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15.6. PROTEIN PEPTIDE SEQUENCING There are several instrumental MS methods that can be used to obtain sequence information from proteins and peptides. ESI-triple-quadrupole is frequently used; this con guration produces a reasonable number of fragments, the resolution is usually suf cient and the equipment is relatively inexpensive. With this MS/MS con guration, peptides up to 2500 Da can be analyzed. A MALDI with a TOF re ectron and Fourier transform ion cyclotron resonance mass analyzers are also beginning to be used.21 A typical procedure for protein sequencing begins by digestion with a protease such as trypsin in order to obtain a collection of tryptic peptides. Other enzymes and their cleavage sites are described elsewhere.22 This peptide collection can be ionized using ESI, separated by the rst quadrupole according to m/z ratios, and then fragmented (CID), with the resulting fragments analyzed in the third quadrupole. The mass spectrum can be analyzed to establish the peptide sequence, or compared directly with a peptide database. Figure 15.12 depicts this typical protocol. The CID procedure causes more or less random peptide bond cleavage. Therefore, a number of fragments are obtained that differ by a single amino acid residue. Several types of fragments are produced, and their nomenclature is shown in Figure 15.13. Two main classes of ions are formed by CID, those that contain the C terminus plus one or more additional residues (ions of types xn , yn, and zn ) and those that contain the N-terminus and one or more additional residues (ions of types an , bn , and cn ). Ions of types yn and bn are formed by the rupture of amide bonds, and the mass differences between these fragments are limited to the masses of the naturally occurring 19 different amino acid residues (Table 15.9). Isoleucine and leucine,

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Be conservative in your ratings; everything can t be a 3, or you will lose credibility. Build the list and the ratings so that it would be very difficult to poke holes in your reasoning or logic. By being conservative and calm, you take away some of the ammunition of your potential critics, and you will make a much more persuasive case. When trying to develop your list of vulnerabilities, it is wise to employ brainstorming techniques and include several people in the process. There are many methods to assist with creative thinking beyond brainstorming that will help you generate a more complete list.

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which are structural isomers and therefore have the same molecular weight, cannot be distinguished with MS. Moreover, lysine and glutamine can only be differentiated if resolution is high, since their mass difference is only 0.0432 Da. The sequencing process consists of the simultaneous measurement of a peptide collection, as shown in Figure 15.14. The sequence is obtained by observation of

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Once your list of vulnerabilities and ratings is complete, it s time to develop a list of recommendations If you have made a solid and sober case, and you can follow that with some equally well-thought-out recommendations, you will maximize the likelihood that you ll get the resources you are looking for Choose no more than three or four of the most serious vulnerability scenarios the ones with the highest likelihoods and impacts Develop complete plans to address each of them, with alternatives at different cost levels Choose one that you like best, and recommend it the most strongly, but make sure that all of the alternatives are palatable The recommendations should include a pure business discussion of costs versus risks, along with those old business school chestnuts return on investment and time to payback (We discussed these in some detail in 3.

) What are the objectives Why are we discussing this What is the potential benefit to the business Be as specific as possible Discuss the impact on current ongoing operations of implementing your solution; will there be downtime How much What will it all cost When estimating costs, be sure that your numbers are realistic If someone challenges you on acquisition or implementation costs, be sure that you can defend your numbers Cite sources for your information Discuss the hidden benefits of your proposal For example, will having better recovery plans result in a reduction in the enterprise s business interruption insurance premiums (You may not be able to accurately determine this, but it s something to include as a potential hidden benefit For example, a completed and tested disaster recovery plan can reduce these very expensive premiums by 20 percent or more.

Figure 15.13. Nomenclature used for the more common fragments produced by CID peptide fragmentation. The b and y fragment families , that occur when the peptide bond is broken, are normally produced at higher concentration.

) If the plan includes purchasing additional computer equipment or real estate for a disaster recovery site, what additional benefits can these resources provide the organization Will you be able to offload backups from primary systems Will you be able to house additional personnel Is there a chance the property value will rise Remember that financial arguments are most likely to get attention from upper management..

Infrastructure services, which provide technical functions, such as: access to the data, access to the communication channels, print services, etc The concept of service did not appear out of nowhere; it draws its roots from technologies of objects and components well known in the computing industry The concept of object aims at the design and the programming of software The notion of Class is a concept from programming and is referred to as a module in programming languages like C++ or Java The class encapsulates the programming logic and the data of the module in such a way that programmers can use the module (and therefore the class) without having to understand how the module is structured or coded internally An object is a particular instance of a class.

Some of the key questions to ask include how long could our business/ enterprise/organization survive without:

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