Research Phases

Biognosys is the world leader in the application of next-generation proteomics solutions to accelerate your research and drug development timelines.

Biognosys’ proteomics platform offers a versatile toolbox to provide integrated functional insights across the drug discovery pipeline, from novel target discovery and validation through to profiling mechanisms of action in experimental models and biomarker discovery in early and late-phase clinical studies.

Our proteomics solutions provide the detailed data you need at every stage of the journey:


Discovery Biology ➜ Pre-clinical Evaluation ➜ Clinical Studies




Discovery Biology

Our proteomics solutions provide the versatility and quick delivery of results needed to inform go/no-go decision-making throughout the drug discovery process. Using Biognosys’s Discovery Proteomics workflows to generate functional data offers the opportunity to discover new pathways and targets, and to develop first-in-class therapeutics.

Here are a few examples of how proteomics has provided a deeper understanding of biology and better characterization of therapeutic profiles to de-risk drug development at an early stage.


Target Discovery

Global proteomic profiling of tumors to identify novel therapeutic targets

Biognosys’ proteomics workflows enable the identification of dysregulated proteins in disease, revealing deep insights into cancer biology and new targets for further exploration.

Biognosys’ Discovery Proteomics approach was used to deeply characterize global tumor proteomes from melanoma FFPE sections to uncover proteins and pathways implicated in the disease, highlighting potential novel therapeutic targets.


Case Study: Novel Target Discovery in Melanoma                

Application: Biomarker Discovery

Small Molecule Target Deconvolution

Proteome-wide characterization of the binding specificity and selectivity of small molecules

Biognosys’ drug Target Deconvolution approach Limited Proteomics Mass Spectrometry (LiP-MS) can effectively identify protein drug targets and characterize their binding properties in complex proteomes without the need for compound modification or labeling.

In this specific example, LiP-MS was used to distinguish the specificity and selectivity of different kinase and phosphatase inhibitors.


Case Study: Target Deconvolution of Drug Specificity and Selectivity

Publication: A machine-learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes (Nature Communications, 2020)

Technology Video: LiP-MS: A Novel Target Deconvolution Approach

Application: Target Deconvolution


«The LiP technology is a very valuable tool to identify target and off-target of novel compounds whatever the organism and to support the process of target deconvolution in research. The interactions with Biognosys are very nice and fruitful. The team is engaged and responsive throughout the project.»

Thomas Knoblauch
Laboratory Manager, Bayer


Pre-clinical Evaluation

Our mass spectrometry-based proteomics tools and techniques provide a flexible platform that works across all types of biological samples, species, and disease indications. This enables proteomics markers identified in cell-based and animal studies to be validated in the pre-clinical setting in order to increase confidence in your therapeutic approach, identify potential off-target interactions or side effects and improve the chances of success in clinical trials.

Here are a few examples of how our proteomics workflows can be applied in the pre-clinical space.


Mechanism of Action

Profiling of the proteomic response to therapy in animal models

Proteomic profiling of tissue or tumor samples from animal models of disease reveals detailed information about the proteins and pathways involved in response to therapy.

For example, Biognosys’ Discovery Proteomics was used to investigate the role of immune cell depletion in the response to PD-1 blockade in syngeneic mouse models.


Case study: Mechanism of Action of Immunotherapy in Syngeneic Mouse Models

Application: Mechanism of Action Studies

Targeted Protein Quantification

Absolute quantification of targeted protein panels

Biognosys’ Target Proteomics workflows provide a precise, sensitive and scalable platform for monitoring simultaneously the expression of hundreds of proteins. The high specificity of the Targeted Proteomics workflows enables proteins with minor sequence differences to be resolved. Assays for specific proteins of interest can be readily developed in a matter of weeks and applied across hundreds or thousands of samples collected at multiple time points, making proteomics an invaluable tool for studying the biology, progression, and treatment of rare diseases.


Case Study: Targeted Protein Quantification

Application: Protein Quantification


Clinical Studies

Our mass spectrometry workflows offer high-precision, quantitative proteomic data at unprecedented depth and reproducibility over thousands of samples taken at multiple timepoints. We are bringing Good Clinical Practice (GCP)-compliant workflows at our service facility in Switzerland, making proteomics the method of choice for large-scale translational and clinical studies.

These case studies show the benefit of proteomics to identify and measure novel biomarkers in samples ranging from biological fluids such as blood plasma/serum or urine to fresh frozen tissue and FFPE sections.


Blood-based Biomarker Discovery

Deep proteomics characterization of biofluids

Biognosys’ Discovery Proteomics approach offers a highly reproducible and scalable workflow for analyzing biofluids such as blood plasma or serum, making it the ideal choice for your biomarker research needs.

Our plasma/serum workflow enables robust and reproducible quantification of 600+ proteins in plasma or serum samples across large-scale studies. The use of our proprietary reference kit PQ500 enables the absolute quantification of up to 500 proteins in human plasma or serum.

For deeper profiling and exploration of lower abundant proteins, we have developed a workflow that depletes samples of the most common plasma proteins to reveal the less abundant informative molecules, allowing the quantification of 1’000+ proteins. 

Browse the case studies below to see the power of our blood-based proteomics workflows to identify novel biomarkers associated with disease progression and response to therapy in lung cancer.


Case Study: Plasma Proteome Profiling and Clinical Outcome Association in Subjects with NSCLC

Product Brochure: PQ500: The Key to the Plasma Proteome

Application: Biomarker Discovery

Large-scale Longitudinal Proteomics Studies in Plasma

Deep proteomics characterization of blood-based biomarkers

Comprehensive, high throughput profiling of the plasma proteome enables a holistic analysis of the health of an individual. In collaboration with Nestlé, Biognosys’ Discovery Proteomics was used in a large-scale plasma study of more than 1'500 samples collected over a longitudinal clinical study of weight loss. The analysis revealed biomarkers associated with obesity, cardiovascular and liver-associated diseases, and diabetes.


Case Study: Next Generation Proteomics in Large-Scale Plasma Clinical Analysis

Publication: Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance (Molecular and Cellular Proteomics, 2019)

Application: Biomarker Discovery

Biomarker Discovery in Neurodegenerative Diseases

Global proteomic profiling of CSF to identify novel disease biomarkers

Progress in neurodegenerative conditions such as Alzheimer’s disease has been hindered by a lack of knowledge about the underlying biological processes and relevant biomarkers. By applying Biognosys’ Discovery Proteomics workflow, we deeply characterized the proteome of cerebral spinal fluid samples (CSF) of Alzheimer’s patients to identify proteins and pathways implicated in the progression of the disease.


Case study: Global Proteomic Profiling of CSF to Identify Disease Biomarkers of Neurodegeneration

Application: Biomarker Discovery

Urine-based Biomarker Discovery in Fibrosis

Global Proteomics Profiling in Urine

There is an increasing need for the identification of non-invasive biomarkers that can reliably predict disease progression and treatment response in the clinical setting. Urine provides a valuable and underexplored source of proteomics biomarkers. In collaboration with Pliant Therapeutics, we used Biognosys’ Discovery Proteomics to profile urine from people with idiopathic pulmonary fibrosis, identifying a number of novel circulating proteins that can serve as biomarkers for monitoring progression and therapeutic response.


Poster: Urine Proteomics Identifies Novel Biomarkers of IPF Disease Progression and Resolution



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