Software Solutions
ProteoScape Package 2025c
Bruker ProteoScape Package 2025c includes Bruker ProteoScape and GlycoScape software applications. They are our software dedicated to bottom-up proteomics and glycoproteomics applications, respectively. Bruker ProteoScape is a GPU-powered platform that integrates third-party tools (such as BPS Novor, TIMSrescore and Spectronaut®) while utilizing the concept of data streaming to realize fully customizable real-time processing workflows including on-the fly decision making based on the data generated. With workflows for the analysis dda-PASEF, dia-PASEF and diagonal-PASEF being supported. GlycoScape extends these functionalities for glycopeptide identification via the Myriad workflow, providing real-time N-glycan identification without a pre-defined glycan database. The ProteoScape Package can only be installed on hardware designated for it and is shipped with purchase of the license.
Disclaimer
You are only eligible to download this installation of ProteoScape 2025c if you already have a valid license for ProteoScape.
You should acquire the license before downloading. Please contact your Bruker sales representative in this case.
Software Download:
TASQ® 2026 & MetaboScape® 2026
MetaboScape® is our all-in-one software suite dedicated to discovery metabolomics, lipidomics and phenomics. It provides the powerful T-ReX® algorithm family together with comprehensive statistics and CCS-aware compound identification workflows. Its main purpose is to allow users to readily pinpoint and identify relevant drugs, metabolites, lipids or glycans to set them in a biological context.
TASQ® provides a turnkey data analysis solution for when there is a requirement to screen, confirm and/or quantify hundreds of compounds in a single analysis.
MetaboScape and TASQ Software Training courses available:
Disclaimer
You are only eligible to download this installation of TASQ® 2026 and MetaboScape® 2026 if you already have a valid license for TASQ® 2026 or MetaboScape® 2026.
Do not download and install this version for TASQ® 2025b / MetaboScape® 2025b or earlier because the licenses are specific to version 2026 and will render your installation inactive.
Older versions of the software solutions require a chargeable license upgrade, and you should acquire the upgrade before downloading. Please contact your Bruker sales representative in this case.”
Software Download:
TASQ® 2025bSR1 & MetaboScape® 2025b
MetaboScape® is our all-in-one software suite dedicated to discovery metabolomics, lipidomics and phenomics. It provides the powerful T-ReX® algorithm family together with comprehensive statistics and CCS-aware compound identification workflows. Its main purpose is to allow users to readily pinpoint and identify relevant drugs, metabolites, lipids or glycans to set them in a biological context.
TASQ® provides a turnkey data analysis solution for when there is a requirement to screen, confirm and/or quantify hundreds of compounds in a single analysis.
MetaboScape and TASQ Software Training courses available:
Disclaimer
You are only eligible to download this installation of TASQ® 2025bSR1 and MetaboScape® 2025b if you already have a valid license for TASQ® 2025 or MetaboScape® 2025.
Do not download and install this version for TASQ® 2024b / MetaboScape® 2024b or earlier because the licenses are specific to version 2025 and will render your installation inactive.
Older versions of the software solutions require a chargeable license upgrade, and you should acquire the upgrade before downloading. Please contact your Bruker sales representative in this case.
Software Download:
SCiLS
The world-leading software for analysis of mass spectrometry imaging data from all major mass spectrometry vendors, including Bruker’s FLEX series and MRMS.
QuPath to SCiLS Export Plugin
QuPath is an open, flexible and extensible software platform for whole slide image analysis. It provides powerful annotation tools like a magic wand and supports multiple histological data formats. This QuPath plugin allows to export images and annotations from QuPath to SCiLS™ Lab.
The QuPathToSCiLS plugin is released under the GNU General Public License, version 3.
For Research Use Only. Not for Use in Clinical Diagnostic Procedures
SCiLS_align_peptides software
Scils_align_peptides is a tool to re-calibrate MALDI imaging datasets of tryptic peptides acquired on axial MALDI-TOF instruments. The re-calibration is based on the peptide pattern in the baseline, is fast and requires no parametrization. Extract the contents of the zip-file to a local folder and follow the steps described in the README.txt file.
The tool implements the re-calibration method described in:
T. Boskamp et al.
Using the chemical noise background in MALDI mass spectrometry imaging for mass alignment and calibration
Anal. Chem. (2019) DOI: 10.1021/acs.analchem.9b04473
ZIP (38 MB)
SCiLS™ Scope: MALDI HiPLEX-IHC made easy
SCiLS™ Scope is a software solution for analyzing MALDI HiPLEX-IHC data allowing for intuitive review of targeted proteins within a pathological context and providing meaningful data from multiplexed images. The lightweight solution and result images can be easily distributed, thereby enabling exchange with collaboration partners.
Compatibility
Hardware: neofleX, timsTOF flex
For the automatic generation of OME-TIFF files are required:
- SCiLS Lab 2024b or higher
- Compass fleX series 2025 or Compass timsTOF 2024b - or higher
For creating OME-TIFF files manually SCiLS Lab 2023c or higher is required.
OmniScape™ 2026
OmniScape™ is our software dedicated to Top-Down protein sequence analysis. It provides a reliable protein sequence confirmation workflow using the powerful OmniWave™ algorithm for in-depth isotope pattern extraction and extended capabilities for PTM and proteoform assessment.
In case of unknowns, it allows to automatically identify sequence tags to be used in downstream MS-BLAST (Sunyaev lab, Harvard) homology searches for de novo protein identification.
Multiple dataset results can be combined into a single high-quality result for further increased sequence coverage and certainty in PTM and proteoform assessment, whether different experimental conditions were applied, or even different type of instruments were used (axial/oTOF-MALDI, ESI-QTOF, timsTOF, MRMS). 3rd party instrument’s data are supported through a text-based spectrum format.
Single spectra as well as LC_MS/MS or DI-MRM datasets can be analyzed.
OmniScape™ provides a unique Top-Down protein sequence data analysis solution addressing the analytical needs in academic research as well as for the biotech industry.
Disclaimer
You are only eligible to download this installation of OmniScape™ 2026 if you already have a valid license for OmniScape™ 2026.
You should acquire the license before downloading. Please contact your Bruker sales representative in this case.
Software Download:
BioPharma Compass® 2026
BioPharma Compass® is our software dedicated to the routine analysis of biopharmaceuticals. It is a workflow-driven software that allows the MAM analysis of intact proteins as well as proteolytic digests and includes the sequence verification of synthetic oligonucleotides and side product quantitation (OligoQuest). Workflows can comprise all steps from automatic data acquisition to report generation. ESI and MALDI data can be used for the workflow Mult Target Screening for oligonucleotide and peptide synthesis QC or clone selection for instance.
The data mover functionality provides data security in the protected database.
BioPharma Compass supports work under regulatory conditions together with the Regulatory Toolkit option with extensive user rights management and audit trail.
Disclaimer
You are only eligible to download this installation of BPC® 2026 if you have a valid license. Installation of BPC® 2026 will render your current installation inactive if you don´t have such license.
Older versions of the software require a chargeable license upgrade and you should acquire such upgrade before downloading. Please contact your Bruker sales representative in this case.
Do not download and install BPC® 2026 if you have a previous version of BPC “Server” (MSSQL database). BPC® 2026 is only compatible with the PostgreSQL database type. Please contact your Bruker sales representative in this case.
Software Download:
BiopharmaCompass 2026 - Tutorials:
MALDI PharmaPulse® 2023c software
MALDI PharmaPulse® 2023c software can be used for triggering acquisition or visualization of data from timsTOF flex MALDI PharmaPulse or timsTOF flex MALDI PharmaPulse MALDI-2 instruments. It supports a broad range of HTS applications for drug discovery. Its automation interface allows for integration in high-throughput environments.
Disclaimer
You are only eligible to download this installation of MALDI PharmaPulse® 2023c if you already have a valid license for MALDI PharmaPulse® 2023c.
Do not download and install this version when using rapifleX®.
Software Download:
BioTools
BioTools™ provides support to mass spectrometry-based proteomics and protein analysis. It is designed for the interpretation of MS and MS/MS spectra of protein digests or peptides obtained with Bruker QTOF and all MALDI instruments. Bio Tools has been developed to translate mass spectral information into knowledge in both major approaches for proteomics and protein analysis: screening approaches generating high amounts of data and in-depth analysis of single or a low number of proteins, such as modifications, polymorphisms or splice variants. Also, MALDI/ESI oligonucleotide MS/MS spectra can be interpreted.
Features of BioTools for automated protein identification via library search
- Protein identification as batch process using MALDI-TOF fingerprint and complete LCMS/MS data. Mascot 2.8 and 3.0 are supported.
- Batch result reporting, including visualization of MALDI-TOF results in MTPviewer format.
- De-novo sequencing support and subsequent protein identification.
Features of BioTools for detailed structural analysis of selected proteins
- Automatic MS and MS/MS spectra annotation based on protein sequences using theoretical digests.
- Sequence Editor for creating and editing sequences, with full support for the definition of modifications and cross-links, including disulfide bonds.
- Screening tools for post-translational modifications (PTMs).
- Fine-structure characterization of proteins.
- De novo sequencing in the RapiDeNovo module.
Data import/export
- Datasets can be exchanged (bidirectionally: JP EAKS only) with DA 6.2 and higher, formats: baf, bsc, mgf.
- MALDI datasets processed in FA can be imported using the XMASS data format.
PolyTools
Industry standard software for the analysis of polymer mass spectrometry data including Kendrick Mass Defect plots.
DataAnalysis 6.2
DataAnalysis is our multi-purpose solution for mass spectrometry data processing. It supports processing of analyses acquired on all timsTOF, QTOF, ion trap and MRMS instruments.
The DataAnalysis 5.2 license (DAL01704) is also valid for DataAnalysis 6.2. Please contact your local sales representative.
The molecular formula tools are included in the DataAnalysis 6.2 setup, yet they are also available as separate Molecular Formula Tools setup without licensing.
DataAnalysis 6.1
DataAnalysis is our multi-purpose solution for mass spectrometry data processing. It supports processing of analyses acquired on all timsTOF, QTOF, ion trap and MRMS instruments.
The DataAnalysis 5.2 license (DAL01704) is also valid for DataAnalysis 5.3, 6.0 and 6.1. Please contact your local sales representative.
The molecular formula tools are included in the DataAnalysis 6.1 setup, yet they are also available as separate Molecular Formula Tools setup without licensing.
DeutEx
DeutEx is a versatile software package designed for the analysis of Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) data. It supports the processing of high-resolution, high mass accuracy MS data from Bruker MRMS (FT-ICR MS) as well as data from timsTOF, q-TOF, and even MALDI-TOF instruments. DeutEx operates on peak-picked data stored in an open format (simple text file), which can be easily exported from Bruker’s DataAnalysis software.
Software Download: