University of Illinois at Urbana-Champaign
Mass Spectrometry Laboratory


Mass Spectrometry/Mass Spectrometry

MS/MS is not an ionization technique but a method for structure determination and analysis of molecules. Traditionally, MS/MS uses two mass spectrometers in tandem. Between the two analyzers (MS1 and MS2) is a collision gas cell. Precursor ions selected by MS1 collide with a high pressure gas (usually He) in the cell and undergo fragmentation. The resulting daughter ions are analyzed in MS2. The collision process is called collision induced dissociation (CID). In the QTof, the collision cell is located between the quadrupole and TOF analyzers. In the LCQ, which is an ion trap instrument, the separation is in time rather than space. The selected ions are trapped, collided, and then analyzed. In the Voyager, MS/MS depends on the decay of ions after they leave the ion source (post-souce decay or PSD).

MS/MS is used for the structural studies of complex molecules and is performed on the QTof and LCQ by ESI or the Voyager by MALDI. Many large molecules such as peptides have spectra with only a few fragment ions. MS/MS has proven useful in the sequence determination of peptides due to the formation of abundant daughter ions in the CID process.

MS/MS can be run on molecular ions or fragment ions. MS/MS can also be performed with high resolution selection of the precursor for isobaric fragment species. The practical upper mass limit for MS/MS is currently about 4000 Da. Beyond that the intensity of precursor ions is too small to produce detectable daughter ions.

MS/MS Instrument: QTof (ESI) Sample size: 1-300 pmole

MS/MS Instrument: LCQ (ESI) Sample size: 1-300 pmole

MS/MS Instrument: Voyager (MALDI) Sample size: 1-500 pmole

A low resolution spectrum must be run before submitting samples for MS/MS, and the exact mass of the quasimolecular ion must be known, either from the known molecular formula or from a previous high resolution spectrum. Submit all low resolution and exact mass forms and spectra with your MS/MS request.