MS2

MS2, in the context of mass spectrometry, refers to the second stage of tandem mass spectrometry (MS/MS). In an MS2 experiment, a selected precursor ion produced in the first mass analyzer (MS1) is isolated and fragmented in a collision cell. The resulting product ions are then measured by a second mass analyzer, producing an MS2 spectrum that provides structural information about the ion.

Fragmentation is typically induced by collision with neutral gas (collision-induced dissociation, CID) or by higher-energy methods (HCD). Other techniques, such as electron-based dissociation (e.g., ETD), are used for specific chemistries or labile post-translational modifications. The pattern of fragment ions, together with their mass differences, helps reveal the composition and sequence of the original molecule.

MS2 is central to proteomics, where it is used to identify and sequence peptides and infer proteins. It is also employed in metabolomics and small-molecule analysis to determine substructures and aid compound identification. In targeted workflows, MS2 data enable quantification and verification of specific molecules of interest.

Data interpretation relies on comparing the MS2 spectrum to theoretical fragmentation patterns or libraries, or on de novo sequencing when databases are incomplete. Software tools and databases (e.g., for peptide spectra) support peptide identification, modification assignment, and confidence scoring.

Instrumentation varies and includes triple quadrupole, ion trap, time-of-flight (TOF), and Orbitrap systems. Acquisition strategies differ, with data-dependent acquisition (DDA) selecting precursor ions for MS2 in real time, and data-independent acquisition (DIA) systematically fragmenting broader mass ranges. MS2 remains a foundational element of structural elucidation in mass spectrometry.

Note: MS2 can also denote other concepts in science, such as the MS2 bacteriophage in biology, but this article describes MS2 as a mass spectrometry stage.