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Technology

Snapshot Proteomics™

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Snapshot Proteomics™

 

Snapshot Proteomics™ is a sensitive and reproducible technology that uses microarrays containing ~20,000 individual human proteins to naturally reveal information about complex mixtures like cells or serum. When a microarray is exposed to a biological sample, the proteins on the chip take on the same post-translational modifications and engage in the same protein-protein interactions as their endogenous counterparts within that sample. We extract this crucial information by developing the arrays in a method analogous to a western blot. Improved sensitivity is afforded by enzymatic amplification, and our process requires no harsh manipulation that could lead to data loss such as trypsin digestion. Unlike a western blot, Snapshot Proteomics™ enables novel discovery by starting with up to 20,000 human proteins identifiable by location and does not depend upon detection reagents specific to individual proteins.

 

Our Snapshots represent the first combination of enzymatic amplification with novel discovery across the proteome. We capture the post-translational modifications and protein interactions in the presence of complexes, cofactors, metabolic inputs, and other enzymatic activities revealing the active proteomic state of the biological sample in a near-physiological context. Differential comparison of samples (i.e. treated versus control) reveals information specific to the experimental or phenotypic differences defined by your own research interests.

 

At AVMBioMed, we functionally characterize the activities of the most critical enzymes in the entire proteome – those that drive PTM – on a platform of up to 20,000 human protein substrates that is more reproducible and informative than MS-based alternatives. By taking a Snapshot of the signatures of these activities across the proteome, we gain insight into cells or other complex mixtures under various user-defined states.

 

~20,000 human proteins is a far larger number of proteins than has ever been identified in any mass spectrometry-based experiment. By allowing physiologically relevant biological machinery to alter and manipulate these proteins in parallel to what was happening endogenously within their source, we gather, elucidate, and exploit the logarithmic expansion of information (beyond 20,000) that is the TRUE proteome. Exactly like nature does.

 

 

We use Snapshot Proteomics™ as a core technology that powers several services, each tailored to the diverse stages of pharmaceutical development and scientific need. Visit out services overview for more information.

 

 

 

Snapshot Proteomics™ vs. Tandem Mass Spectrometry

 

Tandem Mass Spectrometry (MS/MS) is a technique that has driven many discoveries in proteomics. However, MS/MS has two important limitations: inherently poor reproducibility and the inability to feasibly detect novel PTM*. These issues are particularly problematic for applications involving complex biosamples, such as human serum representing different pharmacological treatments.

 

  • Reproducibility from biological duplicates is ~50% for MS/MS, >90% for Snapshot Proteomics.
  • The best MS/MS runs return information on a few thousand of the most abundant proteins. Each and every single experiment utilizing Snapshot Proteomics™ provides information on up to 20,000 human proteins without bias to cellular concentration.
  • MS/MS requires the use of broad and powerful enzyme inhibitors, and requires that case and control samples be mixed prior to analysis, introducing enzymes from one to substrates from the other.
  • The trypsin digestion necessary to MS-based approaches creates variability between samples, and ablates higher order PTM structures.
  • Certain PTM-modified amino acid residues have mass/charge ratios (m/z) identical to other unmodified residues, making distinction difficult or impossible.
  • 10% of the primary amino acids show indistinguishable mass/charge ratio (leucine and isoleucine) and must be inferred from context according to what is already known and present within the database.

*Immunoprecipitation of modified proteins using PTM-specific antibodies prior to analysis (IP-MS) adds variability to a technique already laboring under 50% reproducibility. Top-down approaches report PTM without introducing additional variability, but only provide information about the ~1200 most abundant proteins in the sample.

 

 

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