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Related Concept Videos

Inductively Coupled Plasma-Mass Spectrometry (ICP-MS): Interferences01:20

Inductively Coupled Plasma-Mass Spectrometry (ICP-MS): Interferences

Inductively coupled plasma–mass spectrometry (ICP–MS) is a highly selective and sensitive technique for accurate elemental analysis. Though the analysis of ICP–MS mass spectra is comparatively straightforward, it is affected by spectroscopic and non-spectroscopic interferences. Spectroscopic interferences arise when the plasma contains ionic species with an m/z value the same as the analyte ion. Spectroscopic interference can be categorized as isobaric, polyatomic ions, and refractory oxide ion...
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
Effects of EDTA on End-Point Detection Methods01:18

Effects of EDTA on End-Point Detection Methods

Different methods, such as visual observance of metal-ion indicators, spectroscopic techniques, and potentiometric methods, can determine the endpoint of an EDTA titration.
In the visual method, metal-ion indicators (metallochromic dyes), which have distinct colors in their free and complex forms, are added to the mixture to signal the titration's end point. They form stable complexes with metal ions, but these complexes are weaker than the corresponding metal–EDTA complexes. As a result, EDTA...
Ion-Exchange Chromatography01:09

Ion-Exchange Chromatography

Ion-exchange chromatography, or IEC, is a technique for separating ions based on their affinity for the stationary phase. The stationary phase is a cross-linked polymer resin with covalently attached ionic functional groups. The functional groups can be either positively charged (cation exchangers) or negatively charged (anion exchangers). A cation exchanger consists of a polymeric anion and active cations, while an anion exchanger is a polymeric cation with active anions. The choice of...
π Electron Effects on Chemical Shift: Overview01:27

π Electron Effects on Chemical Shift: Overview

An applied magnetic field causes loosely bound π-electrons in organic molecules to circulate, producing a local or induced diamagnetic field over a large spatial volume. As the molecules tumble in solution, the field generated by π-electrons in spherical substituents results in a zero net field. However, the net field generated by π-electrons in non-spherical substituents is not zero. The effect of this induced field depends on the orientation of the molecule with respect to B0, resulting in...
Atomic Absorption Spectroscopy: Interference01:25

Atomic Absorption Spectroscopy: Interference

Interference leads to systematic error in atomic absorption (AA) measurements by enhancing or diminishing the analytical signal or the background. These interferences can be grouped into three main categories: spectral interference, chemical interference, and physical interference.
Spectral interference occurs when signals from other elements or molecules overlap with the analyte signal, falsely elevating or masking the analyte's absorbance. This interference can be corrected using Zeeman,...

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Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes Using Ion Mobility-Mass Spectrometry
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The effect of interfering ions on search algorithm performance for electron-transfer dissociation data.

David M Good1, Craig D Wenger, Joshua J Coon

  • 1Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Proteomics
|November 10, 2009
PubMed
Summary
This summary is machine-generated.

Spectral processing to remove unique electron-transfer dissociation (ETD) features enhances peptide identification. This method improves search sensitivity and the number of unique peptides identified in proteomic datasets.

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Published on: April 16, 2018

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Collision-activated dissociation (CAD) and electron-transfer dissociation (ETD) produce distinct spectral features in mass spectrometry.
  • Existing database search algorithms are partially adapted for ETD data, primarily by searching for c- and z(*)-ions.
  • Unaccounted ETD-specific spectral features can impede accurate peptide identification.

Purpose of the Study:

  • To investigate the impact of removing ETD-specific spectral features on proteomic database searching.
  • To assess the potential for improving peptide identification sensitivity and accuracy through spectral processing.

Main Methods:

  • Implemented spectral processing techniques to remove unique ETD-specific features from mass spectrometry data.
  • Compared the performance of modified database search algorithms on processed and unprocessed ETD data.
  • Evaluated identification sensitivity and the number of unique peptide identifications using human and yeast proteomic datasets.

Main Results:

  • Removal of ETD-specific features significantly increased total search sensitivity by approximately 20% for both human and yeast datasets.
  • Unique peptide identifications were enhanced by approximately 17% for yeast and 16% for human datasets.
  • Spectral processing effectively addressed limitations of current algorithms in handling ETD data.

Conclusions:

  • Spectral processing to remove extraneous ETD features is a valuable strategy for improving proteomic identification.
  • This approach enhances the performance of existing search algorithms, leading to more comprehensive proteomic analysis.
  • The findings suggest a pathway for refining mass spectrometry data analysis in proteomics research.