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Related Concept Videos

Proteomics01:33

Proteomics

8.3K
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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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
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...
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Related Experiment Video

Updated: Oct 1, 2025

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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Enhanced protein isoform characterization through long-read proteogenomics.

Rachel M Miller1, Ben T Jordan2, Madison M Mehlferber2,3

  • 1Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.

Genome Biology
|March 4, 2022
PubMed
Summary
This summary is machine-generated.

Detecting protein isoforms is vital for biomedicine. This study introduces a long-read proteogenomics approach, integrating RNA sequencing and mass spectrometry, to improve the characterization of human protein isoform diversity.

Keywords:
Alternative splicingIso-SeqLifebit CloudOSLong-read RNA-seqMass spectrometry-based proteomicsNextflowPacBioProtein inferenceProteogenomicsSQANTI

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Area of Science:

  • Biomedical research
  • Genomics
  • Proteomics

Background:

  • Accurate detection of human protein isoforms is critical for biomedical applications.
  • Mass spectrometry (MS)-based proteomics is a primary method for protein detection.
  • Isoform-resolved proteomic analysis requires precise, sample-matched reference databases.

Purpose of the Study:

  • To develop a long-read proteogenomics approach for enhanced protein isoform characterization.
  • To integrate long-read RNA sequencing and MS-based proteomics data.
  • To improve the detection of previously intractable protein isoforms.

Main Methods:

  • Developed a long-read proteogenomics approach.
  • Integrated sample-matched long-read RNA sequencing and MS-based proteomics data.
  • Introduced a novel protein isoform classification scheme and inference algorithm.
  • Released an open-source Nextflow pipeline for isoform-resolved proteomic analysis.

Main Results:

  • Successfully integrated long-read transcriptome data with MS-based proteomics.
  • Discovered novel protein isoforms.
  • Enabled detection of protein isoforms previously undetectable by MS.
  • Established a robust pipeline for long-read proteogenomics.

Conclusions:

  • Incorporating long-read sequencing and proteomic data enhances human protein isoform characterization.
  • The developed pipeline serves as a foundation for future long-read proteogenomics research.
  • This approach has potential applications in both basic and translational research.