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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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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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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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...
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The Proteasome Structure01:17

The Proteasome Structure

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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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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Proteins: From Genes to Degradation02:11

Proteins: From Genes to Degradation

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Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
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Related Experiment Video

Updated: Jun 9, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
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A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

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Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.

Praveen Kumar1,2,3, James E Johnson4, Thomas McGowan4

  • 1Data Sciences & Quantitative Biology, Discovery Sciences, AstraZeneca, Waltham, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|October 22, 2024
PubMed
Summary
This summary is machine-generated.

Proteogenomics integrates proteomics and sequencing to identify novel protein variants and improve genome annotation. A new Galaxy workflow simplifies this complex multi-omics analysis, enhancing reproducibility for researchers.

Keywords:
Galaxy-PMulti-omicsProteogenomicsWorkflows

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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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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Area of Science:

  • Multi-omics research
  • Proteomics
  • Genomics

Background:

  • Proteogenomics combines mass spectrometry-based proteomics with high-throughput sequencing.
  • It aids in genomic annotation and identifies variant proteins from genomic variations like SNPs and Indels.
  • Existing proteogenomic workflows involve complex, disparate software, hindering accessibility and reproducibility.

Purpose of the Study:

  • To describe a user-friendly, reproducible proteogenomic analysis workflow.
  • To leverage the Galaxy platform for integrated multi-omics data analysis.
  • To facilitate the identification and classification of novel protein variants.

Main Methods:

  • Development of an open-source, web-based Galaxy workflow for proteogenomic analysis.
  • Creation of customized protein sequence databases.
  • Matching spectral data against databases to identify peptide sequences and novel proteoforms.
  • Variant classification and genomic visualization.

Main Results:

  • The Galaxy workflow successfully integrates disparate software for proteogenomic analysis.
  • It enables efficient matching of spectral data to customized databases.
  • Novel protein variants are identified, classified, and visualized against the genome.
  • The workflow enhances usability and reproducibility in proteogenomic studies.

Conclusions:

  • The described Galaxy-based workflow simplifies complex proteogenomic analyses.
  • It improves accessibility for researchers lacking extensive computational expertise.
  • This approach enhances the reproducibility and efficiency of identifying and characterizing protein variants.