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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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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.
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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Emerging protein sequencing technologies: proteomics without mass spectrometry?

A S Deshpande1, A Lin2, I O'Bryon2

  • 1Biogeochemical Transformations Group, Pacific Northwest National Laboratory, Richland, Washington, USA.

Expert Review of Proteomics
|March 19, 2025
PubMed
Summary

New non-mass spectrometric protein sequencing methods offer lower costs than traditional liquid chromatography-tandem mass spectrometry (LC-MS/MS). While currently less performant, these emerging technologies could democratize proteomics research.

Keywords:
BioinformaticsEdman degradationfluorosequencingnanoporesnext-generation proteomicsnon-mass spectrometry proteomicsprotein sequencing

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Area of Science:

  • Proteomics
  • Biotechnology
  • Analytical Chemistry

Background:

  • Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has dominated proteomics for three decades.
  • High costs and complexity limit LC-MS/MS accessibility.
  • Emerging non-mass spectrometric methods present alternatives, but their capabilities for complex mixtures are underexplored.

Purpose of the Study:

  • To review and assess recent non-mass spectrometric protein and peptide sequencing technologies.
  • To compare their potential competitiveness against established LC-MS/MS methods.
  • To identify bioinformatics challenges and fundamental limitations of new approaches.

Main Methods:

  • Comprehensive literature review.
  • Analysis of instrument vendor websites, patents, webinars, and preprints.
  • Evaluation of emerging techniques including nanopore sequencing, sequencing by degradation, reverse translation, and short-epitope mapping.

Main Results:

  • Several promising non-mass spectrometric technologies have emerged.
  • No current non-MS methods have demonstrated superior performance to LC-MS/MS in identifying peptides and proteins.
  • Key limitations include dynamic range issues in single-molecule measurements of complex mixtures.

Conclusions:

  • Emerging non-mass spectrometric methods face performance challenges compared to LC-MS/MS.
  • Despite performance gaps, their significantly lower cost may drive widespread adoption.
  • These technologies could revolutionize proteomics by enabling broader participation in research labs.