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Tandem mass spectrometry links multiple mass spectrometry stages to isolate a biomolecule of interest and determine its chemical composition. An ion source converts the sample into ions, and a mass analyzer separates them by mass-to-charge ratio. A quadrupole mass analyzer allows only specific precursor ions through, which then move into a collision cell where energy fragments them into product ions for detection and analysis.

The collision cell, typically another quadrupole, receives the precursor ion and applies energy to fragment it in a predictable pattern. The strength of applied voltage accelerates the precursor ion into the collision cell and determines the degree of fragmentation. Voltage is increased until the precursor reaches roughly 10% abundance compared to the highest product ion, ensuring optimal fragmentation for analysis.

Collision-induced dissociation (CID) transfers energy via neutral atoms to fragment precursor ions, primarily cleaving at peptide bonds between amino acids. This fragmentation pattern is unique for each protein. Analysis software compares the resulting spectrum to a database of known peptide sequences, allowing identification of unknown proteins from overlapping fragments.

Selected reaction monitoring (SRM) is a scanning mode where both mass analyzers are fixed to specific mass-to-charge ratios, focusing on particular precursor and product ions. SRM's high sensitivity allows peptide standards of known concentration to be compared with unknown samples for protein quantification. It also discards all but one product ion, increasing sensitivity and enhancing detection limits by up to 100-fold.

Tandem mass spectrometry fragments proteins into smaller components, allowing determination of post-translational modification (PTM) locations to specific fragments or amino acids. Modifications like phosphorylation and glycosylation are important in cell signaling. For modifications difficult to differentiate by mass alone, such as acetylation and trimethylation, chromatographic separation is performed before mass spectrometry analysis.

Biomolecules have large, complex structures making direct molecular composition determination difficult. Tandem mass spectrometry selects a molecule of interest and fragments it into multiple subunits, revealing its identification and sequence. The unique spectral pattern generated for each biomolecule, combined with database comparison software, enables elucidation of unknown protein structures from overlapping fragments.

Biomolecules are typically ionized using matrix-assisted laser desorption or electrospray ionization. After ionization, the precursor ion signal is optimized by tuning ion optics. The target is then isolated and a fragmentation method such as collision-induced dissociation is chosen, with multiple spectra acquired and averaged until a sufficient signal-to-noise ratio is achieved.