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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
The Proteasome Structure01:17

The Proteasome Structure

The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an...

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Related Experiment Video

Updated: May 21, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Life's simple measures: unlocking the proteome.

Edward Brody1, Larry Gold1, Mike Mehan1

  • 1SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.

Journal of Molecular Biology
|June 23, 2012
PubMed
Summary
This summary is machine-generated.

Researchers developed SOMAmers (slow off-rate modified aptamers) to detect over 1000 proteins in small fluid samples. This novel aptamer technology enables precise protein quantification for medical research and diagnostics.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • Aptamers are nucleic acid-based ligands with high specificity and affinity for target molecules.
  • Traditional aptamer selection (SELEX) can be limited by aptamer dissociation rates.
  • Detecting proteins in complex biological fluids like serum or plasma presents significant analytical challenges.

Purpose of the Study:

  • To develop and validate a novel class of aptamers, SOMAmers, with enhanced binding properties for protein detection.
  • To establish a sensitive assay for quantifying a large number of proteins in minimal volumes of body fluids.
  • To demonstrate the utility of SOMAmer-based proteomics in addressing medical questions.

Main Methods:

  • Evolution of SOMAmers using modified nucleotides and selection for slow off-rates during SELEX.
  • Development of a 1:1 complex formation assay between SOMAmers and cognate proteins in body fluids.
  • Quantification of SOMAmer-protein complexes using hybridization to solid supports or other DNA quantification technologies, including Next-Generation Sequencing.
  • Application of bioinformatics methods, such as principal component analysis, for data interpretation.
  • Evaluation of sample handling procedures to identify potential sources of error in proteomics analysis.

Main Results:

  • SOMAmers exhibit tight and specific binding to target proteins in body fluids.
  • The developed assay accurately reflects protein concentrations by measuring SOMAmer complex concentrations.
  • Measurements of over 1000 proteins were achieved using less than 100 μL of serum or plasma.
  • Bioinformatics tools aided in discovery and analysis of proteomic data.
  • Methods were established to identify parameters affecting proteomics analysis quality.

Conclusions:

  • SOMAmers represent a powerful tool for high-throughput proteomic analysis in clinical samples.
  • This technology enables sensitive and specific protein quantification in small sample volumes, facilitating medical research.
  • The SOMAmer assay platform has the potential to advance biomarker discovery and diagnostic applications.