communicator bar does not appear. |
40409 | Intact Mass Analysis | After copying and pasting the source spectrum into a third-party application, the peak markers are not correctly aligned with the peaks in the pasted image. |
45964 | Intact Mass Analysis | In the Process and Review > Results table, the “Apex RT” value displayed for some components is outside of the range indicated by the “Start Time (min)” and “Stop Time (min)” values. |
119790 | Oligonucleotide Analysis | In the Oligonucleotide Sequence Editor, entering a sequence with a formula that contains any elements with a quantity greater than 100,000 results in an error. |
123294 | Oligonucleotide Analysis | In the Predicted Oligo MS/MS (Kinetic Model) feature, when a sequence is entered using lower case letters, no warning message is displayed stating that the sequence should be entered in capital letters or triplet code format. |
(TFS) 14263 | Peptide Mapping Analysis | When a protein coverage map is copied and pasted to Microsoft Office 2007, some amino acids are not displayed properly. |
(TFS) 16720 | Peptide Mapping Analysis | Disulfide bonds are not properly highlighted on the Protein Sequence tab. |
(TFS) 20965 | Peptide Mapping Analysis | The sequence coverage map does not paste into Microsoft Word™ correctly. |
(TFS) 24538 | Peptide Mapping Analysis | Peptides might not be properly highlighted on the Protein Sequence tab. |
(TFS) 38277 | Peptide Mapping Analysis | A refresh issue occurs when loading a protein sequence after reprocessing an experiment. |
38385 | Peptide Mapping Analysis | If a peptide has more than one modification, the peptide is excluded from the “% Relative Abundance” calculations displayed on the Mapping > Modification Summary page. |
38396 | Peptide Mapping Analysis | For experiments with a single raw data file, the “ID Type” value displayed for some components in the Processing and Review > Results table is “Full”, even though the components have an associated MS2 spectrum. |
38707 | Peptide Mapping Analysis | Processing a large experiment results in the application using only one raw data file for the MS2 spectrum. |
38708 | Peptide Mapping Analysis | The application selects the activation type as ETD over higher-quality CID in the MS2 spectrum. |
38733 | Peptide Mapping Analysis | In an experiment with multiple raw data files, the file-specific “Avg MS Area” and “%CV” columns in the Process and Review > Results table are displayed out of order. |
39285 | Peptide Mapping Analysis | The protein coverage results in the Mapping > Coverage > Results table might not agree with those displayed on the Protein Coverage Map. |
39305 | Peptide Mapping Analysis | Double-clicking on a completed experiment in the run queue does not open the experiment results. |
39309 | Peptide Mapping Analysis | The application might crash if the user cancels an actively processing experiment. |
39324 | Peptide Mapping Analysis | In the Process and Review > Results table, the information in the “Modification” column is displayed incorrectly for a component with seven modifications. |
39371 | Peptide Mapping Analysis | In the Process and Review > Result table, glycosylated peptides are not identified when the user defines an N-glycan as a variable modification in the protein sequence. |
40106 | Peptide Mapping Analysis | The data resolution displayed in the MS2 spectrum on the Process and Review page might be incorrect. |
40109 | Peptide Mapping Analysis | Toggling between fragmentation types (Auto/CID/ETD) in the MS2 spectrum on the Process and Review page results in scaling and data label discrepancies between spectra. |
40197 | Peptide Mapping Analysis | For an experiment using the “Find All Ions with MS/MS” task specified on the Parameters > Component Detection page of the processing method editing wizard, the Modification Results table on the Mapping > Modification Summary page is blank. |
40200 | Peptide Mapping Analysis | Isomerization of the same peptide component shows up as two different modification masses with a large ∆ ppm value in the Process and Review > Results table. |
(TFS) 40794 | Peptide Mapping Analysis | When the MS2/full scan spectra window is changed to "floating" by dragging the window and then changed back to "dockable," the data is not displayed anymore. |
52377 | Peptide Mapping Analysis | In the Process and Review > Results table, the “Theoretical Mass” value does not include Na+ adducts. |
52382 | Peptide Mapping Analysis | In the Process and Review > Results table, the “Theoretical Mass” value does not include K+ adducts in the mass. |
52383 | Peptide Mapping Analysis | In the Process and Review > Results table, the “Theoretical Mass” value does not include glycans in the mass. |
52830 | Peptide Mapping Analysis | In the Process and Review > Results table, the “Theoretical Mass” value is incorrect for dimeric peptide components. |
52831 | Peptide Mapping Analysis | In the Process and Review > Results table, the “Theoretical Mass” value does not include oxidation for gas phase oxidation in the mass. |
52946 | Peptide Mapping Analysis | In the Modification Summary, the “Predicted Time” value is not always the same when processing the same experiment multiple times. |
78060 | Peptide Mapping Analysis | When a user exports checked components in the Process and Review > Results table “As Displayed”, the columns in the exported table overlap and are misaligned. |
138669 | Peptide Mapping Analysis | For a targeted experiment, the “ID Type” values displayed in the Process and Review > Results table is incorrect; components with a “Full” ID type have associated fragment coverage maps. |
150046 | Peptide Mapping Analysis | For host cell protein (HCP) experiments, performance issues could occur when searching extremely large data sets. |
257333 | Peptide Mapping Analysis | Isomerization does not appear as a modification in the Result table. |
39378 | Protein Sequence Editor | The chain mass is not updated after linking disulfide bonds in the Protein Sequence editor. |
230105 | Reporting | For experiments with large data files, shading might not be visible when a chromatogram is added to a report. |
39539 | Run queue | After processing a job, the run queue table displays the bottom of the job list. |