Related Experiment Video
Updated: Jul 14, 2026
17:12
Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)
Published on: December 20, 2010
Composition Profiler: a tool for discovery and visualization of amino acid composition differences.
Vladimir Vacic1, Vladimir N Uversky, A Keith Dunker
1Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA. vladimir@cs.ucr.edu <vladimir@cs.ucr.edu>
BMC Bioinformatics
|June 21, 2007
Summary
Composition Profiler identifies amino acid enrichment or depletion in protein sequences. This tool aids in selecting features for predicting protein function and structure by highlighting compositional differences.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Composition Profiler is a web-based tool for semi-automatic discovery of amino acid enrichment or depletion.
- It analyzes amino acids individually or grouped by physico-chemical or structural properties.
Purpose of the Study:
- To provide an exploratory data mining tool for analyzing protein amino acid composition.
- To guide feature selection for protein function and structure prediction models.
Main Methods:
- The tool accepts two amino acid samples: a query and a reference.
- The reference sample provides a background distribution for comparison.
- Results are presented in both textual and graphical formats.
Main Results:
- Identifies significant differences in amino acid frequencies between query and reference samples.
- Highlights enrichment or depletion of specific amino acids or groups based on properties like hydrophobicity, charge, or helix propensity.
Conclusions:
- Composition Profiler serves as a visual classifier for protein classes with distinct amino acid compositions.
- It aids in understanding protein properties and can inform the development of predictive models.
More Related Videos
Related Concept Videos
01:33Peptide 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...
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...
01:15Mass Spectrometry of Amines
In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic aliphatic amines show...
01:33Proteomics
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 proteomics...
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 proteomics...
01:20¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)
When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
01:19MALDI-TOF Mass Spectrometry
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...