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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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

Updated: Jul 16, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Romancing the "hidden proteome", Anno Domini two zero zero seven.

Egisto Boschetti1, Lee Lomas, Attilio Citterio

  • 1Ciphergen Biosystems, Fremont, California, USA.

Journal of Chromatography. A
|February 27, 2007
PubMed
Summary

This review details a hexapeptide ligand library for capturing low-abundance "hidden proteome" proteins. This method significantly increases protein detection, including small diagnostic peptides.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Analytical Chemistry

Background:

  • The majority of proteins in biological samples are low-abundance, termed the "hidden proteome."
  • Standard proteomic techniques often fail to detect these low-abundance proteins.
  • Small peptides are frequently lost during conventional analysis, hindering comprehensive proteomic studies.

Purpose of the Study:

  • To review the mechanism of action and properties of a solid-phase hexapeptide ligand library.
  • To evaluate methods for capturing and eluting low-abundance proteins and peptides.
  • To highlight the utility of this library for enhancing proteomic analysis.

Main Methods:

  • Utilizing a solid-phase ligand library composed of hexapeptides.
  • Investigating adsorption mechanisms for protein capture.
  • Developing en bloc and sequential elution protocols.
  • Applying the library to various biological samples like serum, platelet extracts, and bacterial extracts.

Main Results:

  • Demonstrated significant capture of low- and very low-abundance proteins.
  • Achieved at least a four-fold increase in the detection of low-abundance species.
  • Successfully adsorbed a high proportion of small peptides (600-8000 Da) typically lost in other methods.
  • Showcased protein capture from diverse sources including human serum and egg white.

Conclusions:

  • The hexapeptide ligand library is effective for accessing the "hidden proteome."
  • This approach substantially enhances the detection of low-abundance proteins and diagnostic peptides.
  • The method offers a valuable tool for comprehensive proteomic analysis and biomarker discovery.