Mass Spectrometry Proteomics Vs. Aptamer-based Approaches

Mass Spectrometry Proteomics Vs. Aptamer-based Approaches

Proteins are highly complex biomolecules that can be involved in the origin of diseases and are vital in the search for cures. Therefore, being able to identify their composition and structure is critical for diagnostics, drug discovery, and to aid in the understanding of key disease pathways and human biology.

Proteomics allows the characterization of proteins’ level of expression, function, and structure. Each of these characteristics is key to fully interpreting the protein’s life cycle and interactomics.

Proteins are very large macromolecules; the largest known protein is the Titin’s human variant that consists of a chain of 34,351 amino acids, while the smallest may comprise just 20 amino acids. The dimension, complexity of structure, and post-transcriptional modifications (PTMs) can make the analysis of proteins challenging. However, there are various technologies available for analyzing proteins. This article will compare two leading methods, mass spectrometry proteomics and aptamer-based technologies.


How Mass Spectrometry Proteomics Can Help


Mass spectrometry is a key technique for a proteomics approach, and a vast range of applications for mass spectrometry have been developed over time.

One of the significant developments for mass spectrometry proteomics was the Orbitrap-based techniques that allowed for extremely high mass resolution and improved mass accuracies. Tandem fragmentation techniques have also proven invaluable for allowing ‘sorting’ of protein fragments and sequencing of short amino acid chains.

Today, mass spectrometry offers fast measurement times, high throughput, while maintaining robustness, scalability, high specificity, and reliability. Mass spectrometry also allows absolute quantification and deep coverage of the proteome. It provides the possibility to close the gap between genotype and phenotype. For years, genomics and transcriptomics have taken over the spotlight, however, it is time for proteomics to shine and unlock another dimension of information in biology.

Mass spectrometry can be used for the quantification and analysis of protein expression, function, and structures. It can analyze the protein structure at the peptide level in a completely unbiased and hypothesis-free way. Furthermore, as no binding markers are required, mass spectrometry proteomics is suitable for use with a wide range of proteins, even those for which there are no known binding antibodies.


Mass Spectrometry Proteomics Vs. Aptamer-based Approaches


Today, many high throughput mass spectrometry proteomics techniques are available, but how do these compare to aptamer-based methods? Aptamers are short, single-stranded oligonucleotides that can selectively bind to a specific protein target. Whilst they have good specificity and selectivity in binding, aptamers only bind specific protein domains and their protein targets need to be identified prior to analysis. In contrast, mass spectrometry offers a deeper insight into the proteome and can be performed in an unbiased and hypothesis-free way.

An unknown protein mixture can be exposed to a range of known aptamers and then screened to determine which ones bind. This is an interactive process, through which unbound aptamers are released and hybridized to an antisense-aptamer oligo bound to a slide, which is then detected via fluorescence. One of the challenges of aptamer-based approaches is that the analysis is lengthy, and the proteins to be analyzed need to be known and synthesizable in a laboratory. This means, that validated tool molecules selective for the proteins of interest are necessary and it can potentially produce false-negative signals if the binding epitope is not accessible. Moreover, aptamer-based approaches cannot give information about post-translational modifications. Historically, the struggle for increasing sensitivity and dynamic range in mass spectrometry proteomics was one of the biggest limitations of the technique. However, developments both in mass spectrometry technologies and new analysis approaches have helped to overcome this. Mass spectrometry remains the most characterized and widely used technique for proteomics analysis, and new workflows continue to be created for highly sensitive measurements in a wide range of sample types, making it the gold standard for proteomics analysis.


For over 14 years, Biognosys has been leading progress and innovation in proteomics. Scientific excellence is the basis of our pioneering proteomics solutions. To find out more about our mass spectrometry proteomics, contact us today.

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