We compare mass spectrometry proteomics with panel-based affinity approaches and discuss why mass spectrometry has established itself as the method of choice for plasma biomarker discovery.
In the search for novel biomarkers in plasma, proteomics technologies should ideally provide deep coverage and unbiased exploration of the entire proteome.
Currently, two proteomics technologies are widely used for identifying and quantifying plasma proteins: affinity-based assays and mass spectrometry (MS).
Here, we explain how these platforms work, the performance you can expect from each technology, and how well they meet the needs of biomarker discovery.
Mass spectrometry proteomics is an established approach that has made significant technological leaps in the last few years. The method uses chromatography to separate proteins, followed by mass spectrometry to measure the mass-to-charge ratio of peptide fragments, allowing identification and quantification of proteins.
While affinity-based proteomics approaches are confined to a pre-determined panel of targets, MS covers the entire proteome to reveal the most important and interesting proteins. This true discovery approach allows exploration of novel biology in the search for new biomarkers, rather than looking for the ‘usual suspects’.
Next-generation proteomics approaches pioneered by Biognosys have been developed to achieve deep proteome profiling with mass spectrometry that is now extremely competitive with affinity-based proteomics.
Biognosys’ proprietary deep plasma and serum proteomics workflow combines enrichment for low abundance proteins with highly optimized chromatography to overcome the challenges of the large dynamic range of the plasma proteome. As a result, Biognosys’ plasma proteomics solution offers unlimited detection of proteoforms and quantification of up to 3,000 proteins across the complete plasma and serum proteome.
Mass spectrometry proteomics is also now highly reproducible. While affinity proteomics approaches quantify proteins based on just one data point per protein, mass spectrometry typically provides over ten thousand peptide measurements per sample. Quantifying an average of ten unique peptides per protein ensures specific identification, precise quantification and high reproducibility.
Besides offering unbiased discovery and deep coverage, mass spectrometry generates additional data with structural insights and detection of proteoforms. In contrast to affinity-based approaches that rely on ligand specificity, mass spectrometry is applicable to all species and sample types, including tissue and biofluids such as plasma, serum, cerebrospinal fluid, and urine.
Biognosys’ high-throughput workflows support biomarker discovery in large-scale clinical trials. Furthermore, our optimized QC workflows and transparent data mean you can always go back in time to re-analyze and compare data across and between studies.
Affinity-based proteomics assays use molecules such as antibodies or aptamers to bind to known protein domains for detection and quantification. Because they rely on known binding sites, they can only provide a targeted, panel-based approach to proteomics. They cannot uncover new, unknown, or less studied proteins, limiting their applicability to novel biomarker discovery.
The precise depth and specificity of affinity-based proteomics depend on the specific assay used. With the right binding molecules, both antibody and aptamer-based assays can provide high specificity.
Leading antibody approaches use dual binding and DNA tags to increase specificity and reduce cross-reactivity. However, binding can be limited if proteins change conformations or aggregate, preventing aptamers and antibodies from reaching the intended binding site and reducing specificity.
Although affinity-based assays can provide relative quantification of the proteins within a sample, they can’t offer absolute quantification. They also have a relatively high false discovery rate of 5-10%.
Affinity-based proteomics assays can’t detect protein isoforms, post-translational modifications or other proteoforms, unlike mass spectrometry methods, so they miss out a whole additional layer of biological information for biomarker discovery.
Affinity-based methods are also limited by the breadth and specificity of the aptamer or antibody panels available. Furthermore, the raw data is often not shared with the customer, reducing data transparency, limiting clinical transferability and preventing later re-analysis of the data following new discoveries.
Mass spectrometry combines unprecedented unbiased discovery with depth and reproducibility and has established itself as the method of choice in biomarker discovery.
It also provides additional advantages, including structural and functional information, transparent data that can be shared with customers, and ease of transferability to absolute quantification assays, making mass spectrometry the leading proteomics approach for plasma biomarker discovery.
For example, researchers at the Parker Institute for Cancer Immunotherapy recently used a multi-omics approach to biomarker discovery in the ongoing PRINCE clinical trial, comparing Biognosys’ unbiased biomarker discovery workflow with a panel-based affinity proteomics assay.
Using this method, they identified and validated several novel biomarkers that could be used as pharmacodynamic markers in future studies, which were not identified through the affinity assay.
In a pan-cancer study, the Biognosys researchers also identified 190 FDA-approved known biomarkers such as STAT3 for colorectal cancer. The identified biomarkers were consistent with the biological mechanisms of the therapies used, proving the power and significance of unbiased discovery with mass spectrometry proteomics.
With mass spectrometry, you can go beyond the pre-defined hypothesis and discover the unknown, revealing new biological insights that will drive your research forward.