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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 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...

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 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...

Mass Spectrometry: Complex Analysis

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)

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 Analyzers: Overview

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...

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Updated: Jun 16, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Current limitations in native mass spectrometry based structural biology.

Esther van Duijn¹

¹Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands. e.vanduijn1@uu.nl

Journal of the American Society for Mass Spectrometry

|February 2, 2010

Summary

Native mass spectrometry is crucial for structural biology, revealing protein complex details and modifications. Current limitations in sample quality and dissociation efficiency are discussed.

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Analyzing Large Protein Complexes by Structural Mass Spectrometry

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

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Last Updated: Jun 16, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Published on: October 15, 2018

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

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Published on: November 28, 2017

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

Area of Science:

Biochemistry
Structural Biology
Biophysics

Background:

Mass spectrometry is a vital tool in modern structural biology.
It offers insights into intact protein complexes (composition, topology, stability, dynamics) and individual proteins (identity, modifications).
Integration of mass spectrometry data enables the creation of detailed models for biological assemblies.

Purpose of the Study:

To provide a perspective on the application of native mass spectrometry in structural biology.
To discuss the potential and current limitations of this technique.
To highlight specific challenges in sample quality, complex dissociation, and ion mobility.

Main Methods:

Application of native mass spectrometry for analyzing intact protein complexes.
Proteomics approaches for protein identification and characterization of modifications.
Tandem mass spectrometry for complex dissociation analysis.
Ion mobility mass spectrometry for structural insights.

Main Results:

Native mass spectrometry provides comprehensive data on protein complex architecture and dynamics.
Proteomics confirms protein identity and reveals post-translational modifications.
Combined approaches facilitate the construction of functional models of biological assemblies.
Identified limitations include sample homogeneity, dissociation efficiency, and ion mobility boundaries.

Conclusions:

Native mass spectrometry is a powerful technique for advancing structural biology.
Addressing current limitations is essential for maximizing the potential of mass spectrometry in this field.
Further development in mass spectrometry techniques will enhance our understanding of complex biological systems.