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Next Generation Proteomics Solutions

Dear Subscriber, 

At Biognosys, we are committed to the continuous development of innovative and intuitive software products that support any quantitative proteomics workflow: data-independent acquisition (DIA), data-dependent acquisition (DDA), targeted proteomics (SureQuant/PRM/SRM), and isobaric labelled quantification (ILQ) experiments. Below we highlight recent examples where our software solutions Spectronaut, SpectroDive, and SpectroMine enabled researchers to complete cutting-edge projects in systems biology.

Unravelling the Ubiquitination of Circadian Clock Proteins with Spectronaut

Fynn M. Hansen F.M. et al. Nature Communications 2021

Ubiquitination plays a pivotal role in the regulation of the circadian clock in mammals. Comprehensive profiling of endogenous ubiquitination is challenging due to its low stoichiometry and varying ubiquitin-chain topologies. Here the authors developed a sensitive workflow that combines diGly antibody-based enrichment, optimized DIA acquisition, and analysis in Spectronaut with spectral libraries that contain over 90,000 diGly peptides. This workflow enabled in-depth diGly proteome coverage in single-shot experiments and uncovered hundreds of cycling ubiquitination sites across the circadian cycle.


Deep Characterization of the HLA Immunopeptidome with Spectronaut

Pak S. et al. MCP 2021

T cells recognize short peptide antigens of 8–11 amino acids in length presented by human leukocyte antigen (HLA) molecules on tumor cells. Deep characterization of the HLA immunopeptidome can advance the development of therapeutics against cancer. Due to the limited amount of HLA peptides eluted from clinical samples, a comprehensive multi-HLA library was generated for DIA analysis in Spectronaut. The use of a complex multi-HLA spectral library, which included sample-specific libraries and libraries that combined up to 40 different immunopeptidomics samples, boosted sensitivity without compromising specificity.


Potential Targets to Treat Drug-resistant Tumors Uncovered with Spectronaut’s directDIA Phosphoproteomics Workflow

Franciosa G. et al. Nature Communications 2021

Deregulation of the Notch signaling pathway has wide-ranging effects across multiple cancer types. The clinical efficacy of γ-secretase inhibitors (GSIs), small molecules that block Notch cleavage and subsequent activation, is limited due to the emergence of drug-resistant tumors. This work systematically compares GSI resistant and sensitive tumor cells by DIA phosphoproteomics, using Spectronaut’s directDIA workflow. The results highlighted a rewiring of the signaling networks upon Notch inhibition and identified druggable pathways in cancer that can be targeted in combination treatments to overcome resistance.


Investigating Age-dependent Changes in Muscle Stem Cell Functionality with Spectronaut and SpectroDive

Schüler S.C. et al. Cell Reports 2021

Muscle stem cells (MuSCs) confer a remarkable regenerative capacity to skeletal muscles, which however, declines during aging due to a reduction in MuSCs number and functionality. Since the interaction of MuSCs with the stem cell niche is critical to provide the proper cues for self-renewal, researchers investigated how aging alters the communication between MuSCs and their niche. Deep proteome DIA analysis in Spectronaut followed by PRM in SpectroDive unraveled aging-affected signaling axes and showed that the accumulation of the secreted protein Smoc2 contributes to their perturbation in MuSCs during aging.


Multi-omics Investigation of Daily Exercise Performance with SpectroMine

Maier G. et al. The Journal of Physiology 2021

Muscle activity has been proposed to be regulated by the circadian clock and to act as an upstream Zeitgeber to synchronize physiological and molecular responses in muscles and other peripheral tissues. Here the authors employed a multi-omic approach to study the circadian regulation of endurance performance and control of the circadian clock by exercise. The quantitative analysis of both the phospho- and total proteome labelled with isobaric TMT tags was conducted in SpectroMine. This study provides a starting point to identify and validate markers of exercise performance, possibly contributing to personalized training design and patient care.

To learn more about how our products could support your research, contact our team at

Best regards, 
The Biognosys Team

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