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Related Concept Videos

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...
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 Spectrometers01:16

Mass Spectrometers

This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:

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Identification and Quantification of Decomposition Mechanisms in Lithium-Ion Batteries; Input to Heat Flow Simulation for Modeling Thermal Runaway
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QuickMod: A tool for open modification spectrum library searches.

Erik Ahrné1, Frederic Nikitin, Frederique Lisacek

  • 1Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland. erik.ahrne@isb-sib.ch

Journal of Proteome Research
|April 20, 2011
PubMed
Summary
This summary is machine-generated.

Spectrum library searches can identify modified peptides, even without prior knowledge of modifications. QuickMod, a new tool, efficiently detects and localizes post-translational modifications (PTMs) in peptides.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • MS2 library spectra offer rich peptide fragmentation data.
  • Spectrum library searches typically identify unmodified peptides.

Purpose of the Study:

  • Evaluate library spectra for identifying post-translational modifications (PTMs).
  • Develop a tool for detecting modified peptide variants in spectrum libraries.

Main Methods:

  • Utilized a modification-rich test dataset.
  • Developed QuickMod, a modification-tolerant spectrum library search tool.
  • Employed a support vector machine (SVM) for spectrum-spectrum match scoring.
  • Implemented a rapid modification site assignment algorithm.

Main Results:

  • Library spectra effectively identify modified peptides.
  • QuickMod successfully detects and localizes PTMs.
  • QuickMod demonstrates favorable speed and identification rates compared to existing software.

Conclusions:

  • Spectrum library searching is a viable strategy for PTM identification.
  • QuickMod offers an efficient and accurate solution for PTM analysis in proteomics.