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Related Concept Videos

Proteomics01:33

Proteomics

10.0K
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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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Related Experiment Video

Updated: Mar 6, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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ProteoModlR for functional proteomic analysis.

Paolo Cifani1, Mojdeh Shakiba2, Sagar Chhangawala2

  • 1Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

BMC Bioinformatics
|March 6, 2017
PubMed
Summary
This summary is machine-generated.

ProteoModlR is a new R package for analyzing post-translational modifications (PTMs) in proteomics. It quantifies PTM abundance and stoichiometry, enabling systems-level analysis of cellular signaling pathways.

Keywords:
Functional analysisMass spectrometryPost-translational modification stoichiometryQuantitative proteomicsR

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Area of Science:

  • Proteomics
  • Systems Biology
  • Mass Spectrometry

Background:

  • High-accuracy mass spectrometry enables comprehensive quantification of cellular proteomes and their modified variants.
  • Availability of quantified synthetic peptides allows absolute quantification of modified proteoforms for systems-level analyses.
  • Existing computational tools lack integrated functions for quantitative analysis of post-translationally modified proteins and their stoichiometry.

Purpose of the Study:

  • Develop a computational program for quantitative analysis of post-translational chemical modification abundance and stoichiometry.
  • Support analysis of experiments using isotopically labeled reference peptides for absolute quantitation.
  • Enable functional analysis of quantitative mass spectrometry experiments by inferring missing values.

Main Methods:

  • ProteoModlR program development for quantitative analysis of PTMs.
  • Support for absolute and relative quantitation using labeled and label-free data.
  • Inference of missing values for sparsely sampled quantitative mass spectrometry experiments.
  • Implementation of parsing and normalization functions to control for technical variation.
  • Modular design for integration with existing computational proteomics tools.

Main Results:

  • ProteoModlR enables quantitative analysis of PTM abundance and stoichiometry across biological states.
  • The program supports various experimental designs, including absolute and relative quantitation.
  • ProteoModlR facilitates functional analysis by inferring missing quantitative data.
  • Integrated parsing and normalization functions address technical variations.
  • Modular design promotes integration with other proteomics tools for comprehensive analysis.

Conclusions:

  • ProteoModlR is a novel R package for quantitative analysis of PTMs.
  • The software supports diverse quantitative mass spectrometry experiments.
  • ProteoModlR aids in the comprehensive quantitative analysis of cellular signaling.