One of the most powerful tools available to the mass spectrometrist is MS/MS. Whereas fragmentation is virtually absent in electrospray mass spectrometry, it can be deliberately induced by MS/MS techniques. Tandem MS employs collision-induced dissociation (CID) to fragment a precursor ion. For a sample mixture (even after chromatography, a mixture of different species can be present), the first quadrupole mass analyzer (Q1 in the QSTART XL) generates a spectrum of ions. The ion of interest is then selectively allowed to progress into the collision cell (Q2), containing an inert gas typically argon, which is allowed to collide with the selected ion. This induces fragmentation, caused by collision-induced dissociation (CID) and the resulting ions are then analyzed as product ions. Sequence as well as other structural information can be derived from these fragments. Tandem MS/MS can be used to elucidate the structure of a variety of small to medium sized molecules, including organic molecules, lipids and fatty acids, peptides, carbohydrates, oligonucleotides, as well as DNA and RNA adducts, etc.In the past a few years, researchers have begun to use mass spectrometry to determine peptide sequence. Improvements in machinery sensitivity as well as software now allows for the confirmation of peptide sequence with virtual certainty. When fragmented, a series of ions are produced, termed a, b, and c ions for those with N-terminal charge and termed x, y and z ions for those fragments with C-terminal charge. The b and y ions are the ions generated when the fragments are due to the cleavage at the peptide bond, whereas the a, c, x, and z ions are generated when cleavages occur on the N-terminal side of the peptide bond carbon (a and x) C-terminal side of the peptide bond amine (c and z). These ions are then matched up with known amino acids and amino acid fragments, and the mass difference between consecutive ions reveals the identities of the consecutive amino acids. From this map, an accurate peptide sequence can be determined.The QSTART XL is so accurate in determining mass of the various CID fragments, that with the exception of leucine and isoleucine, two amino acids with identical molecular weights, all other amino acids can be differentiated. Even glutamine, with a mass of 128.0586 and lysine, with a mass of 128.0950, can be differentiated. Similarly, various amino acid modifications can be determined due to the gentle nature of ESI (versus MALDI, which tends to remove some modifications, such as phosphates). These include phosphorylation, glycosylation, acylation, nitronation, and many others.