What is large-scale discovery proteomics?

What is large-scale discovery proteomics?


Proteomics has the potential to bring about transformative changes in our understanding of biology and the therapeutic targets linked to genetic alterations, drug pharmacology and disease. The application of modern proteomics is already enabling researchers to study disease proteomes with a precision never before possible. Proteomics also holds many potential advantages over genomics alone, giving functional and actionable information linked to the phenotype – as proteins themselves can be clinical biomarkers and therapeutic targets. The use of proteomics can help to speed up drug development by reducing risks and increasing the efficiency of the process.


How can large-scale discovery proteomics help drug research and development?


Biognosys has perfected its mass spectrometry (MS) based proteomics technology so that large-scale analyses can be conducted using high throughput automation, meaning that thousands of proteins can be quantified across thousands of biological samples. Importantly, our large-scale discovery proteomics approach is untargeted, not limited to a narrow, pre-defined set of proteins that were previously already known to have clinical significance. This enables unbiased, true discovery of novel biomarkers and therapeutic targets. Also, having analyzed a vast amount of proteomics data across various species and biological matrices, we have an extensive understanding of the proteome; meaning our study reports will provide you with actionable insights to inform your decision making.

“Leveraging our extensive knowledge of the proteome to advise our customers on the best proteomics strategy for their research needs is fundamental to our approach.”

Jakob Vowinckel, PhD
Head of Discovery Proteomics

How does large-scale mass spectrometry proteomics works in practice?


Step 1: Getting to the heart of your objectives


We work with you to really understand your research, and then design the most suitable proteomics strategy for you, working alongside you as a partner. Next, a scientific project manager is assigned to you and the project starts the moment we receive your tissue or biofluid samples.



Step 2: Mass spectrometry analysis begins


We take your samples first through our Hyper Reaction Monitoring (HRM™) workflow, a highly parallelized data analysis method based on Data Independent Acquisition (DIA), invented and patented by Biognosys. HRM is a label-free discovery proteomics workflow that is ideal for identifying differentially expressed proteins or highly multiplexed protein quantification on a proteome level. Spectronaut™, our industry-leading DIA software, is then used to generate highly accurate, deep, and specific quantitative information, delivering huge volumes of reliable data at the peptide level.


MS-based proteomics has the advantage over other technologies that it provides high specificity and allows direct quantification of analytes. Biognosys has further standardized the MS process so that we are now conducting high throughput automation and parallelization, meaning study samples can be processed across multiple instruments with high reproducibility.


As of today, we can quantify up to 1,700 proteins in blood plasma (known to be a less approachable sample type) in a single experiment. This is set to increase to 3,300 proteins for large-scale plasma discovery projects by the end of 2022. We are operating one of the largest high-end MS facilities in the world, allowing us to scale up our throughput for large-scale discovery proteomics to 250,000 samples per year, enabling industry-leading project turnaround times.



Step 3: Development of your actionable insights report


Finally, and most importantly, we convert your data into actionable insights. Our data analysts are PhD-level scientists with strong backgrounds in proteomics and other omics who highlight and pre-digest the most interesting aspects of your data. Because we apply machine learning and artificial intelligence, your project report gives meaningful insights which may be applied directly to your R&D and clinical research. Specifically, you will receive a simple and complete data matrix with precise quantity values for each protein in each sample, which can be interpreted by any researcher without the need for expert knowledge. HRM also turns a physical sample into a digital proteome map – so the data can be revisited and reinterpreted at any time without the need for re-measuring the original sample.

Biognosys can quantify up to 10,000 proteins from tissue in a single experiment.

Illustration of Indivumed large-scale discovery proteomics study results from 1,755 NSCLC clinical samples

(Vowinckel J et al.; presented as poster at AACR 2020)

The addition of our large-scale discovery proteomics capability to our existing, diverse range of products and services, allows us to support our customers in performing studies comparable in scale to genomics population screening or genome-wide association studies. The range of applications of our technology so far includes among others Tissue Biomarker Discovery, Biofluid Biomarker Discovery, and Phospho Profiling Studies.


“Delivering truly actionable insights for our pharma and biotech customers is at the heart of our mission, translating their investment into efficiencies for their biomarker discovery and drug development programs.”

Karel Novy, PhD
Chief Operating Officer

Allow Biognosys’ cutting-edge proteomics technology, facility and data competence to transform your R&D.

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