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Related Concept Videos

Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
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: Amine Fragmentation00:55

Mass Spectrometry: Amine Fragmentation

Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via ⍺-cleavage. The ⍺-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single or...
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...
Mass Spectrometry of Amines01:15

Mass Spectrometry of Amines

In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic aliphatic amines show...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: Jul 2, 2026

Nitropeptide Profiling and Identification Illustrated by Angiotensin II
07:31

Nitropeptide Profiling and Identification Illustrated by Angiotensin II

Published on: June 16, 2019

NITPICK: peak identification for mass spectrometry data.

Bernhard Y Renard1, Marc Kirchner, Hanno Steen

  • 1Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany. bernhard.renard@iwr.uni-heidelberg.de

BMC Bioinformatics
|August 30, 2008
PubMed
Summary
This summary is machine-generated.

NITPICK, a novel peak picking method, accurately deconvolves complex mass spectra for proteomics. This non-greedy, iterative template-based approach improves feature extraction in mass spectrometry (MS) analysis.

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Applications of Liquid-Chromatography Tandem Mass Spectrometry in Natural Products Research: Tropane Alkaloids as a Case Study
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Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
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Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Published on: February 21, 2018

Related Experiment Videos

Last Updated: Jul 2, 2026

Nitropeptide Profiling and Identification Illustrated by Angiotensin II
07:31

Nitropeptide Profiling and Identification Illustrated by Angiotensin II

Published on: June 16, 2019

Applications of Liquid-Chromatography Tandem Mass Spectrometry in Natural Products Research: Tropane Alkaloids as a Case Study
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Applications of Liquid-Chromatography Tandem Mass Spectrometry in Natural Products Research: Tropane Alkaloids as a Case Study

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Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
11:44

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Published on: February 21, 2018

Area of Science:

  • Proteomics
  • Mass Spectrometry (MS) analysis
  • Computational Biology

Background:

  • Reliable feature extraction is crucial for automated proteomic mass spectrometry (MS) analysis.
  • Automated analysis of MS data requires robust methods for identifying spectral features.

Purpose of the Study:

  • To introduce NITPICK, a novel sparse template regression method for peak picking in mass spectrometry.
  • To address the challenge of deconvoluting complex overlapping isotope distributions in multicomponent mass spectra.

Main Methods:

  • Developed NITPICK (Non-greedy, Iterative Template-based peak PICKer).
  • Utilized fractional averaging, an extension of Senko's averaging model.
  • Employed a modified sparse, non-negative least angle regression with a statistically derived early stopping criterion.

Main Results:

  • NITPICK effectively deconvolves overlapping isotope distributions in mixture mass spectra.
  • Comparative evaluations on simulated and real-world datasets demonstrate NITPICK's performance.
  • NITPICK outperforms the existing non-greedy feature extraction routine, pepex.

Conclusions:

  • NITPICK offers a robust solution for feature extraction in complex mass spectra.
  • The software package for R is publicly available for download.
  • This method enhances the automated analysis of proteomic MS data.