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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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Ribosome Profiling02:24

Ribosome Profiling

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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.
Applications of ribosome profiling
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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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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Updated: Aug 8, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry.

Hayley M Bennett1, William Stephenson1, Christopher M Rose1

  • 1Department of Next Generation Sequencing and Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.

Nature Methods
|March 2, 2023
PubMed
Summary
This summary is machine-generated.

Single-cell RNA sequencing and protein measurement technologies are advancing our understanding of biological systems. New mass spectrometry methods offer potential for single-cell proteome characterization, but challenges remain.

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Proteomics

Background:

  • Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of biological system heterogeneity.
  • Technological progress now allows for protein measurements, aiding cell type and state elucidation.
  • Recent mass spectrometry (MS) advancements bring single-cell proteome characterization closer.

Purpose of the Study:

  • To discuss challenges in single-cell protein detection using MS and sequencing-based methods.
  • To review the current state-of-the-art in single-cell proteomic technologies.
  • To identify opportunities for technological advancement and complementary approaches.

Main Methods:

  • Review of existing literature on single-cell sequencing and mass spectrometry techniques.
  • Analysis of current technological capabilities and limitations for protein detection at the single-cell level.
  • Comparative assessment of sequencing-based and MS-based proteomic approaches.

Main Results:

  • Significant progress has been made in single-cell RNA sequencing, revealing cellular heterogeneity.
  • Protein measurement technologies are emerging, complementing transcriptomic data.
  • Mass spectrometry shows promise for single-cell proteome analysis, though challenges persist.

Conclusions:

  • Detecting proteins in single cells presents distinct challenges for both MS and sequencing-based methods.
  • There is a need for technological innovation to overcome current limitations in single-cell proteomic analysis.
  • Integrating complementary approaches can maximize the advantages of different technologies for comprehensive single-cell characterization.