What Is Fragmentation Analysis in Mass Spectrometry?
Mass spectrometry (MS) is an analytical technique used to determine the mass and relative abundance of molecular or atomic species within a sample. In MS, the sample is ionized to generate charged particles (ions), which are then accelerated and separated based on their mass-to-charge ratio (m/z) within a magnetic or electric field. The resulting data enable the identification and quantification of molecules present in the sample.
Fragmentation analysis in mass spectrometry is commonly performed using tandem mass spectrometry (MS/MS). In MS/MS, selected precursor ions undergo collision-induced dissociation (CID) within a collision cell by interacting with an inert gas such as argon or nitrogen. This process generates fragment ions, which are subsequently analyzed to produce a fragmentation spectrum. The fragmentation spectrum provides critical information for deducing the structural composition of the original molecule.
In peptide fragmentation analysis, two primary types of fragment ions are commonly observed: b ions and y ions. b ions result from the cleavage of the peptide bond at the N-terminal (amino terminus), whereas y ions are produced when the bond breaks at the C-terminal (carboxyl terminus). By analyzing the m/z values of these fragment ions, researchers can systematically reconstruct the amino acid sequence of the peptide, making this approach a fundamental tool in proteomics and biomolecular research.
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