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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

IsoformResolver: A peptide-centric algorithm for protein inference.

Karen Meyer-Arendt1, William M Old, Stephane Houel

  • 1Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA.

Journal of Proteome Research
|May 24, 2011
PubMed
Summary
This summary is machine-generated.

IsoformResolver is a new peptide-centric algorithm for protein inference in mass spectrometry. It resolves ambiguity by clustering proteins based on experimental and in silico identified peptides, improving protein profile organization.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Protein inference from tandem mass spectrometry data is often ambiguous, even with validated peptides.
  • Challenges include determining minimal vs. exhaustive protein lists and quantifying shared peptides.
  • Existing methods struggle with complex protein relationships and ambiguous inferences.

Purpose of the Study:

  • To introduce IsoformResolver, a novel peptide-centric protein inference algorithm.
  • To address ambiguities in protein identification and quantification in complex proteomic samples.
  • To provide a comprehensive and concise method for organizing protein profiles.

Main Methods:

  • IsoformResolver clusters proteins using two approaches: experimentally identified MS/MS peptides and in silico-digested database peptides.
  • It groups proteins based on shared peptides, distinguishing between minimal and all possible protein inferences.
  • The algorithm summarizes spectral count information and facilitates multi-experiment comparisons.

Main Results:

  • MS/MS-derived groups present minimal protein lists within the context of all possibilities, avoiding redundant peptide listings.
  • In silico-derived groups consolidate functionally related proteins, offering stable identifiers.
  • The peptide-centric strategy enables clear organization of protein profiles, even with shared peptides.

Conclusions:

  • IsoformResolver offers a robust solution for peptide-centric protein inference, enhancing clarity in complex proteomic analyses.
  • Its dual clustering approach provides both minimal and functionally related protein groupings.
  • The algorithm improves the organization and comparison of protein profiles from LC-MS/MS experiments.