This mass spectrometer uses Matrix Assisted Laser desorbtion ionization and a time of flight mass analyzer to produce highly accurate mass spectra. The ionization source is suited to compounds that do not ionize well using other ionization sources, for example electrospray ionization. Examples of such compounds are lipids, carbohydrates and synthetic polymers. A variety of matrices allow for the ionization of specific classes of compounds. The matrix predominantly used is a-cyano-4-hydroxycinnamic acid for peptide analyses but other matrices are also available for intact protein analysis, carbohydrates, lipids, DNA and synthetic polymers. The tandem time-of-flight (ToF/ToF) analyzer allows for the acquisition of high mass accuracy spectra – typically sub 5ppm with internal calibration while also allowing for true MS/MS. The tandem mass spectra are generated by introducing the parent ions into the collision induced dissociation (CID) cell filled with air. This is in contrast to conventional ToF analyzers using Post Source Decay (PSD). The advantage of true MS/MS capability lies in better fragmentation and high mass accuracy. Samples can be analyzed using either the Peptide Mass Fingerprinting approach (PTM) for pure proteins or using the liquid chromatography-mass spectrometry (LCMS) approach for complete proteome digests. The mass accuracy of the mass spectrometer enables the acquisition of high quality data. In terms of proteomics this results in more positive protein identifications per analysis.