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Matrix-Assisted Laser Desorption Ionization (MALDI)

Matrix-Assisted Laser Desorption Ionization (MALDI)

Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI spectrometry is widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.
The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix material. The...

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Updated: Aug 20, 2025

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

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Dissolve-spin: Desalting oligonucleotides for MALDI MS analysis.

Alexander Apostle¹, Shiyue Fang¹

¹Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA.

Journal of Mass Spectrometry : JMS

|November 23, 2022

Summary

A novel dissolve-spin method effectively desalted oligonucleotides (ONs) for mass spectrometry. This technique uses organic solvents and centrifugation to remove salts, improving ON analysis via MALDI MS.

Keywords:

DNA MALDI MS RNA desalt oligonucleotide sample preparation

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Published on: June 20, 2025

Area of Science:

Analytical Chemistry
Biochemistry
Molecular Biology

Background:

Oligonucleotides (ONs) require desalting for accurate analysis.
Traditional desalting methods can be complex or inefficient.
Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) is a key technique for ON analysis.

Purpose of the Study:

To develop a simple and effective method for desalting oligonucleotides (ONs).
To enable ON analysis using MALDI MS by removing interfering salts.
To demonstrate the utility of organic solvents for ON desalting.

Main Methods:

A novel dissolve-spin approach was employed for ON desalting.
Oligonucleotides were dissolved in organic solvents like acetonitrile with a proton source.
Insoluble inorganic salts were removed via centrifugation.
The effectiveness was validated by comparing MALDI MS spectra.

Main Results:

Oligonucleotides demonstrated solubility in organic solvents when a proton source (e.g., pyridinium chloride) was present.
Inorganic salts remained insoluble, allowing for their separation.
The developed method effectively removed salts from ON samples.
MALDI MS analysis showed significantly improved spectra after desalting.

Conclusions:

The dissolve-spin method provides an efficient and simple approach for desalting ONs.
This technique enhances the quality of ON analysis by MALDI MS.
The findings offer a valuable new tool for researchers working with oligonucleotides.