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Related Concept Videos

IR Spectroscopy: Molecular Vibration Overview01:24

IR Spectroscopy: Molecular Vibration Overview

When Infrared (IR) radiation passes through a covalently bonded molecule, the bonds transition from lower to higher vibrational levels. The fundamental vibrational motions that result in infrared absorption can be classified as stretching or bending vibrations.
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...
UV–Vis Spectroscopy: Molecular Electronic Transitions01:16

UV–Vis Spectroscopy: Molecular Electronic Transitions

In Ultraviolet–Visible (UV–Vis) spectroscopy, the absorption of electromagnetic radiation is used to probe the electronic structure of molecules. This technique provides insights into molecular electronic transitions, particularly the movement of electrons between different molecular orbitals. Radiation is absorbed if the energy of the electromagnetic radiation passing through the molecule is precisely equal to the energy difference between the excited and ground states. During this process,...
Raman Spectroscopy Instrumentation: Overview01:26

Raman Spectroscopy Instrumentation: Overview

A conventional Raman spectrophotometer includes a laser source, a sample holding system, a wavelength selector, and a detector.
The monochromatic laser source, typically using visible or near-infrared radiation, generates a highly focused beam of light. This light interacts with the molecules of the sample, scattering some of the light. Liquid and gaseous samples are usually tested in ordinary glass capillaries, while solids can be analyzed as powders packed in capillaries or as potassium...
Mass Spectrum01:23

Mass Spectrum

A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations01:08

IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations

Identical bonds within a polyatomic group can stretch symmetrically (in-phase) or asymmetrically (out-of-phase). Similar to hydrogen bonding, these vibrations also influence the shape of the IR peak. Generally, asymmetric stretching frequencies are higher than symmetric stretching frequencies. For example, primary amines exhibit two distinct IR peaks between 3300–3500 cm−1 corresponding to the symmetric and asymmetric N-H stretching, while secondary amines exhibit a single stretching vibration...
Raman Spectroscopy: Overview01:20

Raman Spectroscopy: Overview

The underlying principle of Raman spectroscopy is based on the interaction between light and matter, specifically molecules' inelastic scattering of photons. When a monochromatic beam of light, typically from a laser source, interacts with a sample, most scattered light has the same frequency as the incident light. This is known as Rayleigh scattering.
However, a small fraction of the scattered light exhibits a frequency shift due to the exchange of energy between the incident photons and the...

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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MaRiMba: a software application for spectral library-based MRM transition list assembly.

Carly A Sherwood1, Ashley Eastham, Lik Wee Lee

  • 1Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.

Journal of Proteome Research
|July 17, 2009
PubMed
Summary
This summary is machine-generated.

MaRiMba software automates the creation of targeted mass spectrometry (MRM-MS) analysis lists. This tool enhances proteome exploration by streamlining the design of MRM transition lists for mass spectrometers.

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Multiple reaction monitoring mass spectrometry (MRM-MS) is a sensitive, high-throughput technique for targeted proteome analysis.
  • Automating the generation of MRM transition lists is crucial for efficient experimental design.

Purpose of the Study:

  • To develop MaRiMba, an open-source software tool for automating the creation of MRM transition lists.
  • To facilitate the programming of triple quadrupole mass spectrometers for targeted proteomic analyses.

Main Methods:

  • MaRiMba utilizes spectral libraries to generate MRM transition lists.
  • The software allows for filtering based on specified proteins, peptides, and ion properties.
  • It supports the inclusion of transitions for isotopically labeled peptides.

Main Results:

  • MaRiMba successfully automated the design of MRM transition lists.
  • The tool was demonstrated in an MRM-MS experiment targeting proteins in a standard mixture.
  • The software integrates with the Trans-Proteomic Pipeline via a graphical user interface.

Conclusions:

  • MaRiMba provides an automated and efficient solution for generating MRM transition lists.
  • This tool enhances the sensitivity and throughput of proteomic studies using MRM-MS.
  • MaRiMba is an accessible, open-source application for mass spectrometry-based proteomics.