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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 Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
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: Overview01:19

Mass Spectrometry: Overview

Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...
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...
Mass Spectrometry: Branched Alkane Fragmentation01:29

Mass Spectrometry: Branched Alkane Fragmentation

This lesson delves into the mass spectrometry of branched alkane fragmentation. Branched alkanes possess secondary or tertiary carbon atoms, which generate relatively stable carbocations if the cleavage occurs at the branching point. The high stability of carbocations drives the instant fragmentation of branched alkanes. Accordingly, the branched alkane's molecular ion peak is very weak or invisible in the mass spectra, especially in comparison to a linear alkane.

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Related Experiment Video

Updated: May 30, 2026

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics
13:02

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Published on: October 5, 2016

The volatile compound BinBase mass spectral database.

Kirsten Skogerson1, Gert Wohlgemuth, Dinesh K Barupal

  • 1Genome Center, University of California, Davis, CA 95616, USA.

BMC Bioinformatics
|August 6, 2011
PubMed
Summary
This summary is machine-generated.

A new database system, vocBinBase, automates the analysis of volatile compounds in complex mixtures. This tool enhances chemical ecology research by providing accurate identification and quantification across large datasets.

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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

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Last Updated: May 30, 2026

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics
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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Ecology

Background:

  • Volatile compounds are diverse, originating from secondary metabolism and playing key roles in plant and animal chemical ecology.
  • Advancements in sampling and instrumentation for volatile analysis have outpaced the development of robust database tools.

Purpose of the Study:

  • To develop an automated peak annotation and database system for analyzing complex volatile mixtures using GC-TOF-MS data.
  • To extend the existing metabolite BinBase software for volatile compound identification.

Main Methods:

  • The volatile compound BinBase (vocBinBase) system utilizes deconvoluted spectra and peak metadata from ChromaTOF software.
  • A multi-tiered filtering system with stringent thresholds annotates peaks, referencing the Adams mass spectral-retention index library.
  • Novel compounds are automatically added based on strict mass spectral and experimental criteria.

Main Results:

  • vocBinBase successfully annotates large datasets (thousands of chromatograms) with quantitative information.
  • The database currently contains 1,537 unique mass spectra from 1.7 million deconvoluted spectra across 3,435 samples (18 species).
  • Mass spectra and volatile profiles are available for download under a CC-BY agreement.

Conclusions:

  • BinBase algorithms are effectively adapted for tracking and identifying volatile compounds in complex mixtures.
  • The system is suitable for large-scale data annotation and cross-study comparisons, including chemotaxonomy.
  • This volatile compound database is applicable to diverse fields from chemical ecology to human health.