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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 electrospray 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...

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 signal-to-noise ratio for the analyte. 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 collision-induced...

High-Resolution Mass Spectrometry (HRMS)

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...

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: 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...

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

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A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data.

Jessica Henning¹, Rob Smith²

¹Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA.

BMC Bioinformatics

|September 25, 2020

Summary

JS-MS 2.0 is a new software suite for creating ground truth data for mass spectrometry (MS) analysis. This tool simplifies the evaluation of MS1-aware algorithms, improving data processing accuracy and coverage.

Keywords:

MS1 feature finding Mass spectrometry Mass spectrometry viewer Open source mass spectrometry software

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Area of Science:

Analytical Chemistry
Biochemistry
Computational Biology

Background:

Mass spectrometry (MS) is vital for molecular identification and quantification.
Interpreting raw MS data requires sophisticated processing algorithms.
Evaluating the performance and bias of MS data processing is crucial for accurate results.

Purpose of the Study:

To develop improved software for creating ground truth datasets for quantitative MS.
To facilitate more extensive evaluation and enhancement of MS data processing algorithms.

Main Methods:

JS-MS 2.0 is a browser-based, cross-platform software suite.
It allows loading, viewing, and navigating MS1 data in 2D and 3D.
Includes tools for capturing, editing, saving, and viewing isotopic envelope and extracted isotopic chromatogram features.

Main Results:

JS-MS 2.0 offers a dependency-free solution for creating MS1 ground truth.
The software enables efficient capture and editing of isotopic features.
It also facilitates the exploration of feature-finding algorithm outputs.

Conclusions:

JS-MS 2.0 accelerates the creation and inspection of MS1 ground truth data.
The software is publicly available under an MIT license.
This tool supports the advancement of quantitative MS data processing.