Comparison of Several Methods of Protein Mass Spectrometry

Mass spectrometry technology ionizes sample molecules into ions and achieves qualitative and quantitative identification of samples by detecting mass-to-charge ratios and other mass spectrometry information. It is an important tool in proteomics research. It can identify the molecular mass, content, and amino acid sequence of proteins, as well as detect post-translational modifications of proteins. For analyzing the molecular mass or amino acid sequence of proteins, single-stage mass spectrometry is sufficient. However, to characterize post-translational modifications, special ions must be selected for fragmentation analysis via a collision cell, which is tandem mass spectrometry. A mass spectrometer mainly consists of three core components: an ion source, mass analyzer, and ion detector. The ion source ionizes sample molecules into ions, the mass analyzer separates ions based on different mass-to-charge ratios, and the ion detector is used for detection. With the development of life sciences technology, various mass spectrometry ionization techniques and mass analyzers have emerged, each with unique characteristics in terms of physical principles, performance parameters, operating modes, and applicability.

Comparison of Different Ionization Methods:

Ionization Method	Type of Compounds Detected	Sample Introduction Method	Main Characteristics
Electron Impact Ionization (EI)	Small molecules, low polarity, volatile	GC or liquid/solid Adsorbed onto a probe	Hard ionization, high reproducibility, rich structural information
Chemical Ionization (CI)	Small molecules, medium-low polarity, volatile	GC or liquid/solid Adsorbed onto a probe	Soft ionization, provides molecular ion information
Electrospray Ionization (ESI)	Small molecules, proteins, peptides, non-volatile	Liquid chromatography or direct injection of sample solution	Soft ionization, multiple charged ions
Fast Atom Bombardment Ionization (FAB)	Carbohydrates, organometallic compounds, proteins, non-volatile	Sample dissolved in a viscous matrix	Soft ionization, harder than ESI and MALDI
Matrix-Assisted Laser Desorption/Ionization (MALDI)	Peptides, proteins, nucleic acids	Sample mixed with solid matrix	Soft ionization, suitable for macromolecules

Comparison of Different Mass Analyzers:

Type	Measured Parameters	Mass Range	Resolution	Characteristics
Quadrupole	Mass/Charge	m/z 3000	2000	Suitable for electrospray, easy to switch between positive and negative ion modes, small size, low cost
Ion Trap	Frequency	m/z 2000	1500	Small size, medium resolution, simple design, low cost, suitable for multi-stage mass spectrometry, easy to switch between positive and negative ion modes
Magnetic Field	Motion/Charge	m/z 2000	10000	High resolution, accurate molecular weight measurement, medium test range
Time of Flight	Flight Time	m/z ∞	15000	Wide mass range, fast scan speed, simple design
Fourier Transform Ion Cyclotron Resonance	Frequency	m/z 10000	30000	High resolution, suitable for multi-stage mass spectrometry, requires high vacuum and superconducting magnet

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