Diphtheria toxin is a single, 60,000 dalton molecular weight protein composed of two peptide chains, fragment A and fragment B, held together by a disulfide bond.In pairwise-end sequencing, both ends of each fragment are analyzed for overlap.Originally, shotgun sequencing only analyzed one end of each fragment for overlaps.A third fragment shows only the lake, but it reveals that there is a cabin on the shore of the lake.By matching overlapping sequences at the end of each fragment, the entire DNA sequence can be reformed.Then, with the help of a computer, the fragments are analyzed to see where their sequences overlap.When the complete collection of fragments has been sequenced, comparing the sequences of all the fragments will reveal which fragments have ends that overlap with other fragments.From the order of fragments formed, the DNA sequence can be read.Each fragment is sequenced and sophisticated computer algorithms compare all the different fragments to find which overlaps with which.As a result, each copy of the same chromosome is fragmented at different locations and the fragments from the same part of the chromosome will overlap each other.They can only be sequenced in tiny fragments and the tiny fragments have to put in the correct order to generate the uninterrupted genome sequence.Odd-electron fragment ions are often formed by characteristic rearrangements in which stable neutral fragments are lost.By localizing the reactive moiety, certain fragmentation processes will be favored.All of the significant fragment ions in this spectrum are even-electron ions.Alcohols, ethers and highly branched alkanes generally show the greatest tendency toward fragmentation.The fragmentation of molecular ions into an assortment of fragment ions is a mixed blessing.The third diagram above displays a Grob-like fragmentation, favored by the relief of ring strain in the four-membered ring.Other examples of Grob fragmentations will be shown above in the second diagram. A Grob fragmentation takes place in the top example, because the orbitals of the bonding and non-bonding electron pairs participating in the reaction are aligned properly.Here a simple nucleophilic fragmentation at M is converted to an ethylagous analog by the insertion of a two carbon (ethyl) segment between the reacting moieties.An interesting and generally useful skeletal transformation, involving specific carbon-carbon bond cleavage with accompanying conversion of certain sigma-bonds to pi-bonds, is known as the Grob fragmentation.Spectrum diagrams are followed by the fragmentations leading to the chief fragment ions.
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