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Overview
Complete biotherapeutic characterization includes intact mass analysis, peptide mapping, oligonucleotide analysis, top- and middle-down analysis or Multi-Attribute Method (MAM) workflows. Access workflows that facilitate comprehensive interpretation and data visualization, allowing you to confidently characterize your biologics with speed and ease. From novel deconvolution algorithms generating complete results to easy-to-understand data visualization tools, Thermo Scientific BioPharma Finder software helps you choose the right path for confident characterization.
Simplify and streamline your analysis workflows using a single software platform including everything from batch processing to in-depth data analyses. Workflows guide experts and non-experts to easily set up, interpret and visualize results, accessing the information contained within any analyzed sample. Fully characterize protein-based therapeutics using peptide mapping analysis to provide complete sequence confirmation, post-translational modifications (PTMs), disulfide bonds, host cell proteins, and hydrogen-deuterium exchange (HDX). Comprehensive oligonucleotide analysis capabilities enable the identification and detection of impurities, metabolites, and the sequence mapping of large mRNA therapeutics.
On-demand webinar: Comprehensive workflows for oligonucleotide sequence confirmation
Complete biotherapeutic characterization with BioPharma Finder software
Comprehensive oligonucleotide analysis with BioPharma Finder software
Key benefits of BioPharma Finder software
Utilize the accuracy of high-resolution data for confident intact mass analyses
For absolute confidence in your deconvoluted molecular weights in both acidic and native conditions, advanced algorithms make the most of high-quality Thermo Scientific Orbitrap mass analyzer data.
Use all your data, not just a slice, for greater accuracy in deconvolution and relative quantitation of isoforms and drug-to-antibody ratios with the Sliding Window algorithm.
Xtract deconvolution using sequence-specific isotope tables provides accurate results for deconvolution of complex biotherapeutics, including heavily modified oligonucleotides.
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Know more than ever about peptide or oligonucleotide sequences
Rapidly process single or multiple data files to confidently identify sequence coverage, expected and unexpected PTMs, disulfide bonds and sequence variants.
Full MS, MS2 experimental vs. predicted spectra and fragment coverage maps increase confidence in peptide and oligonucleotide sequences, with data visualization tools to facilitate deeper insights into identifications and a faster time to meaningful results.
Enable identification, mapping, and relative quantitation of peptides or oligonucleotides and their impurities, even those present at very low levels, in a single experiment.
Workflow-driven and built to be easy to execute without a need to build a target mass list.
Leverage the advantages of HRAM, fast scanning speed, and multiple fragmentation techniques provided by Thermo Scientific Orbitrap mass spectrometers.
Completely characterize process and product quality attributes for high throughput QC monitoring
Confidently discover, identify, quantify and monitor product quality attributes with easy-to-understand data visualization within a single software platform.
For those requiring GxP compliant monitoring, seamlessly transfer all information from BioPharma Finder software into Thermo Scientific Chromeleon Chromatography Data System (CDS) software for targeted quantitation and new peak detection of peptides and intact proteins.
Comprehensive and confident characterization of mRNA vaccines and therapeutics
Confirm the identity of mRNAs through direct sequence confirmation using an innovative LC-HRAM MS solution with controlled partial digestion. Obtain confident identification of oligonucleotide fragments using a mass analyzer algorithm with MS2 kinetic prediction model. Achieve reproducible and comprehensive sequence coverage with fast data processing, confident assessment through mRNA sequence randomization tools, and an intuitive user interface for data review.
Enable confident characterization of critical quality attributes (CQAs), including 5’ capping efficiency and 3’ poly(A) tail distribution. Ensure accurate identification and quantification of capped and uncapped 5’ fragments using HRAM MS and MS/MS. Achieve high-resolution profiling of poly(A) tail distribution using high-quality MS spectrum and a powerful deconvolution algorithm.
Download the mRNA solution guide to learn more.
Learn more about BioPharma Finder software
The complexity of lifesaving therapies under investigation in the biopharmaceutical industry brings significant challenges from research and discovery, through to development, lot-release and quality control. Some of the toughest tasks for analysts and QC chemists are adequately characterizing these complex molecules and subsequently monitoring their quality attributes throughout the manufacturing process.
Find out what it takes to go smoothly from sample to knowledge.
Whether you are analyzing your protein under denaturing conditions or in its native state or determining the mass of a heavily modified oligonucleotide therapeutic, default methods and an automated parameter optimizer deliver accurate and confident deconvolution, simplifying your analyses.
BioPharma Finder software can perform batch-to-batch comparisons, or help you confirm the identity of antibody-drug conjugates (ADCs). With improved detection of low abundance species using the Sliding Window algorithm, powerful data visualization tools allow you to gain structural insights into your protein with confidence.
Incorporation of chemical modifications into therapeutic oligonucleotides in order to resist degradation by naturally occurring nucleases is common. One of the most frequently used modifications are phosphorothioates, which replace oxygen with sulfur in the linker region. By leveraging the HRAM data produced by Orbitrap mass spectrometers that reveal the unique abundance distribution of the sulfur isotopes, BioPharma Finder software automatically computes the chemical formula for phosphorothioated molecules and uses this information to generate a sequence-specific isotopic model, in order to obtain accurate deconvolution results.
BioPharma Finder software gives you the ability to store your intact mass analyses and processed data within a workbook, as well as the ability to edit the contents of each workbook. This provides easy data archiving and sharing, making sure results are transparent and accessible.
As with peptide mapping, analysts increasingly need to perform intact deconvolution under compliant conditions. For laboratories that need to acquire, process and report results within a compliant environment, the Intact Mass Workbook can be seamlessly imported directly into the Chromeleon Chromatography Data System (CDS) software. The ability to maintain compliance-ready workflows by performing method development within the BioPharma Finder software, and then intact mass deconvolution within the BioPharma Finder software or Chromeleon CDS software creates a powerful solution serving the entire biopharmaceutical development pipeline.
Sliding Window algorithm
The advanced Sliding Window algorithm provides a more thorough interpretation of LC/MS data for intact protein and oligonucleotide analysis by calculating a moving averaged spectrum across the chromatogram (i.e. "Sliding Window"). This powerful approach generates deconvoluted spectra for each component, resulting in a single deconvoluted spectrum of all protein components. The Sliding Window algorithm supports both high resolution (Xtract) and lower resolution (Respect) data.
Native separations can pose a challenge, especially when it comes to analyzing the resulting data. The Sliding Window algorithm ensures that all data is used, not just a slice that may be missing key information on low abundance species, for deconvolution to make sure your drug to antibody ratio (DAR) calculations are accurate.
BioPharma Finder software provides comprehensive tools to characterize and ensure the safety and efficacy of oligonucleotide-based biotherapeutics.
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The oligonucleotide sequence editor provides an easy-to-use interface for quickly and easily building and visualizing customized oligonucleotide sequences.
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Expanded sequence matching for oligonucleotides is provided by the intact mass analysis workflow, including Terminal Truncation Searching capabilities from the 3’ or 5’ terminus, allowing for easier identification of impurities. The annotated deconvolution spectrum produced by the Sliding Window algorithm deconvolution (Xtract) can be combined with an oligonucleotide sequence search for both the 5’ and 3’ removal and several different variable modifications.
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LC-MS fragmentation data provides a powerful tool for structural and sequence confirmation. BioPharma Finder software MS2 fragment identification can be seamlessly implemented to enhance oligonucleotide sequence confirmation. With the implementation of a novel kinetic model for oligonucleotide fragmentation prediction that incorporates predicted fragment intensity, spectral matching is performed with greater confidence to improve fragment identification.
- Easily review annotated MS2 fragmentation and compare with predicted MS2 spectrum
- Access color coded fragmentation maps for easy fragmentation visualization
- Display predicted fragment tables to evaluate fragment mass accuracy
- Implement dynamic filters to customize data display across multiple windows
- Customize window docking for simplified data review
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Automatic sequencing of the MS2 spectrum provides confidence in identification and confirmation of the true sequence of impurities. Without MS2 information the identification of oligonucleotide impurities cannot be confidently determined due to the prevalence of isomeric species that share the same accurate mass.
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The size and complexity of mRNA samples present analytical challenges for analysis at the intact level. mRNA digestion utilizing restriction endonucleases provides a suitable approach for the generation of predictable mRNA fragments that can be further analyzed to generate a complete mRNA sequence map. BioPharma Finder software provides advanced in silico digestion tools designed to support the identification of mRNA digestion fragments and fragment modifications to enable advanced mRNA mapping workflows.
- Perform mRNA mapping using in silico mRNA digestion tools
- Select from predefined RNase options or specify user defined cleavage locations
- Assess overall mRNA sequence coverage using interactive coverage map tools
- Identify mRNA sequence fragments as well as expected and unexpected modifications
- Visualize sequence map coverage for unique and non-unique mRNA sequence fragments
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The intact mass analysis of heavily modified oligonucleotides presents analytical and data processing challenges due to the frequent usage of sulfur modifications. Pairing Orbitrap mass spectrometers with BioPharma Finder software allows for confident intact mass identification of phosphorotioate conversion of oligonucleotides with less than 5 ppm error.
Confidently confirm amino acid sequences, with the ability to utilize mass and intensity-based MS2 kinetic fragmentation model predictions to ensure everything is captured, including the identification and localization of both expected and unknown PTMs. From disulfide bond mapping, to de novo sequencing for unknown components, rapidly visualize data to ensure that you see everything, including low-level impurities and sequence variants, as well as calculate relative abundances.
BioPharma Finder software simplifies comprehensive biotherapeutic attribute characterization with advanced capabilities to increase throughput and confidence for BioPharma workflows with built for purpose data processing, curation, and reporting in a connected environment to streamline and enable collaboration on a global scale powered by Thermo Scientific Ardia Platform.
Connectivity streamlines and enables collaboration on a local and global scale with seamless data processing capabilities by multiple users across any computer connected to the virtual private cloud or on-premises server. BioPharma Finder software with the Ardia Platform enables an all-encompassing solution for peptide mapping analysis including data processing, review, and reporting. Dynamically collaborate, compare, track, and finalize peptide results and workbooks using versioning history. Access and save results in a single secure location using shared sign-on for the entire workflow for enhanced data integrity and security.
Comprehensive and easy to use built-in peptide mapping reporting functionality
- Utilize pre-built or design and share your report templates to publish curated result reports in PDF or .xls formats
- Tailor report content with the report designer functionality, including dynamic data tables, column filters, custom calculations, charts and graphs, and images, such as peptide coverage maps
- Share and easily import custom report templates to implement standardized result reporting protocols
- Easily export workbooks to the Chromeleon CDS software as part of the multi-attribute method workflow
Detect and quantify host cell proteins
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Detection and quantification of residual HCPs as process-related impurities is critical per regulatory guidelines. BioPharma Finder software provides a complete HCP workflow that identifies product-specific peptides and their modifications, and then searches the unidentified MS2 spectra against user-selected protein databases (i.e., Cricetulus griseus (CHO), Homo sapiens (Human), Mus musculus (Mouse)) and merges the information together into one simple report. The software automatically selects the top three most abundant peptides from each HCP for relative quantitation. The user can adjust the peptides used for quantitation and generate quantitation profiles of HCPs across multiple conditions to demonstrate clearing. The integrated workflow allows for identification and quantification of target molecules, PTMs (including n-linked glycopeptides) and HCPs in the same sample and in one comprehensive analysis.
Ardia Platform connectivity enables local and global collaboration
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Faster data review
- Review a result generated by another colleague without having to import the results, open it from the shared secured Ardia Platform data repository, make comments or changes, and the software will automatically generate a new version to record the changes.
Better data management with centralized secured data
- All results are securely saved in one place, no more finding the “right” computer or hard drive that contains the experiment and data
Dynamic versioning history
Comparison view of changed values within the processing parameters
Enable collaboration on a global scale in a secure fashion to collaborate, compare, track, and finalize peptide results and workbooks using dynamic versioning history. Accelerate method optimization and review through a shared secure environment.
Default report templates
Easy to use report designer and viewer
Comprehensive and easy to use built in customizable peptide mapping reporting functionality to enhance data review and streamline collaboration.
- Default templates provide a simple starting point
- Report designer facilitates customization, including; dynamic data tables, column filters, custom calculations, charts and graphs, plot images, and more
- Report templates can be managed across multiple page tabs within the report display, saved, and stored as templates for future implementation and easily shared with colleagues to standardize reporting
- All reports can be exported in excel for PDF format
Streamline Hydrogen Deuterium Exchange workflows
BioPharma Finder software automates HDX data processing. The HDX workflow generates a protection factor plot that can be used to quickly assess and compare protein folding across batches of biopharmaceuticals.
HDX protection factor plot for the light and heavy chains of the antibody Herceptin.
When you utilize high resolution to obtain the highest quality data and combine that with the ability to operate in multiple fragmentation modes, you need to be sure that you can confidently process and visualize the resulting data.
Simple workflows for sequencing top- and middle-down analyses allow the comparison of multiple data files, if required, as well as providing interactive combined fragmentation coverage maps. BioPharma Finder software provides unparalleled sequence coverage for the top- and middle-down analysis of biotherapeutics by supporting multiple modes of fragmentation: CID, HCD, ETD, EThcD and UVPD.
An example of a middle-down analysis in BioPharma Finder software showing chromatographic separation of the light and heavy chains, with excellent mass accuracy observed upon deconvolution. Additionally, the sequence coverage when using both ETD and UVPD fragmentation is illustrated for each of the chains.
During the research and discovery stages of biopharmaceutical characterization, high-resolution mass spectrometry is commonly used to provide an accurate and confident understanding at both the intact and peptide level. However, during lot-release and quality control (QC), a number of release methodologies are performed. Currently, these methods are time consuming, and provide limited information on a single or very few critical quality attributes (CQAs) that need to be monitored.
The Multi-Attribute Method (MAM) is of significant interest to the industry, as it not only allows the implementation of a robust mass spectrometry-based assay for the characterization and release of biotherapeutics, but also offers the potential to reduce the number of ‘traditional’ lot release assays while increasing both product knowledge and the quality and depth of information acquired.
Discovery and early development laboratories operating outside compliance requirements can benefit from straightforward and automated peptide identification, attribute monitoring and new peak detection, as well as relative quantitation for targeted peaks, as defined using the powerful peptide workbook within the BioPharma Finder software. The workbook allows fast screening of large data sets for potential CQA identification, which is verified by a unique MS2 spectra prediction algorithm, isotope distribution and accurate mass information.
For laboratories that need to acquire, process and report results within a compliant environment, the Peptide Workbook can be seamlessly imported directly into the Chromeleon Chromatography Data System. The ability to maintain compliant workflows by performing method development within the BioPharma Finder software, and then intact mass deconvolution within the BioPharma Finder software or Chromeleon CDS creates a powerful solution serving the entire biopharmaceutical development pipeline.
Learn how innovation and monitoring strategies can reduce the number of tests and enhance the methodology of validating impurity.
Representation of the multi-attribute method workflow, where the BioPharma Finder software is used to comprehensively characterize biotherapeutics and determine any potential CQAs to be monitored. The flexibility afforded within the BioPharma Finder software is designed for the discovery environment where compliance is not always necessary. When compliance is required for the routine environment, the knowledge gained can be seamlessly transferred into the Chromeleon CDS software for CQA and new peak monitoring.
Featured resources
LC/MS characterization of lysine-linked antibody drug conjugate
Peptide mapping of trastuzumab using LC-MS workflow
Monoclonal antibody mass confirmation using intact protein deconvolution
HCP identification and monitoring
Download application note ›
mRNA Direct Sequence Mapping
Use MAM 2.0 workflow for seamless transition to quality control
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