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Related Concept Videos

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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
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...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
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 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...

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Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
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Published on: January 20, 2022

Combinatorial approaches for mass spectra recalibration.

Sebastian Bocker, Veli Makinen

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |February 5, 2008
    PubMed
    Summary

    Automated mass spectra recalibration is crucial for large proteomics datasets. New deterministic methods improve matching accuracy and efficiency for peptide and protein identification in mass spectrometry analysis.

    Area of Science:

    • Proteomics
    • Systems Biology
    • Computational Biology

    Background:

    • Mass spectrometry is a key technique in proteomics and systems biology.
    • Increasing dataset sizes necessitate automated mass spectra recalibration for accurate peak assignment.
    • Robust and efficient algorithms are vital for handling measurement errors in mass spectrometry data.

    Purpose of the Study:

    • To develop robust and efficient deterministic methods for mass spectra recalibration.
    • To address the problem of optimal matching between mass spectra with measurement errors.
    • To improve existing algorithms for mass spectra matching.

    Main Methods:

    • Developed a computational geometry approach to find parallel lines stabbing maximal points.
    • Developed a maximal common approximate subsequence method for spectral matching.

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    Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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    Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

    Published on: November 28, 2017

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    Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
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    Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry
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    Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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    Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

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  • Exploited the sequential nature of the matching problem for algorithmic improvement.

    • Main Results:

    • Achieved robust computation of optimal matching between mass spectra.
    • The common approximate subsequence method improved existing algorithms by an order of magnitude.
    • Compared results against a computational geometry algorithm using topological line-sweep.

    Conclusions:

    • The developed deterministic methods offer robust and efficient solutions for mass spectra recalibration.
    • These algorithms enhance the accuracy of peptide and protein identification in large-scale proteomics.
    • The study contributes significant advancements to computational methods in mass spectrometry analysis.