Biopharmaceutical Analysis Software

BioPharma Compass®

A workflow-based software platform, suitable for mass spectrometry experts and routine users alike

Increase your productivity

Simplify routine workflows through automation

BioPharmaceutical Analysis Software

BioPharma Compass® methods secure highest reproducibility

Comprehensive workflows for automated biopharmaceuticals characterization from acquisition to report generation in a single process.
Well documented and preinstalled workflow methods provide for an easy operator’s onboarding and fast return on investment. Automated result interpretation supports shortening analysis turn-around times.
Adapts to user requirements and can be scaled from a single workstation to a client server network spanning a global biotech enterprise.
The regulatory toolkit supports work under regulated conditions. The data mover enables data transfer to a protected server for utmost data security and access is limited through the database under audit trail.
BioPharma Compass®

MAM analyses are enabled on the intact protein level as well as on the protein digest level

  • Automation – entire workflows can be automatically performed, from acquiring LC-MS data to generating a report it’s a single process
  • CFR 21 part 11 – compliance tools are on board, right after acquisition the data mover transfers data to a protected server
  • Multi Attribute Methods (MAM) - allow to bring the focus of analysis where you need it. Fast and in-depth MAM assays are supported on the protein as well as on the peptide level, respectively
  • QC analysis - high throughput analyses by ESI and MALDI provide synthesis quality information, e.g., for peptides or oligonucleotides, and provide QC reports automatically based on intact mass measurements
  • Ion mobility – using timsTOF instrument datasets, PASEF® data vastly increase the sequence coverage of biopharmaceuticals, the sensitivity in Host Cell Protein analysis (HCP) and provide CCS values as further molecular property of biomolecules

Workflow-based software solution
BioPharma Compass® 2023 is a wizard-driven, workflow-based software platform, suitable for mass spectrometry experts and routine users alike. Methods developed in a non-regulated environment can be locked down for routine biopharmaceutical analysis deployment. The customizable workspace adapts to the task at hand, including user interface, method development and data review, all from the comfort of your office PC.

The software simplifies routine biopharmaceutical analysis by offering dedicated LC-MS workflows from automated measurements to report generation. Such workflows are increasingly important in biopharmaceutical development, e.g., to verify protein sequences and to quantify product and process related heterogeneities such as modification profiles. These Multi-Attribute Methods (MAM) are implemented in BioPharma Compass® to reduce report turnaround times and increase throughput using high isotopic fidelity ESI-QTOF mass spectrometry.

MAM-assays can be carried out at the intact, domain (subunits) or peptide level using MS-only or MS/MS for top-down/middle-down and bottom-up analysis. Dedicated similarity scoring enables automatic result assessment and reporting with color-coded results to accelerate data review. Butterfly plots enable visual dataset comparisons.

BioPharma Compass®

BioPharma Compass® provides answers for biopharma R&D and process development

BioPharma Compass® automates common biopharmaceutical analysis workflows from acquisition and analysis to full reports. Laboratories under 21 CFR Part 11 compliance will benefit from the regulatory options, including leading data security features.

MAM protein screening workflow for intact protein analysis: glycoform and heterogeneity quantification

The high isotopic fidelity data from Bruker’s high resolution QTOFs and timsTOFs are uniquely beneficial to the identification of low level protein isoforms, clipping variants, ADCs or glycoforms during mAb characterization.

With Bruker's patented SNAP II algorithm and True Isotopic Pattern (TIP™) data quality, monoisotopic masses - e.g., of mAb subunits - are automatically assigned with low-ppm accuracy. Scoring as key element of the workflows provides automated quality assessment and simplifies batch comparisons. Butterfly plots allow visual dataset comparison.

RNA and oligonucleotides characterization with OligoQuest™
Building on algorithms designed for the annotation of high isotopic fidelity MS and MS/MS spectra, OligoQuest™ adds tools to simplify the characterization of oligonucleotides or RNA samples such as ASOs, siRNAs or sgRNAs.

Users can define oligonucleotide sequences in spreadsheet-type sample tables using their preferred syntax based on customized building blocks. Full length products and side-products are annotated with high confidence based on accurate mass assignment of MS and MS/MS peaks. Automatically generated visual quality attributes use a traffic light reporting system to reduce analysts time to verify results. In addition, the dynamic interface simplifies the manual review of the spectra used for identification for maximum trust in the results. Impurities are quantified both based on UV alone and by including the MS signal composition of LC-UV peaks. 

Top-Down Protein Sequencing: Sequence Variant Localization
Bruker's market-leading MALDI-TOF/TOF and ESI-QTOF-ETD high resolution platforms make top-down and middle-down analysis straightforward.

Automatic sequence confirmation and sequence curation help with N/C-terminal status assessment (clipping variants), localization of sequence variants and other quality attributes.

Peptide Level Analysis for Sequence Confirmation, Attribute Identification and Multi Attribute Monitoring (MAM)

Peptide Mapping: BioPharma Compass® simplifies peptide mapping data handling for high quality sequence confirmation, PTM identification and targeted MAM assay design.

MAM Peptide Screening: Clear overviews and detailed EIC-based validation make multi-attribute methods simple, delivering reliable results quickly. Results can be used for comparability assessments and time course analysis to monitor critical quality attributes (CQAs) quickly.

MAM Peptide Screening for PTM quantification based on Extracted Ion Chromatograms (EICs)

Host Cell Protein (HCP) Analysis: Taking full advantage of the benefits of Bruker’s timsTOF systems with trapped ion-mobility, BioPharma Compass® further extends Bruker’s expertise in biopharmaceutical characterization with the support for database searches of PASEF® datasets. Increased sensitivity from PASEF® leads to high sequence coverage and facilitates the confident identification of host cell proteins (HCP).

Butterfly plot showing a deconvoluted spectrum from a test sample and a reference.

OligoQuest™ output to confirm the sequence of an oligonucleotide and to quantify side products of its synthesis


Middle-Down sequence analysis of deglycosylated Cetuximab Fd subunit fully confirms the sequence.


Low ppm HCPs detected by PASEF®. Confirmed by CCS.
BioPharma Compass®

Suitable for a wide range of applications

Multi-Target Screening workflows for LC-ESI and LC-free MALDI-TOF workflows open a broad range of applications. Depending on application and throughput requirements, both ionization techniques can be used synergistically to provide fast and in-depth analysis reports. Reports can be exported in various formats to the file system. The analysis results are reported in a traffic light overview, covering different quality attributes to reduce operator time. Ion mobility data acquired on the timsTOF Pro allow to extend the molecular characterization by the highly accurate determination of collision cross sections (CCS).

A single method will work on 1000s of different samples, the information about them is provided as a sample table. The generic format supports very broad applications:


The QC analyses of synthetic oligonucleotides is one of several applications enabled by the Multi-Target Screening workflow.

BioPharma Compass® related information