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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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UV–Vis Spectrometers01:14

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The absorbance of UV and visible (UV–visible) radiations is measured using a UV–visible spectrophotometer. Deuterium lamps, which emit UV radiation, and tungsten lamps, which produce radiation in the visible region, are used as light sources in UV–visible spectrophotometers. A monochromator or prism is used for diffraction grating, i.e., to split the incoming radiation into different wavelengths. A system of slits is used to focus the desired wavelength on the sample cell.
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Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...
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Ultraviolet–visible (UV–visible or UV–Vis) spectroscopy is an analytical technique that investigates the interaction between matter and UV–Vis light within the electromagnetic spectrum. This method is widely used for its versatility, simplicity, and relatively quick data acquisition, making it valuable for both qualitative and quantitative analysis. When UV–Vis radiation passes through a material,  molecules absorb light depending on the energy required for...
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The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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MS-viewer: a web-based spectral viewer for proteomics results.

Peter R Baker1, Robert J Chalkley

  • 1Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158.

Molecular & Cellular Proteomics : MCP
|March 5, 2014
PubMed
Summary

MS-Viewer simplifies sharing proteomic data by enabling interactive viewing of peptide identification results. This tool accepts easy-to-create tabular files, overcoming format challenges from diverse analysis engines.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Sharing and viewing peptide identification results from mass spectrometry-based proteomics is challenging due to diverse analysis tool output formats.
  • Standardized formats exist but are often difficult to generate, hindering data accessibility for researchers.
  • Annotated results are crucial for journal articles but difficult to query by the wider scientific community.

Purpose of the Study:

  • To introduce MS-Viewer, a program within the Protein Prospector Web package.
  • To provide a solution for the interactive viewing of peptide identification results from various search engines.
  • To facilitate easier data sharing and accessibility in proteomics research.

Main Methods:

  • MS-Viewer utilizes easy-to-create tabular files as input.
  • The program leverages a web interface for interactive result viewing.
  • It is part of the Protein Prospector Web package.

Main Results:

  • MS-Viewer successfully displays search engine results through an interactive web interface.
  • The tool accommodates results from a wide variety of search engines.
  • The simplicity and flexibility of the input format are key to its success.

Conclusions:

  • MS-Viewer enhances the accessibility and usability of peptide identification data.
  • The tool addresses the challenge of diverse output formats in proteomics data analysis.
  • It promotes easier data sharing and querying among researchers in the field.