Breaking the Barrier: Achieving Unprecedented Coverage in Tissue Proteomics

At Biognosys, we have always believed that mass spectrometry (MS) can play a revolutionary role in quantitative proteomics. Yet mass spectrometers have historically proven unreliable and inaccessible. Our mission was to leverage the power of MS technology to cell proteomics, creating a high-throughput research service capable of reproducibly analyzing many thousands of proteins across thousands of samples.

This month, we are delighted to announce another milestone. We can now reliably identify and quantify more than 13,000 proteins from a tissue sample in a single measurement.

This represents a near doubling of coverage in just a few years and, to our knowledge, is the deepest single shot proteome analysis that has been achieved to date.

Here’s how we did it and how you can access our groundbreaking TrueDiscovery™ tissue proteomics solution to accelerate your drug discovery and biomarker research.

Revealing True Biology Through Tissue Proteomics

Tissue remains the gold standard in pathology. Biopsies are commonly taken as part of many healthcare pathways, such as cancer treatment, as they contain a wealth of information about the underlying biology of health and disease.

But while genomic and transcriptomic analysis have their place, only proteomic profiling can truly reveal what’s happening at the phenotypic level within tissues as a disease develops and progresses.

Our TrueDiscovery mass spectrometry platform, TrueDiscovery, powered by our proprietary Hyper Reaction Monitoring (HRM) technology, allows identification and quantification across all the proteins present in a sample without the need for chemical labeling. It is also the only proteomics technology that can simultaneously identify a wide range of post-translational modifications, as well as truncations and other proteoforms.

This unbiased, hypothesis-free approach enables you to explore novel biology and targets beyond the ‘usual suspects’, finding what is not yet known but waiting to be discovered. It also works across all species and sample types, allowing smooth transferability of findings from one research phase to the next.

We’ve been busy optimizing the platform for tissue and tumor samples, whether fresh frozen or formalin-fixed paraffin-embedded (FFPE), as well as cultured cells.

We’ve been focusing on automating and perfecting our sample preparation protocols to minimize contamination and processing artifacts on the input side. And we’ve also optimized our chromatography and mass spectrometry processes to get as much information as possible from each precious sample.

Achieving Unprecedented Depth in Tissue Proteomics

In our latest pilot study, which we’ll be presenting at the ASMS Conference later this year, we used our tissue proteomics workflow to analyze 12 fresh frozen non-small cell lung cancer biopsies and 12 matching healthy samples.

We measured more than 250,000 peptides in total, including post-translational modifications, covering a ten-fold range in abundance. This translates to the identification and quantification of more than 13,000 individual proteins – an average of nearly 20 peptides per protein – and represents more than 90% of the total number of genes that are typically expressed in lung tissue.

We could clearly identify 414 oncogenes, 392 transcription factors, 837 plasma membrane proteins, including 25 G-protein coupled receptors, and 316 kinases. We also detected around 20 different post-translational modifications on thousands of proteins, including phosphorylation, deamidation, citrullination, hydroxylation, acetylation, mono-, di- and tri-methylation, and carboxylation.

Not only were we able to clearly distinguish different subtypes of lung cancer (squamous cell carcinoma versus adenocarcinoma) based on whole proteomic profiling, selective data analysis of the phosphoproteome analysis revealed clear clustering of healthy (red) versus tumor (green) samples, suggesting that these patterns may contain biologically relevant information.

To our knowledge, this is the deepest single shot proteome profiling reported to date. It also represents a near doubling of the depth of coverage from our previous analysis of the same lung cancer samples, published in 2020, where we identified 7097 proteins.

True Biology at Your Fingertips

Our TrueDiscovery platform provides an unbiased exploration and near-complete quantification of tissue proteomes. So whether you’re searching for novel drug targets or potential biomarkers, we help you unlock new biological insights from your precious tissue samples.

Importantly, we’re with you every step of the way, from study design to data analysis. We don’t just provide you with an incomprehensible data file or confusing list of hits. Instead, our team of experts bring their years of experience analyzing and interpreting proteomics datasets to provide you with actionable, biologically relevant insights that you can really use.

This latest breakthrough puts us at the leading edge of tissue proteomics and is the market’s deepest, single-shot proteomics service. We are also the only global proteomics provider to be GLP certified and GLP compliant, providing the regulatory data you need to get new therapies to market.

But we won’t stop here. We continue to refine and optimize our technology and analytical tools, working towards our goal of being able to analyze all the proteins and post-translational modifications present in a tissue or biofluid sample and bringing you ever deeper insights into true biology.

Contact us today if you would like to learn more.