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Related Concept Videos

Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
Isotopes and Radioisotopes01:28

Isotopes and Radioisotopes

In the early 1900s, English chemist Frederick Soddy realized that an element could have atoms with different masses that were chemically indistinguishable. These different types are called isotopes — atoms of the same element that differ in mass. Isotopes differ in mass because they have different numbers of neutrons but are chemically identical because they have the same number of protons. Soddy was awarded the Nobel Prize in Chemistry in 1921 for this discovery.
An isotope containing more...
Isotopes01:12

Isotopes

Elements have a set number of protons that determines their atomic number (Z). For example, all atoms with eight protons are oxygen; however, the number of neutrons can vary for atoms of the same element. The sum of the number of protons and the number of neutrons is the mass number (A). Atoms with the same atomic number but different mass numbers are called isotopes. Elements can have multiple isotopes, for example, carbon-12, carbon-13, and carbon-14.An element's atomic mass, or weight, is a...
Nuclear Overhauser Enhancement (NOE)01:06

Nuclear Overhauser Enhancement (NOE)

Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling. This phenomenon, called the nuclear Overhauser enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring spin-active...
Inductively Coupled Plasma–Mass Spectrometry (ICP–MS): Overview01:19

Inductively Coupled Plasma–Mass Spectrometry (ICP–MS): Overview

In inductively coupled plasma–mass spectrometry (ICP–MS), an inductively coupled plasma (ICP) torch is used as an atomizer and ionizer. Solid samples are dissolved and volatilized before being introduced into the high-temperature argon plasma, while solution samples are nebulized and passed through the high-temperature argon plasma. Plasma dissociates the analytes and ionizes their component atoms to form a mixture of positive ions and molecular species. The positive ions are then passed on to...

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Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline
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Envelope: interactive software for modeling and fitting complex isotope distributions.

Michael T Sykes1, James R Williamson

  • 1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. sykes@scripps.edu

BMC Bioinformatics
|October 22, 2008
PubMed
Summary
This summary is machine-generated.

Envelope software simplifies the analysis of complex isotope distributions in mass spectrometry. It interactively calculates and visualizes isotopic patterns from labeled macromolecules, aiding in data interpretation and experimental design.

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Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling
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Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Computational Biology

Background:

  • Interpreting isotope distributions in mass spectrometry is crucial for analyzing labeled macromolecules.
  • Complex labeling patterns, especially from in vivo metabolic labeling, pose challenges in distinguishing species and calculating theoretical distributions.
  • Existing methods often struggle with interactive fitting of complex isotope distributions to experimental data.

Purpose of the Study:

  • To develop user-friendly software for calculating and fitting complex isotope distributions from mixtures of labeled macromolecules.
  • To provide interactive visualization and analysis of isotopic patterns for mass spectrometry data.
  • To aid in the design and interpretation of metabolic labeling experiments.

Main Methods:

  • Developed the Envelope software with a graphical user interface.
  • Implemented simultaneous calculation of isotope distributions for multiple labeling patterns (2H, 13C, 15N).
  • Enabled interactive adjustment of labeling contributions, baseline correction, and instrument accuracy.
  • Integrated display of experimental data with calculated distributions and least-squares goodness-of-fit analysis.

Main Results:

  • Envelope can simultaneously calculate and sum isotope distributions for various labeling patterns (fractional or complete).
  • The software provides interactive visualization, allowing individual adjustment of contributions from different labeling patterns.
  • Envelope facilitates comparison with experimental data, including baseline correction and instrument accuracy adjustments.
  • High-quality output of distributions and a goodness-of-fit measure are provided.

Conclusions:

  • Envelope is a powerful, interactive tool for calculating and visualizing complex isotope distributions.
  • The software aids in fitting experimental mass spectrometry data and understanding contributions from different labeled species.
  • Envelope serves as a valuable resource for experimental design and as a teaching tool in isotopic analysis.