Peptide Identification Using Tandem Mass Spectrometry

Unlike MALDI-TOF, tandem mass spectrometry, or MS/MS, employs two mass analyzers placed in series, separated by a collision cell. This technique can identify the amino acid sequence of a peptide from a complex mixture for detailed analysis.

First, an electrospray ionizer generates peptide ions and accelerates them to the first mass analyzer like a quadrupole. This analyzer acts as a mass filter allowing selection of a single peptide ion called a precursor ion of a specific mass-to-charge ratio.

Once inside the collision cell, the selected peptide ion collides with the gas molecules, primarily breaking the peptide bonds, and generating smaller ions.

These ions move into the second mass analyzer like a time of flight that separates ions based on their mass-to-charge ratio.

The obtained product-ion spectrum helps identify the peptide's amino acid sequence.

Combining MS/MS with liquid chromatography aids in continuous peptide analysis from complex biological samples.

MS/MS can also characterize lipids, identify post-translational protein modifications, and detect low levels of disease-specific biomarkers in biological samples.