BioPharmaView™ Software Release Notes

BioPharmaView™ Software Release Notes
BioPharmaView™ Software
Release Notes
RUO-IDV-03-1798-A
July 2015
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Contents
Chapter 1 Introduction ..............................................................................................................................4
Related Documentation.....................................................................................................................................................4
Changes from Version 1.0 to Version 1.5...........................................................................................................................5
Contact Us.........................................................................................................................................................................7
Chapter 2 Workstation Requirements.......................................................................................................8
Supported Equipment........................................................................................................................................................8
Chapter 3 Installation.................................................................................................................................9
Notes on Installation..........................................................................................................................................................9
Install the BioPharmaView Software..................................................................................................................................9
License the BioPharmaView Software..............................................................................................................................11
Chapter 4 Known Issues and Limitations................................................................................................15
Chapter 5 Remove the BioPharmaView Software..................................................................................20
Appendix A Download the Software from the SCIEX Web Site............................................................21
Revision History........................................................................................................................................22
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1
Introduction
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The BioPharmaView software is a post-acquisition processing software used for performing characterization
and analysis of biologics. Use the software to complete the following tasks:
• Enter or update assay information
• Characterize standards
• Batch process files
• Review batch results
• Create reports
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®
The BioPharmaView software processes data files generated by SCIEX TripleTOF systems to support protein
and peptide analysis during therapeutic drug development.
The BioPharmaView
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software supports the following workflows:
• Intact Protein Analysis: Determines the molecular weight of intact proteins, based on the deconvolution
of a charge series envelope resulting from LC-MS/MS.
• Peptide Mapping Analysis: Determines the sequence of peptides resulting from the enzymatic digestion
of a protein from the mass-to-charge (m/z) ratio of TOF MS/MS data.
Each workflow enables the user to characterize samples and store the results, perform automated batch analysis,
and generate reports.
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All of the BioPharmaView
software report templates, processing settings, and modifications can be customized.
Related Documentation
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• BioPharmaView Software User Guide: Available on the installation DVD or click Start > All
Programs > AB SCIEX > BioPharmaView > BioPharmaView User Guide.
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• BioPharmaView Software Help: Click the Help icon in the bottom left corner of the BioPharmaView
software window, press F1 from any location in the software, or click Start > All Programs > AB SCIEX
> BioPharmaView > BioPharmaView Help.
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Introduction
Changes from Version 1.0 to Version 1.5
• A new column, Score, has been added to the Peptide Results table in version 1.5 of the software. This column
provides an estimate of the probability that a candidate match is correct. During the review of results, users
can differentiate between true-positive and false-positive identifications based on an assigned score value.
• A new tab, Modifications Summary, has been added to the Intact Protein Characterize Standard Results table.
This tab summarizes Modification to Protein Ratios, including the average count of modifications attached to
a single protein molecule. The Drug-Antibody Ratio (DAR) is an example of this. A DAR value of three indicates
that, on average, the protein is modified with three drug attachments. Other examples include the average
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level of oxidation, glycosylation, or any other modification. In addition, the BioPharmaView software reports
the fraction of the total intact protein signal that comes from versions containing "n" number of each
modification.
• A new column, Modification Percent, has been added to the Peptide Results table in version 1.5 of the software.
The column captures post-translational modifications which are considered to be critical quality attributes for
biological therapeutics. Using this information, users can assess the level to which individual amino acids are
modified over the range of all observed modifications for the same charge state.
• A new column, Validated Match, containing a check box for each entry, has been added to both the Intact
Protein workflow Results table and the Peptide Mapping workflow Peptide Results table in version 1.5 of the
software. All check boxes are selected by default for matched results in Intact Protein and for matched results
with a Score value above the user-defined threshold in Peptide Mapping. By clearing a check box, users can
exclude individual results that they consider problematic from the results list. Users also have the option to
update the Assay Information with only those results identified as a Validated Match by selecting the Use Only
Validated Matches to Update Assay Information option, or all results can be used to update the Assay Information
by clearing that selection. It is the responsibility of the user to confirm the correct results are being reported.
• Filtering dialogs have been incorporated into many of the workflows in version 1.5 of the software. Filtering
enables users to minimize the number of entries shown. Filtering preferences can be exported and saved as a
.FilterSet file. This file can then be imported into subsequent results tables to filter. When filters are applied,
users have the option to create reports containing all of the generated batch results or only the results that
match the filter criteria applied. Refer to Appendix A in the BioPharmaView™ Software User Guide.
• Improvements have been made to the MS1 feature detection for LC chromatograms in the Peptide Mapping
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workflow. In version 1.5 of the BioPharmaView software, the generation of theoretical fragment ions is
followed by MS/MS matching for any MS1 identified peptides that have MS/MS spectra available. During
matching, all theoretical peptide forms within the m/z tolerance are evaluated and scored if an MS2 spectrum
is available. The set of matches for each MS1 signal is inspected and if the top scoring match meets or exceeds
the minimum score, then the result is identified as valid.
• Disulfide bond information can be imported into the Disulfide Bonds table from a .txt file or from another
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BioPharmaView software project. All information is validated during import. In addition, disulfide bond
information can be exported from the Disulfide Bond table to a .txt file.
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Introduction
• When drug-linker modifications are attached to an antibody through a partial reduction, this results in the
breaking of some disulfide bonds, followed by modification of the free cysteines that were produced. A new
check box has been added to the Modifications table. When this check box is selected, the application considers
disulfide bonds as eligible for replacement with any defined cysteine modifications during the generation of
theoretical Intact protein and peptide forms. For this option to function correctly, the modification Type must
be Internal and the Position undefined. In addition, non-reduced disulfide bonds are required.
• The option to view a Base Peak Chromatogram (BPC) has been added for both intact proteins and peptides in
the same graph pane used to show Total Ion Chromatogram (TIC) traces in version 1.5 of the software. A BPC
is a more useful single-trace depiction of an LC/MS data set than the TIC is. The BPC shows the momentary
intensity of the most intense ion at any given time, over time. However, the response time of the
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BioPharmaView software when opening a project might be increased when the Show BPC option is selected.
As a workaround, select the Show TIC option before closing the project.
• A new column, Workflow Usage, has been added to the Modifications table in version 1.5 of the software.
This column enables the user to define modifications for use only in the Intact Protein workflow, modifications
for use only in the Peptide Mapping workflow, and modifications for use in both workflows. The default value
for this column is Both. Workflow usage information can be assigned in the Add Modifications dialog or in the
Modifications table.
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• In previous versions of the BioPharmaView software, only the first sample in the selected .wiff file could be
analyzed. Any additional samples were ignored. In version 1.5 of the software, the .wiff file is automatically
opened to Sample # 1 and Experiment # 1. However, if the .wiff file contains additional samples and experiments,
then users can select a different TOF MS sample or experiment from the list provided.
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• In previous versions of the BioPharmaView software, multiple peptide entries that were identical except for
the protein chain of origin were generated. In version 1.5 of the software, chemically unique peptides with
multiple protein chains are amalgamated into one entry, resulting in a final set of peptides that contains one
entry for each unique peptide.
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• In previous versions of the BioPharmaView software, users could identify only one chain per modification
row. In version 1.5 of the software, users can identify multiple chains in sequential order (1-3) or non-sequential
order (1,4) in a single row for each modification being added to the protein sequences. Chain information can
be assigned in the Add Modifications dialog or in the Modifications table.
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• Improvements have been made to the response time of the BioPharmaView software when the user is
reviewing the results of characterization or results generated through the batch processing workflows.
• A new setting, Minimum Peptide Length, has been added to the Peptide Mapping Settings dialog in version
1.5 of the software. This setting enables the user to define the minimum number of amino acids on all peptide
chains. This can be useful for filtering smaller peptides that contain less relevant information about the sample
out of the results.
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Introduction
• A new column, Abundance Ratio, has been added to both the Results table in the Intact Protein—Review
Results workflow and the Peptides Results table in the Peptide Mapping—Review Results workflow in version
1.5 of the software. The Abundance Ratio, which measures the relative abundance levels of quality attributes
between experimental and reference standards, is calculated by comparing the protein or peptide to the values
obtained through the Characterize Standard workflow. Quality attributes can be any user-defined property,
such as proteins or peptides with specific modifications, disulfide bonds, sequences, and so on. The relative
Abundance Ratio is reported for any batch results that were matched to characterized proteins or peptides.
Contact Us
SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout
the world. They can answer questions about the system or any technical issues that might arise. For more
information, visit the SCIEX Web site at http://sciex.com.
SCIEX Support
• http://sciex.com/contact-us
• http://sciex.com/request-support
Customer Training
• In North America: NA.CustomerTraining@sciex.com
• In Europe: Europe.CustomerTraining@sciex.com
• Outside the EU and USA, visit http://sciex.com/education for contact information
Online Learning Center
• http://training.sciex.com
• http://elearning.sciex.com
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2
Workstation Requirements
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CAUTION: Potential Data Loss. The BioPharmaView software should not be installed on
the acquisition computer. Software errors and data integrity issues can result if the
BioPharmaView software and acquisition software are used concurrently.
The workstation must be configured with the following applications:
• English version of Microsoft Windows 7 (32-bit or 64-bit) operating system with SP1
• Microsoft .NET Framework 4.0
• Adobe Reader
Note: Visit www.adobe.com and follow the instructions to install the latest version of Adobe Reader.
• Microsoft Office 2010 or 2013.
Note: If a trial version of Microsoft Office is installed on the computer as a temporary measure, then the
full version of the Microsoft Office software must be activated before the trial period expires. The license can
be purchased from your regional division of Microsoft or from an authorized distributor in your region.
Supported Equipment
• Dell OptiPlex 9010
• Dell OptiPlex XE2
Note: Newer systems might become available. For more information, contact the local sales representative.
Older computer models might be compatible. However, they have not been tested and might result in degraded
performance.
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Installation
Notes on Installation
• The user must be logged on to the computer as a user with Administrator privileges.
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• Any existing version of the BioPharmaView software that is installed on the computer must be removed
before this version of the software can be installed. Refer to Remove the BioPharmaView Software
on page 20.
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• The BioPharmaView software is not backward compatible with previous releases. Before upgrading an
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existing version of the BioPharmaView software (version 1.0) installed on a system configured with the
Microsoft Windows 7 32-bit operating system, the user must remove the installed version of the
TemplateContentControlManager software through the Control Panel (BPV-335).
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• If using a .zip file that contains the BioPharmaView software installer, extract All Files from the .zip file
before running the installer from the location containing the extracted files. Errors will occur if the installer is
run from within the .zip file.
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• During installation of the BioPharmaView software, the system might determine that Microsoft .NET
Framework 4.0 is not installed. If this occurs, then the system needs to be connected to the Internet to download
additional components for the Microsoft .NET Framework 4.0 installation process. If the system fails to install
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the Microsoft .NET Framework 4.0, then the BioPharmaView software installation also fails. Resolve the
situation by connecting the workstation to the Internet or contacting your local IT department to install the
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Microsoft .NET Framework 4.0, and then install the BioPharmaView software again.
Install the BioPharmaView
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Software
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CAUTION: Potential Data Loss. The BioPharmaView software should not be installed on
a computer used for acquisition. Software errors and data integrity issues can result if the
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BioPharmaView software and acquisition software are used concurrently.
1. To begin, log on to the computer as a Microsoft Windows user with administrator privileges.
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2. Remove any existing version of the BioPharmaView
Software on page 20.
software. Refer to Remove the BioPharmaView
3. Make sure that all of the applications are closed.
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Installation
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4. Insert the BioPharmaView
software installation DVD into the DVD drive.
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Note: If any version of the BioPharmaView software is already installed on the computer, then a Windows
Installer error dialog opens before the installation starts.
Figure 3-1 Windows Installer Error Dialog
Note: Click OK and then remove the software.
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The BioPharmaView
Software Setup dialog opens.
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Tip! If the BioPharmaView
double-click setup.exe.
Software Setup dialog does not open, then navigate to the DVD drive and then
Figure 3-2 BioPharmaView Software Setup Dialog
5. Click Next.
6. On the End-User License Agreement dialog, click the I accept the terms in the License Agreement
check box and then click Next.
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Installation
7. On the Destination Folder dialog, click Next.
Tip! The user can change the software installation locations and the data folders before clicking Next.
8. Click Install.
9. After installation is complete, click Finish.
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10. If this is a new installation of the BioPharmaView software, then continue with License the
BioPharmaView Software. If this is an upgrade to an existing version of the software, then the previous
license file activates this version.
License the BioPharmaView
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Software
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The BioPharmaView software is a licensed product. If a current license is not installed, then processing and
saving functions are not available.
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1. Open the BioPharmaView
software.
2. View the software title bar.
• If a valid license file exists, then the title bar only contains the software name.
• If a valid license file does not exist, then the title bar contains the software name and a message indicating
that there is an issue with the license.
3. If there is a licensing issue, then click About in the lower left corner of the software.
The About BioPharmaView
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Software and Software License Activation dialog opens.
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Installation
Figure 3-3 About BioPharmaView Software and Software License Activation Dialog
Any of the following conditions can result in the "This software is not licensed" message being shown:
• A current license is not installed.
• The computer network connection is not available. The licensing components used by SCIEX software
require that the computer's network adapter be enabled, although a physical connection to the network is
not required.
4. Click Software Activation.
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The BioPharmaView
Software Activation dialog opens.
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Installation
Figure 3-4 BioPharmaView™ Software Activation Dialog
5. Type the license key, exactly as shown, in the appropriate field.
If a license key is not available, then contact the SCIEX Sales Representative.
6. Click Generate Computer ID.
This creates a unique identifier for the workstation.
7. Click Copy ID to Clipboard.
8. Click the SCIEX licensing link and then paste the copied computer ID in the Computer ID field.
9. Follow the instructions to obtain the license.
Note: Internet access is required to obtain the license. If the computer does not have Internet access, then
make a copy of the generated computer ID. On a computer with Internet access, go to the licensing page of
the SCIEX Web site and then follow the instructions to obtain a license.
After the required information is submitted, a license file is sent to all e-mail addresses provided.
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Installation
10. Close the browser window.
11. When the e-mail containing the license file is received, copy the license file to the workstation desktop.
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12. Click Install License File on the BioPharmaView
Software Activation dialog.
The Select the new license file to be installed dialog opens.
13. Browse to and select the license file and then click Open.
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Both the Select the new license file to be installed and the BioPharmaView
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14. Click OK to close the About BioPharmaView
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Software Activation dialogs close.
Software and Software License Activation dialog.
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4
Known Issues and Limitations
Everyone should read this section of the Release Notes. This section applies specifically to issues that are known
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in the BioPharmaView software, version 1.5.
Note: The numbers in brackets are reference numbers to each issue or feature in our internal tracking system.
Performance Issues
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• The improvements made to increase the number of detected peptides in version 1.5 of the BioPharmaView
software might result in an increase in the response time in the Peptide Mapping workflow when compared
with version 1.0 of the software.
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• When a large number of peptides (>20 000) is included in the Peptides list, the BioPharmaView software
might become slow to respond or indicate that it is not responding when Process or Update Assay Information
is clicked in the Peptide Mapping—Characterize Standard workflow. No user action is required. The requested
task will be completed. (BPV-67)
• As the number of entries in the Peptides table increases in the Peptide Mapping workflow, the response time
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of the BioPharmaView software increases each time the number of Maximum Missed Cleavages is increased
and Digest is clicked. Occasionally, the software will indicate that digestion has completed but the Peptides
list is empty. Other actions, for example, save the project, open the project, and so on, continue to function as
expected. (BPV-110)
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• When a large number of peptides (>20 000) is included in the Peptides list, the BioPharmaView software
might become slow to respond or indicate that it is not responding when the user is editing information on
the Sequence Features tab. No user action is required. The requested task will be completed. (BPV-670)
• In the Intact Protein—Review Results workflow, when the Copy All Data in Table option is selected from the
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right-click menu, the BioPharmaView software might become slow to respond or indicate that it is not
responding. No user action is required. The requested task will be completed. (BPV-806)
• If large data files or batches are processed multiple times under certain conditions, then all of the available
RAM might be consumed and the software stops responding. If this occurs, close and then open the
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BioPharmaView software.
Filtering Issues
• When invalid criteria is added to a Filtering dialog, an error icon is shown in the field containing the invalid
information. If the invalid information is not corrected and the project is closed without saving the changes,
then when the project and the Filtering dialog are opened, the invalid criteria is retained, but the error icon is
not. When filtering is turned on, a red funnel is shown in the header of the filtered column but the invalid filter
is not applied to the contents of the column. To determine which filter criteria is invalid, clear and then select
each check box. An error icon is shown in the field containing the incorrect Filtering Criteria. (BPV-727)
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Known Issues and Limitations
• When an imported .FilterSet file is used to populate a Filtering dialog, the project must be saved to persist the
filter criteria. If the project is closed without saving, the filter criteria is discarded and must be imported again.
(BPV-808)
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• Occasionally, the BioPharmaView software does not apply the active filters when alternating between the
different tabs in the Intact Protein—Review Results workflow. To resolve this issue, close and then open the
project again. (BPV-850)
• If filtering is applied to the Modification Percent column in the Peptide Mapping—Review Results workflow,
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but no filtering criteria is specified, then the BioPharmaView software filters the Peptide Results table
resulting in the information in the filtered table being removed. Clear the Modification Percent check box on
the Filtering dialog to remove the filter and populate the Peptide Results table again. (BPV-856)
Reporting Issues
• When a Peptide Mapping report is generated, the user might find that there are labels included in the LC-MS
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TIC section of the report that are not visible in the BioPharmaView software interface. To view the additional
labels in the software, zoom in on the specific timeframe containing the extra labels. (BPV-74)
• When a Microsoft Word (.docx) version of a report is generated, the Created by BioPharmaView {timestamp}
information in the report header contains the date and time that the selected report template was last modified
instead of the date and time the report was created. However, when a .PDF version of a report is generated,
the Created by BioPharmaView {timestamp} information in the report header is correct. (BPV-314)
• When the batch contains Drug-Antibody Ratio (DAR) information, and a report is requested, the Detailed
Modifications section of an Intact Protein Single Sample Report or the Intact Protein Batch Results Report does
not contain the multiplicity data. However, the multiplicity data is included at the beginning of the Modification
Summary section. (BPV-846)
• In Microsoft Windows 7, when saving a report to either the C:\ or C:\Program Files folder, an error message is
shown and the report is not created. Reports must be saved to a different location, preferably to a folder on
the D:\ drive.
• When editing a report template for the first time, the message “Are you sure you want to install this
customization?” might be shown. To resolve the issue, close any open report templates and any open copies
of Microsoft Word. Navigate to the C:\Program Files (x86)\AB SCIEX\ReporterOfficeAddins\
TemplateContentControlManager folder, double-click the TemplateContentControlManager.vsto file,
and then install the component.
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• After installing the MasterView software on a 64-bit workstation where the BioPharmaView software is
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installed, an error might occur when editing a BioPharmaView software report template. To resolve the
issue, close any open report templates and any open copies of Microsoft Word. Navigate to the C:\Program
Files (x86)\AB SCIEX\ReporterOfficeAddins\TemplateContentControlManager folder, double-click the
TemplateContentControlManager.vsto file, and then install the component.
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Known Issues and Limitations
• When attempting to open a report template for the first time on a system with Microsoft Office 2010 Professional
installed, a message "Exception from HRESULT: 0x8004063E", a Microsoft Office Document Customization
error message might open. This occurs because the Visual Studio 2010 Tools for Office Runtime is missing from
the system. To resolve this issue, download the component from the Microsoft Web site using the following
URL: http://www.microsoft.com/en-us/download/details.aspx?id=44074, and then double-click the
vstor_redist.exe file and follow the installation prompts.
• After the processing of a large batch (for example, 50 data files), generation of the Peptide Mapping Batch
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Report might fail. If this occurs, close and then open the BioPharmaView software and then create the batch
report.
Labeling Issues
• Occasionally, in the Peptide Mapping—Characterize Standard and the Peptide Mapping—Review Results
workflows, the chromatogram label for a selected peptide in the BPC graph is slightly different than the RT
value listed for the peptide in the Peptide Results table. (BPV-695)
• In the MS/MS Graph pane of the Peptide Mapping—Characterize Standard workflow, the Experiment numbers
included in the labels of the graph are the Information Dependent Acquisition (IDA) experiment numbers and
not the experiment number selected in the Characterize Standard for Peptide Mapping pane. (BPV-701)
• In the Peptide Mapping—Characterize Standard workflow, the labels in the BPC/TIC/XIC pane applied to
peptides with disulfide bonds are formatted incorrectly. Refer to Table 4-1. (BPV-721)
Table 4-1 BPC/TIC/XIC Labels
Label formatted as ...
Label should be formatted as ...
2,3= 2,3 T19-20 =T24
2,3. T19-20 = 2,3. T24
90.64
90.64
• In the Intact Protein—Review Results workflow, when the batch contains multiple files, the information shown
in the BPC/TIC graph pane is inconsistent between files. For example, if two files are submitted in a batch and
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both files are selected, then, when the user is navigating through the results of the first file, the BioPharmaView
software zooms the x-axis to an area that is ± 2 minutes of the RT and a blue, vertical line identifies the protein.
However, when the user is navigating through the results of the second file in the batch, the x-axis returns to
the default view (non-zoomed) and there is no blue, vertical line identifying the peak. If the batch contains
two files but only one file is selected, then when the user is navigating through the results of the selected file,
the x-axis is not zoomed and the blue, vertical line identifying the protein is missing. If the batch contains three
files and all three files are selected, then when the user is navigating through the results of the first file, the
x-axis is zoomed correctly and the blue, vertical line identifying the protein is shown in the correct location.
However, when the user is navigating through the results of the second file in the batch, the x-axis is zoomed
correctly but the blue, vertical line identifying the protein is shown at an incorrect retention time. (BPV-807)
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Known Issues and Limitations
Error Messages
• "The project could not be opened. Sequence contains no matching element."
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• The BioPharmaView software incorrectly allows the user to import a peptide list containing a modification
that has not been defined in the Assay Information into the Peptides table in the Assay Information—Peptide
Mapping workflow and then save the project. However, when the user attempts to open the project, the
message "The project could not be opened. Sequence contains no matching element." opens. To resolve
this issue, the user must create a project and import a valid peptide list. (BPV-858)
• “The image format is unsupported.”
• If the message “The image format is unsupported.” is shown, then click Control Panel > Display
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Settings > Color Quality > Highest (32 bit). The BioPharmaView software cannot be opened
on a system that is unable to display 32-bit graphics.
• "The assay information has been modified and no longer matches the Intact Protein
[Peptide Mapping] characterization results. You must reprocess and update the assay
information before saving the project."
• In the Intact Protein—Characterize Standard and the Peptide Mapping—Characterize Standard workflows,
if the user clicks Process and then clicks Cancel before the processing is completed, the software incorrectly
instructs the user to reprocess and update the assay information before the project can be saved. To resolve
this issue, click Process and then click Update Assay Information before saving. (BPV-119)
• "The assay information has been modified and no longer matches the characterization
result. You must reprocess and update the assay information before saving the result."
• If the message “The assay information has been modified and no longer matches the characterization
result. You must reprocess and update the assay information before saving the result.” is shown, then click
Update Assay Information. This might need to be done in the workflow that is not currently active. For
example, when working in the Peptide Mapping workflow, the Intact Protein workflow assay information
might need to be updated.
Sorting Issue
• When sorting the information in the Peptide column of the Peptide Results table, the information is sorted first
alphabetically and then numerically, one digit at a time. For example, if the column contains four entries, T2,
T3, T19, and T25, then after the column is sorted, the entries are listed in the following order: T19, T2, T3, and
T29. (BPV-646)
Miscellaneous Issues
• The columns of information being imported into the Peptides table or the Characterized Proteins table must
TM
be in the same order as the default column order in these tables the BioPharmaView software. In addition,
all columns must be present. If the user has modified the column order in the .txt file and then attempts to
import peptides or characterized proteins, the import fails.
• When adding Position or Maximum Mods per Chain information to the Modifications table, users must
double-click inside the appropriate cell to move the focus from the previous cell. (BPV-83)
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Release Notes
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Known Issues and Limitations
• If all of the Peptide Results are selected in the Peptide Mapping—Characterize Standard and the Peptide
TM
Mapping—Review Results workflows, then the BioPharmaView software shows a maximum of 10 traces
in the XIC, TOFMS, and MS/MS graphs. In the Characterize Standard workflow, the visible traces are based on
the last results selected and are updated when the information is sorted and different results are selected.
However, in the Review Results workflow, the visible traces are always the same, regardless of how the
information is sorted and the results that are selected. (BPV-94)
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• When assay information includes both matched and unmatched theoretical peptides, the BioPharmaView
software occasionally matches two different peptides to the same observed m/z ion. (BPV-113)
• When characterizing standards, only the last processing result for each workflow can be saved and opened.
Previously saved results are overwritten by more recent results and cannot be saved or opened.
• When importing peptides or proteins, the software searches the list of modifications, attempting to find the
imported modification by name or by symbol. If the imported modification name matches the symbol of an
existing modification, then the imported modification is replaced by the existing modification.
• The values shown in the XIC Area column of the Peptide Results table in the Characterize Standard for Peptide
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Mapping workflow are determined by the processing functionality and are used by the BioPharmaView
software for evaluation purposes. The peptide values are also shown in the Area column of the XIC Peaks tab
in the BPC/TIC/XIC pane. However, because there might be slight differences in the values, the values in the
XIC Peaks tab should be used for information purposes only. (BPV-868)
• If the Assay Information contains multiple versions of the same peptide, but the peptide has different Batch
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Usage settings (for example Optional, Required, and so on), then during batch processing, the BioPharmaView
software might match peptides with different batch settings. To resolve this issue, make sure that all versions
of the same peptide have the same Batch Usage setting. (BPV-874)
• When a peptide list containing a modification that has not been defined in the Assay Information is imported
into the Peptides table in the Assay Information—Peptide Mapping workflow, the software incorrectly enables
the user to complete the characterization, update the Assay Information, and save the project. However, when
the user creates and submits a batch using this updated file, the software does not add the invalid batch to
the queue. No information is provided to the user, indicating why the batch cannot be submitted. (BPV-875)
Release Notes
RUO-IDV-03-1798-A
BioPharmaView™ Software
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Remove the BioPharmaView
Software
5
1. Log on to the computer as a Microsoft Windows user with Administrator privileges.
2. Click Start > Control Panel > Programs and Features.
Tip! If the control panel components are shown by Category, click Start > Control Panel > Programs
> Programs and Features > Uninstall a program.
3. Select BioPharmaView
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Software and then click Uninstall.
The software removed, with no user intervention required.
During the removal, the software name is removed from the Installed Programs list, the shortcut to the
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BioPharmaView software is removed from the desktop, and the shortcuts to the software and the user
documentation are removed from the Start menu.
Note: The following components remain on the computer:
• The C:\AB SCIEX\BioPharmaView\Data folder, which might contain software project data.
• If the product is licensed, the C:\Program Files (x86)\AB SCIEX\BioPharmaView folder, which contains the
license file.
• The AB SCIEX Reporter Template suite.
• Microsoft .NET Framework 4.
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Release Notes
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Download the Software from the
SCIEX Web Site
1. Download the BioPharmaView
TM
A
software from the SCIEX Web site.
Note: To prevent potential installation issues, it is recommended that the file is saved to a location other
than the computer desktop.
2. After the download is complete, double-click the BioPharmaView_1.5.exe file.
The BioPharmaView Setup dialog opens.
3. Click Install.
Tip! By default, the files are extracted to the C:\AB SCIEX\BioPharmaView\BioPharmaView Installer v1.5
folder. However, the user can choose the location.
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After the extraction is complete, the BioPharmaView
Software Setup dialog opens.
Figure A-1 BioPharmaView Software Setup Dialog
4. Continue with step 5 of Install the BioPharmaView
Release Notes
RUO-IDV-03-1798-A
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Software on page 9.
BioPharmaView™ Software
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Revision History
Revision
A
Reason for Change
Date
First release.
July 2015
BioPharmaView™ Software
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Release Notes
RUO-IDV-03-1798-A
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