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Mass Spectrometers

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:

Mass Spectrometry: Overview

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...

MALDI-TOF Mass Spectrometry

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...

Tandem Mass Spectrometry

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...

Mass Spectrometry: Molecular Fragmentation Overview

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: Interpretation

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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The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

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MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile

Tomás Pluskal¹, Sandra Castillo, Alejandro Villar-Briones

¹G0 Cell Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan. pluskal@oist.jp

BMC Bioinformatics

|July 24, 2010

Summary

This summary is machine-generated.

MZmine 2 is a new open-source software for processing mass spectrometry data in metabolomic and proteomic research. It offers enhanced features for data analysis, including improved peak identification and alignment, aiding biomarker discovery.

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Area of Science:

* Scientific research and data analysis
* Bioinformatics and computational biology

Background:

* Mass spectrometry (MS) coupled with online separation methods is crucial for metabolomic and proteomic research.
* Applications include systems biology, functional genomics, and biomarker discovery.
* Development of advanced data processing methods remains a challenge.

Purpose of the Study:

* To introduce MZmine 2, a new generation of a popular open-source data processing toolbox.
* To enhance usability and support for high-resolution spectra processing in molecular profiling.
* To provide improved tools for differential and quantitative profiling of biological samples.

Main Methods:

* MZmine 2 features a modular design separating core functionality from data processing.
* Utilizes embedded visualization tools for immediate parameter setting previews.
* Incorporates new methods for peak identification using online databases and MSn data support.
* Implements a novel peak list alignment method based on the random sample consensus (RANSAC) algorithm.

Main Results:

* MZmine 2 offers improved isotope pattern support and scatter plot visualization.
* RANSAC algorithm-based alignment evaluated using synthetic and experimental datasets.
* Performance comparison of RANSAC alignment with other existing algorithms.
* Enhanced capabilities for processing large batches of data in targeted and non-targeted metabolomic analyses.

Conclusions:

* MZmine 2 is freely available under a GNU GPL license.
* Suitable for processing large datasets in both targeted and non-targeted metabolomic analyses.
* Facilitates advanced data processing for systems biology and biomarker discovery.