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Related Concept Videos

High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

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 example, the mass of helium...
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Mass Analyzers: Common Types

The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
Inductively Coupled Plasma–Mass Spectrometry (ICP–MS): Overview01:19

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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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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...
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Atomic Absorption Spectroscopy: Instrumentation

An atomic absorption spectrophotometer (AAS) comprises several components: a radiation source, an atomizer, a monochromator, and a detector. The radiation source can be a hollow-cathode lamp (HCL) or an electrodeless-discharge lamp (EDL), both of which provide a narrow emission line of the required wavelength. However, some instruments use continuum sources and high-resolution monochromators to achieve a narrow range of radiation.
The atomizer used in AAS can be either a flame atomizer or an...

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An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome
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Balancing robust quantification and identification for iTRAQ: application of UHR-ToF MS.

Saw Yen Ow1, Josselin Noirel, Malinda Salim

  • 1ChELSI Institute, Department of Chemical and Process Engineering, University of Sheffield, Sheffield, UK.

Proteomics
|March 31, 2010
PubMed
Summary

This study optimizes iTRAQ (isobaric tag for relative and absolute quantification) analysis on maXis UHR-Qq-ToF instruments. Adjusting MS/MS ion transmission parameters balances peptide identification and quantification for better proteomic data quality.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Analytical Chemistry

Background:

  • iTRAQ reagents enable simultaneous multiplex identification and quantification of proteins.
  • Effective peptide fragmentation is crucial for generating both sequence and reporter ions.
  • Balancing ion transmission across the MS/MS mass range is key for iTRAQ success.

Purpose of the Study:

  • To describe an analytical strategy for implementing iTRAQ on maXis UHR-Qq-ToF instruments.
  • To discuss the impact of MS/MS ion transmission parameters on data quality.
  • To highlight maXis-specific parameters affecting quantification and identification.

Main Methods:

  • Implementation of iTRAQ workflow on maXis UHR-Qq-ToF mass spectrometers.
  • Systematic adjustment of MS/MS ion transmission parameters.
  • Analysis of peptide fragmentation, ion transmission, and detection across the MS/MS range.

Main Results:

  • Demonstrated an analytical strategy for iTRAQ on maXis UHR-Qq-ToF.
  • Showcased the impact of adjusting MS/MS ion transmission on data quality.
  • Identified maXis-specific parameters influencing protein identification and quantification.

Conclusions:

  • Optimized iTRAQ implementation on maXis UHR-Qq-ToF instruments is achievable.
  • Careful adjustment of MS/MS ion transmission parameters is critical for robust proteomic analysis.
  • Understanding maXis-specific parameter interactions enhances proteomic data reliability.