Suggested recovery actions
- For some issues, restarting the application is the appropriate recovery action.
- As a fix, we generally do not recommend reinstalling the software or the operating system, which more commonly occurs after you install a new hard drive.
- After the installation on the software on some PCs, there is an issue with viewing the IQ report using the displayed link. If this occurs, the IQ report can be found in
C:\Program Files\Thermo\IQ Reports.
Feature requests and other omitted items
- We do not include issues where there is insufficient information logged to successfully reproduce the reported problem.
- We do not list feature requests as software issues, regardless of the reported significance or severity of the request. Product managers evaluate logged feature requests for future releases.
- We report only discrepancies in the documented software as known issues.
Terminology
The following tables define the terms used to describe the severity and risks associated with the known defects detailed in the Known Defects for BioPharma Finder 5.4 table. Product management assesses risk, which can differ significantly from the reported severity.
Severity | Interpretation |
|---|---|
Critical | A problem that renders the system unusable because either an entire function is unusable and no workaround exists or use of the current system compromises data integrity or results in data loss. Catastrophic problems also include significant and non-obvious quantitative errors and all human and instrument safety issues. |
High | A serious issue that does not affect data integrity (meaning data loss, corruption of data, or the wrong answer), but affects the customer’s ability to use the product as designed. It can be a failure, design issue, or documentation error or omission. A workaround might or might not exist. |
Medium | A minor error or poor behavior of a product feature. There is likely a workaround. |
Low | An issue that has a limited effect on customer usage of the product, including defects with visibility so low that a customer might never see it or ease-of use-issues or other items not causing any performance degradation. |
Risk | Interpretation |
|---|---|
High | Occurrence is likely to happen and can compromise operation. |
Medium | Occurrence is uncommon, but if it occurs, can compromise operation. |
Low | Issue is minor; however, the software might operate differently from a user’s expectations. A workaround is often available. |
No risk | This issue causes no problems but is a common inconsistency or an issue with a low severity level. |
Known defects
The following table lists the known defects in the BioPharma Finder 5.4 software, categorized by software section, including a brief description and information related to each defect’s severity and risk. The item ID is the internal number assigned to each issue.
Severity | Risk | Item ID | Software area | Description |
|---|---|---|---|---|
High | High | (TFS) 9716 | General | Images copied from the BioPharma Finder application and pasted into Microsoft Word or PowerPoint™ that are then saved as PDF images might be corrupted. |
High | High | (TFS) 32986 | Intact Mass Analysis | Duplicate copies of the chromatogram and deconvoluted and source spectra (from the same raw file) are created for Multiconsensus experiments when the raw data file contains more than one component that satisfies the multiconsensus merge parameters. |
High | Medium | 40410 | Intact Mass Analysis | Running an experiment using the “Auto ReSpect” processing method does not identify the expected components. |
High | Low | 38374 | Installation | When upgrading from BioPharma Finder version 3.0 to 3.1, if there is not enough disk space and the user selects “Ignore” in the warning message, the application still attempts to create a backup folder and the installation fails. Workaround: First, uninstall version 3.0 and then install version 3.1 as a clean install. |
High | Low | 38699 39292 | Peptide Mapping Analysis | The “ID Type” value (Full, MS2) displayed for some components in the Processing and Review > Results table is incorrect. Workaround: Select the component in the Results table and then select the MS2 Spectra tab to check if a MS2 spectrum is displayed for the component. |
Medium | Medium | (TFS) 81000 | Installation | When the BioPharma Finder installer is run on some Windows 7 machines, the installer stalls at the "Initializing" step. |
Medium | Medium | 49511 | Intact Mass Analysis | When using the “Default Native Above 1 Million” processing method for QB files, users might not be able to set an appropriate retention time (RT) range. |
Medium | Medium | (TFS) 14462 | Intact Mass Analysis | When a user is connected to a remote desktop computer and runs the BioPharma Finder application on a trial license, the Intact Mass Analysis workflow is disabled. |
Medium | Medium | 51171 | Intact Mass Analysis Top Down Analysis | On the Parameters > Component Detection page of the processing method editing wizard, the “Resolution at 400 MHz” parameter is incorrect. |
Medium | Medium | 185972 | Oligonucleotide Analysis | The theoretical masses of some modifications in the Oligonucleotide Analysis workflow are incorrectly calculated for full-scan MS data. |
Medium | Medium | 179638 | Peptide Mapping Analysis | In the Theoretical Protein/Peptide Manager, custom proteases that cleave at both the C- and N-terminals might not cleave correctly at the N-terminal. |
Medium | Medium | 39357 | Peptide Mapping Analysis Intact Mass Analysis | Users are able to save a processing method that contains errors. |
Medium | Medium | 52372 | Peptide Mapping Analysis Oligonucleotide Analysis | In the Process and Review > Results table, the “Peptide ID” values include component mass (m) information, but the “Mono. Mass Exp.” values are “0.000”. |
Medium | Medium | 747861 | Reporting | After navigating pages containing charts, the Report utility produces an error when the user selects the “Preview” button. |
Medium | Low | 749147 (INC) 758078 | Ardia Platform | There is a registration error when upgrading from BioPharma Finder version 5.1 to version 5.2 or 5.3 when connected to the Ardia Platform version 1.1. Workaround: If you encounter this error, please contact Technical Support at digital.support@thermofisher.com for assistance. |
Medium | Low | 758151 | Ardia Platform | When a user updates the raw data file paths associated with an experiment on a given PC, on a second PC, the experiment either cannot be opened from the Ardia Platform data repository or the application prompts the user to specify the raw data files. Workaround: After updating the raw data file paths, on the original PC, save the experiment in a new location in the Ardia Platform data repository before opening the experiment on the second PC. |
Medium | Low | 123001 | Installation | If a user declines the EULA when installing BioPharma Finder version 3.0 (or earlier), subsequently attempting to upgrade to version 4.0 (or later) fails. |
Medium | Low | 119656 | Installation | Post-installation IQ Report link does not work. Workaround: Access the IQ Report via |
Medium | Low | 52888 | Intact Mass Analysis | For experiments using the sliding windows deconvolution method with a single raw data file, the “Matched Mass Error % CV” value should be “0.” |
Medium | Low | 39296 | Intact Mass Analysis | After recalculating the average DAR using selected components, the drug loads are zero for non-selected components. Workaround: Uncheck all components and select “Recalculate”. |
Medium | Low | 39318 | Intact Mass Analysis | When reprocessing an experiment with updated sequence matching/DAR parameters, the application should not reprocess the entire deconvolution experiment, but only the updated tasks. |
Medium | Low | 39279 | Intact Mass Analysis | The retention time (RT) range displayed on the chromatogram is incorrect (smaller) than the range specified in the raw data file. |
Medium | Low | 122165 | Peptide Mapping Analysis | When BioPharma Finder version 3.0 (or earlier) is upgraded to version 4.0 (or later), the Beginning Peak Width and Ending Peak Width parameters display “0” for Peptide Mapping Analysis experiments. Workaround: After upgrading, use the real-time optimization (RTO) feature to set the Beginning Peak Width and Ending Peak Width parameters to the same value as the Typical Chromatographic Width parameter. Save the method and reprocess the experiment. |
Medium | Low | 178056 | Peptide Mapping Analysis | For host cell protein (HCP) experiments, the default “Find All Ions with MS/MS” task may generate components with associated MS2 spectra that have both average and monoisotopic masses of “0”. |
Medium | Low | 164107 | Peptide Mapping Analysis | For host cell protein (HCP) experiments, HCP identifications are incorrect for protein sequences with a negative variable terminal modification. |
Medium | Low | 177288 | Top Down Analysis | The application may freeze when the user is loading or viewing experiment results with more than 25 proteoforms. Workaround: Reduce the total number of proteoforms searched in per experiment by performing multiple experiments with less than 10 proteoforms per experiment. |
Low | Low | 466619 (INC)758085 | Ardia Platform | When signing out of the Ardia Platform via ThermoAD IdP, the user is not automatically signed out of the current BioPharma Finder session. |
Low | Low | 38718 | General | The application does not fully support display on 4K monitors. |
Low | Low | 647675 | Installation | When downgrading from version 5.0 (or later) to 3.0 (or earlier), the expected warning message is not displayed. |
Low | Low | 56143 | Intact Mass Analysis | For an experiment containing multiple raw data files, the deconvoluted spectrum is not displayed due to a refresh error after filtering component results. |
Low | Low | 51273 | Intact Mass Analysis | When the run queue is empty, the Queue page table header is missing. |
Low | Low | 39295 | Intact Mass Analysis | When processing an experiment in Manual mode, specifying a retention time (RT) range greater than the range of the actual chromatogram causes the chromatogram and source spectrum to be empty. |
Low | Low | 39283 | Intact Mass Analysis | Single-scan QB raw data files cause the source spectrum to be blank when switching from Sliding Windows to Average Over Selected RT deconvolution. Workaround: Create a processing method for a Sliding Windows deconvolution with a “Target Avg. Spectrum Width” parameter set to less than 0.02(RT). |
Low | Low | 40032 | Intact Mass Analysis | On the Parameters > Deconvolution Parameters (ReSpect) page of the processing method editing wizard, the “Resolution at 400 MHz” parameter is incorrect for experiment containing both FTMS and ITMS full-scan data. |
Low | Low | 40011 | Intact Mass Analysis | When there are many jobs submitted to the run queue, experiment processing is stalled for an experiment using the Xtract with Sliding Windows deconvolution method. Workaround: Delete the stalled experiment from the run queue and then resubmit the experiment once the run queue is smaller. |
Low | Low | 39544 | Intact Mass Analysis | When the retention time (RT) range is manually set to [0.0 to 0.0] for a Sliding Windows experiment, the expected warning message is not displayed when the experiment is subsequently submitted for processing in Automatic mode. Workaround: Set the RT range to an appropriate value. |
Low | Low | 39358 | Intact Mass Analysis | Drug load cannot be set for a component with no identification. |
Low | Low | 39350 | Intact Mass Analysis | On the Parameters > Identification page of the processing method editing wizard, the list of modifications in the “Select a variable modification candidate for the DAR calculation” area is missing several N- and C-terminal modifications. |
Low | Low | 39325 | Intact Mass Analysis | When other components are selected in the Process and Review > Average DAR table, users cannot update the drug load value for an unchecked component. Workaround: Select the component in the Results table before updating the drug load value. |
Low | Low | 39322 | Intact Mass Analysis | If a raw data file does not contain any matches for a DAR experiment, the “Raw File Name” column in the Process and Review > Average DAR table is blank. |
Low | Low | 39304 | Intact Mass Analysis | For a ReSpect with Sliding Windows deconvolution experiment, the “Mass Std Dev” and “PPM Std Dev” parameters are shown in the deconvolution report, but not in the Results table or exported results file. |
Low | Low | 39291 | Intact Mass Analysis | When a ReSpect deconvolution experiment is submitted to the run queue, the experiment is processed, but the “Number of Components Detected” column displays “0” if the raw file name, experiment name, or file path exceed 256 characters. Workaround: Keep file names, experiment names, and file paths under 256 characters. |
Low | Low | 39288 | Intact Mass Analysis | For a Multiconsensus experiment with raw data files containing multiple peaks, only the first component is exported for each peak when a user exports the top-level results as a Microsoft Excel™ file. Workaround: Export all components as an Excel file. |
Low | Low | 38720 | Intact Mass Analysis | Enhancement request: Optimize layout of elements on the Process and Review page. |
Low | Low | 38717 | Intact Mass Analysis | For an Automatic Peak Detection experiment, the extracted ion chromatogram (XIC) might not appear on the Process and Review page. Workaround: Reload the experiment results. |
Low | Low | 38704 | Intact Mass Analysis | If the run queue is paused and BioPharma Finder is upgraded to version 3.0, a dialog box appears asking the user if they would like to restart the run queue. If the user selects “Yes”, the application crashes. Workaround: Process all experiments in the run queue before upgrading BioPharma Finder to a later version. |
Low | Low | 39374 | Intact Mass Analysis | If experiment data is collected at multiple resolutions, to obtain best results, the user must run multiple experiments in which each processing method specifies a particular resolution value. |
Low | Low | 40211 | Intact Mass Analysis | On the Parameters > Chromatogram page of the processing method editing wizard, the user can specify different retention time (RT) ranges in the “Chromatogram Parameters” and “Sliding Windows Parameters” areas. |
Low | Low | 51905 | Licensing | In the License Activation dialog box, if a user declines to activate a permanent license and then selects “Back” to activate a trial license instead, the application gives an error. Workaround: Close and restart the application. In the License Activation dialog box, activate a trial license. |
Low | Low | 38713 | Licensing | During an offline deactivation, the response file for "Deactivation.req" is incorrectly named "Activation.xml". |
Low | Low | 117056 | Oligonucleotide Analysis | Oligonucleotide sequences with a 3’-terminal modification are not completely highlighted in the Process and Review > Real Time Optimization > Oligo Sequence Map area. |
Low | Low | 117286 | Oligonucleotide Analysis | Oligonucleotide Analysis only supports one variable modification for a given oligonucleotide sequence. |
Low | Low | 117636 | Oligonucleotide Analysis | When users export checked components in the Modification Summary > Components table “As Displayed”, the file is blank when viewed with Apache™ OpenOffice™. Workaround: Export all or checked components in the Modification Summary table as an Excel worksheet. |
Low | Low | 117583 | Oligonucleotide Sequence Editor | An error results when users import FASTA files containing oligonucleotide sequences in two-letter code format. Workaround: Import FASTA files containing sequences in single-letter or triplet code format. |
Low | Low | 38703 | Peptide Mapping Analysis | Loading an incorrectly formatted MSQC file causes an unexpected dialog box to appear. |
Low | Low | 38709 | Peptide Mapping Analysis | After submitting an experiment to the run queue, the Peptide Mapping Analysis page shows the last used processing method checked. |
Low | Low | 54723 | Peptide Mapping Analysis | The application displays an unexpected arrangement of workflow page tabs following experiment processing. |
Low | Low | 53410 | Peptide Mapping Analysis | Users might experience a refresh error on the Mapping > Modification Summary page after performing manual integration of the chromatogram. |
Low | Low | 39281 | Peptide Mapping Analysis | When an experiment is deleted from the Load Results page, the Mapping tab is not removed. Workaround: Close and restart the application. |
Low | Low | 40198 | Peptide Mapping Analysis | The ∆ ppm value for a component with a “Gasphase-NH3Loss” modification is larger than expected. |
Low | Low | 40110 | Peptide Mapping Analysis | When a user subsequently loads a new raw data file, it overwrites the previously added file. |
Low | Low | 40081 | Peptide Mapping Analysis | When there is no protein sequence coverage determined for an experiment, the signal intensity color coding is incorrect. |
Low | Low | 39528 | Peptide Mapping Analysis | For dimers, the MS2 spectrum shows the predicted data for a single peptide instead of the dimer. Workaround: Confirm the presence of the dimer using the full-scan MS data; MS2 data displays the fragmentation of the constituent peptide monomers. |
Low | Low | 39527 | Peptide Mapping Analysis | When a user performs a disulfide bond search, the ∆ ppm value is larger than expected for components predicted to be Na+ or K+ adducts. |
Low | Low | 38701 | Peptide Mapping Analysis | The application selects the activation type as ETD over higher-quality CID in the MS2 spectrum. Workaround: Right-click on the MS2 spectrum, select “Predict Peptide MS/MS (Kinetic Model)", and then select the correct fragmentation method in the dialog box. |
Low | Low | 38389 | Peptide Mapping Analysis | In the Target Peptide Workbook Editor, if you edit the retention time (RT) range of a peptide such that it creates an error, the red error message on the communicator bar does not disappear even after fixing the RT range. Workaround: Select the row for another peptide in the workbook to clear the error message. |
Low | Low | 38387 | Peptide Mapping Analysis | For a very large experiment (100 raw data files), the Process and Review page > Trend MS Area is missing the raw data file labels on the x-axis due to space limitations. |
Low | Low | 38384 | Peptide Mapping Analysis | In the Process and Review > Results table, resetting the filter for an individual column does not return the column to its default state. |
Low | Low | 38378 | Peptide Mapping Analysis | For targeted experiments, the “% Abundance” values displayed on the Mapping > Modification Summary page might be incorrect for peptides with “nonunique” modifications |
Low | Low | 38377 | Peptide Mapping Analysis | Multiple labels for a single glycan might appear in the MS2 spectrum. |
Low | Low | 38376 | Peptide Mapping Analysis | In the Process and Review > Results table, the “Mono Mass Exp.” value for some components might differ slightly between a targeted and non-targeted experiment. |
Low | Low | 39302 | Peptide Mapping Analysis, Intact Mass Analysis | When a user is connected to a remote desktop (Windows 10 machine) and attempts to open or load experiment results, the application displays a blank screen instead of opening the Process and Review page. Workaround: Close and restart the application, load or open the experiment results again. The results are displayed on the Process and Review page. |
Low | Low | 38719 | Protein Sequence Editor | When a user pastes peptide chains beginning with “> name” into the Sequence Box, the Protein Sequence Manager does not correctly differentiate the chains. |
Low | Low | 645518 | Reporting | When switching between modules in the Reporting tool, the user is prompted to save the report template before saving the report, even if no changes to the template have been made. |
Low | Low | 750629 | Run queue | Canceling an experiment in a given workflow with a “Preparing” status in the run queue also cancels other experiments with the same name in other workflows. |
Low | Low | 38738 | Top Down Analysis | On the Parameters > Identification page of the processing method editing wizard, UI items are not properly aligned. |
Low | Low | 38712 | Top Down Analysis | After inputting experiment information on the Top Down Analysis page, selecting the Home tab triggers a warning message that the application will clear the experiment settings. |
Low | Low | 38700 | Top Down Analysis | On the Parameters > Component Detection page of the processing method editing wizard, if the “Intact Deconvolution” parameter is unselected, the m/z range displayed on the source spectrum header does not correspond to the range set in the processing method parameters. Workaround: In the Intact Deconvolution area on the Parameters > Component Detection page of the processing method edition wizard, manually change the “m/z range” parameter and save the method. |
Low | Low | 38698 | Top Down Analysis | On the Top Down Analysis page, if you select a protein sequence for the experiment, but then delete the sequence from the Global Reference table on the Parameters > Identification page of the processing method editing wizard, proteoforms associated with the deleted sequence are not included in the experiment results. Workaround: Do not delete sequences from the Global Reference table if the sequence is used in an experiment that is currently processing or submitted to the run queue. |