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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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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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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Related Experiment Video

Updated: Jun 6, 2025

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

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ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics.

Ziyi Li1,2, Cory A Weller1,2, Syed Shah1,2

  • 1Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.

Genomics, Proteomics & Bioinformatics
|November 22, 2024
PubMed
Summary
This summary is machine-generated.

ProtPipe streamlines mass spectrometry (MS) data analysis for proteomics and peptidomics. This open-source tool automates complex data processing, enabling robust biological insights and discoveries.

Keywords:
Data analysis pipelineImmunopeptidomicsMass spectrometryProtPipeProteomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Mass spectrometry (MS) is crucial for protein identification and characterization in various biomedical fields.
  • Analyzing MS data is complex, involving peptide/protein identification, quantification, and functional exploration.
  • Existing workflows often require significant manual intervention and expertise.

Purpose of the Study:

  • To develop an automated and user-friendly pipeline for high-throughput MS data analysis.
  • To streamline the processing of proteomics and peptidomics datasets.
  • To facilitate downstream biological interpretation of MS data.

Main Methods:

  • Developed ProtPipe, an open-source software pipeline with preinstalled DIA-NN.
  • Integrated automated data quality control, sample filtering, and normalization.
  • Implemented downstream analyses including differential abundance, pathway enrichment, and protein-protein interaction analysis.

Main Results:

  • ProtPipe automates the end-to-end analysis of MS proteomics and peptidomics data.
  • The pipeline ensures robust data quality and reliable downstream analysis.
  • Generates annotated tables and visualizations for experimental design comparisons.

Conclusions:

  • ProtPipe offers a streamlined and automated solution for complex MS data analysis.
  • The tool enhances the understanding of protein function, signaling, and biological systems.
  • Facilitates personalized medicine and systems biology research through efficient data interpretation.