New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

14 CHAPTER 2. PRELIMINARIES
Further analyses of these discriminating peaks can lead to (at least partial)
identification of the underlying peptides by tandem mass spectrometry
(MS/MS) and might allow new insights into the actual function of these proteins
in the organism (see section 6.2.3 for an example).
Drug Development & Pharmacokinetics
Mass spectrometry based techniques are frequently used in many drug development
stages such as “Peptide Mapping”, “Bioaffinity Screening”, “In Vivo
Drug Screening”, “Metabolic Stability Screening”, “Degradant Identification”
or “Quantitative Bioanalysis” (Lee and Kerns, 1999).
Pharmacokinetics as a branch of pharmacology can be used to analyze the
metabolism of substances (e.g. newly developed drugs) brought into a living
organism. MS based pharmacokinetical studies can help determining how
quick a drug will be cleared from the Hepatic Blood flow and organs of the
body. Advantages of MS based technologies over commonly used methods such
as UV based detection techniques are its high sensitivity and specificity and a
very short analysis time (see e.g. (Covey et al., 1986; Hsieh and Korfmacher,
2006)).
Peptide Quantification
Peptide quantification is a method to compare the amounts of a given protein
among two or more samples. (For an introduction see e.g. (America et al.,
2006; Wang et al., 2006; Wang, Zhou, Lin, Roy, Shaler, Hill, Norton, Kumar,
Anderle and Becker, 2003).) There are two main strategies for quantification:
Label-based approaches (e.g. ICAT, MeCAT, SILAC) use chemical labels
to mark individual peptides as coming from one or the other sample and
measure the difference in one MS run. For example additional neutrons
are added to one of the samples by introducing stable isotopes in one
or more of the atoms comprising the peptide under scrutiny (e.g., 2 H
replacing 1 H). The peak intensities of the respective peptides can then
be compared to obtain a relative quantification of the peptide in sample
1 vs. sample 2. See (Ong and Mann, 2005) for a good overview of
different labeling strategies.
Label-free approaches depend on comparison of two (or more) individual
MS runs of the same peptide (in different samples) and comparing the
peak intensities. Obviously, two main critical factors are the mass accuracy
of the mass analyzer used and the ionization quality of the sample,
since the quantification depends on the identification of peaks belonging
to the peptide. The main advantage of this approach is the low cost,
since peptides do not have to be biochemically modified.
2.1.3 Proteomics
The neologism “omics” refers to some (usually but not only) biological field of
study such as genomics or proteomics. The actual object of this study is then
built with the related neologism “omes”, such as the genome or proteome.
Most of the first scientists to use the “-ome” suffix were Bioinformaticians
and molecular biologists who wanted to refer to some sort of wholeness or