Spectronaut 21 (DIA) and SpectroMine 6 (DDA): cloud-enabled processing, increased identifications, enhanced PTM identification and site localization confidence, improved ion mobility metrics, and open search capabilities for detection of rare modifications
Collaboration with SISCAPA Assay Technologies (SAT): qualification of ultrasensitive targeted protein assays for clinical research, including UBE3A quantification in CSF for monitoring of Angelman syndrome
iST-S optimized low-input proteomics: affordable, reproducible deep proteome coverage from low input material with robust performance across diverse platforms and cell models
Optimized P2 single-particle enrichment for serum and plasma proteomics: affordable, robust ultra-deep proteome coverage with further increased protein group IDs
Enhanced LC-MS workflow for FFPE tissues: Combines BeatBox, iST, PepSep Advanced, nanoElute 2, timsTOF and Spectronaut to enable scalable, high-throughput FFPE proteomics with deep coverage from minimal input materials
Advances in PepSep nanoLC: improved robustness, throughput, and reproducibility through integration of ProteoElute, PepSep Advanced, timsTOF and Spectronaut workflows
MxQuant kit hybrid metabolomics on timsMetabo: unified targeted and untargeted metabolomics within single PASEF measurement to increase depth while reducing complexity
The Biognosys Group, a leader in mass spectrometry-based multiomics, announces advancements across its integrated multiomics portfolio, highlighting next-generation software, sample preparation, enrichment, and separation technologies for proteomics and metabolomics. With the launch of Spectronaut 21 and SpectroMine 6, continued innovation in ultrasensitive targeted assays, and optimized workflows including iST-S, P2 single-particle enrichment, FFPE tissue workflows, and PepSep nanoLC solutions, the Biognosys Group further enhances sensitivity, reproducibility and throughput, enabling scalable, high-quality molecular profiling for discovery, translational, and clinical research applications.
Spectronaut 21 and SpectroMine 6 set new benchmarks in DIA and DDA proteomics:
increased identification rates with ~10% more protein groups across a cohort of 65 proteomics datasets and ~11% more peptides across a cohort of 27 immunopeptidomics datasets, enabled by advanced directDIA, next-gen AI-driven PTM prediction, enhanced PTM localization and stoichiometry, improved computational efficiency up to 15% faster processing of directDIA data, and new user-centric features for PTM and labeling workflows.
Yansheng Liu, PhD, Associate Professor, Yale University School of Medicine, Department of Pharmacology, said: “Spectronaut is our preferred DIA analysis software due to its high performance and user-friendly interface, which makes analyzing our complex and multiplex DIA datasets both easy and reliable.”
Prof. Dr. Matthias Mann, Director Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, said: “Spectronaut is an excellent addition to our informatics capabilities, especially for its thorough analysis large scale DIA phosphopeptide data and advanced modification localization algorithm.”
Biognosys and SISCAPA Assay Technologies partner to advance ultra-sensitive targeted proteomics for clinical research applications: the partnership combines Biognosys’ expertise in proteomics and data analysis with SISCAPA’s peptide antibody enrichment for high-sensitivity absolute protein quantification. An ultrasensitive assay for quantifying UBE3A protein levels in human cerebrospinal fluid (CSF) supports therapeutic research monitoring in patients with Angelman syndrome. This highlights the potential of targeted proteomics to enable precise, clinically actionable biomarker measurements.
Oliver Rinner, PhD, Senior Vice President of the Biognosys Group commented: “Clinical development requires not only promising therapeutic approaches, but also reliable tools to measure whether those therapies are having their intended effects. By combining Biognosys’ expertise in highly sensitive, quantitative proteomics with MJFF’s LITE framework, we aim to accelerate the development of biomarkers that can guide Parkinson’s drug development and de-risk clinical trials.”
iST-S enables high-throughput, reproducible deep proteomics from ultra-low input samples: Biognosys presents iST-S, an optimized extension of the trusted PreOmics iST workflow, enabling robust proteomic depth from sub-microgram sample inputs. The optimized iST-S technology delivers affordable and highly reproducible proteomic depth from as low as 0.5 µg starting material. Internal benchmarking across diverse LC-MS platforms, including timsTOF HT and Orbitrap Astral, demonstrates consistent identification of ~7,500 protein groups across 0.5–10 µg inputs from HeLa and HEK293 cells. Importantly, preserved peptide physicochemical properties ensure reliable detection of proteins such as CDK9, HDAC1, and ERBB2 even at the lowest input levels. Across commonly used cancer cell lines, iST-S enables up to 10,000 protein identifications with high reproducibility (CV ~10%), underscoring its suitability for high-throughput, standardized low-input proteomics and large-scale screening applications.
Optimized P2 single-particle enrichment expands deep proteome coverage to serum samples: Biognosys presents the novel P2 single-particle enrichment optimized for serum and alternative plasma matrices, extending the performance of protein corona-based enrichment beyond EDTA plasma. P2 leverages protein corona formation on a single engineered particle to enable reproducible, high-throughput enrichment in a single-well format. Compared to the original P2-iST plasma kit and neat measurements, the optimized workflow demonstrates up to 4-fold increased protein IDs in serum and heparin plasma, with robust quantitative performance. Linearity experiments show excellent correlation (R² up to ~0.97–0.98) across spike-in levels, supporting reliable quantification. In addition, the P2 workflow shows robustness across plates, batches, laboratories, and blood collection methods, highlighting its suitability for large-scale clinical proteomics studies.
A recent independent study (Völlmy et al., Journal of Proteome Research 2026) reported the first direct comparison evaluating the quantitative performance of different technologies for deep plasma proteomic enrichment. The bead-based enrichment technologies outperformed antibody-based depletion workflows in proteomic depth, while ENRICH iST, only using 20 uL of input material, maintains a high correlation to neat plasma (r ≈ 0.7), suggesting that the relative abundance profiles of the plasma proteins are not substantially altered. The new P2 technology achieved the highest depth (~4,040 proteins at 50 µL input) with a median CV of 18.4%. The authors reported that measurements of proteins annotated as secreted were not significantly affected, enabling reliable quantification of biologically relevant plasma proteins.
Markku Varjosalo, PhD, Program Director, Institute of Biotechnology, HiLIFE, Faculty of Medicine, University of Helsinki & Scientific Director, Helsinki Proteomics Center, said: “At the Helsinki Proteomics Center, we have benchmarked essentially all major plasma depletion/enrichment strategies on the market. When depth matters, P2-iST consistently comes out on top. For us it has been a game changer — it puts robust, deep plasma proteomics into the hands of any lab without expensive proprietary hardware. The reproducibility and depth with P2-iST makes it ideal for medium-scale clinical and translational plasma studies.”
Carina Sihlbom Wallem, PhD, Head of Unit, Proteomics Core Facility, University of Gothenburg, BioMS and SciLifeLab, said: “By adding P2 Plasma Proteomics Enrichment, we can now offer a broader and more comprehensive range of solutions to our users. We are grateful to the Biognosys team for the excellent partnership, and for their professionalism and effort in helping us establish the workflow at our facility.”
Integrated LC-MS workflow enables scalable, high-depth proteomics from FFPE tissue:
Biognosys presents an optimized end-to-end FFPE proteomics solution combining best-in-class sample preparation, separation, and data analysis. The integrated workflow leverages PreOmics BeatBox and iST, paired with Bruker’s PepSep Advanced columns on the nanoElute 2, timsTOF, and Spectronaut, to enable scalable and high-throughput FFPE analysis from sample to result. The plate-based workflow eliminates the need for deparaffinization, facilitating efficient processing of retrospective clinical cohorts. It supports diverse FFPE formats, including curls, punches, and microdissection and enables identification of ~5,000 protein groups from as little as two FFPE curls, making it suited for large-scale biomarker discovery studies.
Salla Keskitalo, PhD, Unit Director, Viikki Proteomics Unit, University of Helsinki, Finland, said: “The BeatBox has streamlined our proteomics workflows, particularly for challenging FFPE and tissue samples. Its robustness, ease of automation, and compatibility with Evosep One coupled to either timsTOF or Astral systems have made BeatBox essential for high-throughput and reproducible clinical proteomics."
Biognosys advances PepSep nanoLC performance for high-throughput proteomics:
Advanced nanoLC performance integrates the Bruker proteoElute LC system with PepSep Advanced columns coupled to timsTOF and Spectronaut 21. The workflow demonstrates robust, high-throughput proteomics with stable operation over extended acquisitions up to 12 days without intervention, maintaining retention time deviations below 1%. High proteome depth is achieved with up to ~10,600 protein groups depending on gradient length, while ensuring strong quantitative precision (CV ~20%). The system minimizes carry-over to below 1% even at high sample loads, supported by optimized wash strategies reducing residual contamination, enabling reliable, reproducible analysis in demanding high-throughput settings.
MxQuant kit introduces hybrid targeted and untargeted metabolomics on timsMetabo:
Bruker and biocrates are expanding standardized quantitative metabolomics, while previewing a novel workflow that unifies quantitative targeted metabolomics with untargeted discovery on the timsMetabo platform. biocrates’ quantitative kits are now also available for workflows using the EVOQ triple quadrupole, enabling standardized, kit-based targeted and absolute quantitation approaches within familiar LC-TQ-MS operations. This expands routine access to reproducible, comparable metabolomics data with integrated quality control and streamlined methods designed for scale across translational and applied research settings. Biognosys is now offering these targeted workflows in its Massachusetts lab as a CRO service for biocrates targeted, absolute quant metabolomics. This CRO option enables high-quality quantitative metabolomics without in-house method deployment, supporting rapid project start up, capacity scaling, and standardized data generation for multi-site studies.
Bruker is previewing a novel hybrid metabolomics workflow that combines quantitative measurement enabled by biocrates kits with discovery on the timsMetabo in a single integrated experiment. This hybrid quantitation plus discovery workflow addresses a central challenge in metabolomics: the need to combine standardized quantitative rigor with exploratory breadth without doubling sample consumption, instrumentation time, or method complexity to gain disease biology insights in population-scale translational research and exposomics.
“By combining quantitative metabolomics with discovery on timsMetabo, we are unifying targeted and untargeted workflows in a way that produces data-rich and future-proof digital metabolome archives,” said Matthew Lewis, PhD, Bruker’s Vice President - Metabolomics and Lipidomics.
About Biognosys Group
The Biognosys Group brings together the Bruker Corporation (Nasdaq: BRKR) affiliates Biognosys, biocrates, and PreOmics to deliver integrated solutions across proteomics, metabolomics, and lipidomics. The Group enables seamlessly connected mass spectrometry workflows, making advanced multiomics technologies accessible to laboratories worldwide.
Its ecosystem spans high quality consumables, software, and contract research services. Committed to a vendor neutral approach, the Biognosys Group supports open collaboration and broad compatibility across leading mass spectrometry platforms. All solutions are modular by design, allowing customers to choose the level of support that best fits their needs, from ready to use kits and software to guided implementation, or fully integrated end to end CRO services.