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102 CHAPTER 4. (BIO-)MEDICAL APPLICATIONS in human cancer research (see above) but also in understanding a biological system. These studies usually aim at the identification of protein fingerprints that characterize the difference between a system at the different stages. Below we give some success stories in this area of mass spectrometry-based research. Identification of Proteins in Kinase Pathways A compelling example of the value of comparative proteomics for assigning unique cellular functions to uncharacterized members of protein classes was done by (Khan et al., 2005). They developed an innovative cell-biological strategy based on mass spectrometry proteomics to enrich distinct sexual stages of P.berghei life cycle that allowed the generation of high-quality cellular models for in-depth analysis. The result of this study was the most comprehensive inventory of sex-specific parasite proteins generated so far, including the discovery of novel protein kinasis regulating sex-specific signalling pathways. Identification of ATM/ATR candidates in DNA-damage Response Pathways An excellent example how quantative mass spectrometry-based methods can used for mapping protein phosphorylation sites in proteomes is given by (Matsuoka et al., 2007). Identification of Proteins in Insulin Pathways (Dong et al., 2007) show that quantitative mass-spectrometry-based proteomics using stable isotope labelling can be applied to intact organisms, as well as cell-culture preparations, thus greatly expanding the potential applications of this method. 4.6.3 Fingerprinting the Influenza Virus Influenza is still a deadly virus that continues to cause illness all over the world. The Influenza type A virus (most virulent in humans) genome is contained on eight single (non-paired) RNA strands that code for eleven proteins. One of these proteins, HA, encodes hemaglutinin which determines the extent of an infection into a host organism. Screening of the virus is necessary for the development of effective vaccines, since even a point mutation in the HA gene sequence can render a vaccine ineffective. Usual screening techniques such as enzyme immunoassays, complement fixation and heagglutination inhibition (HI) assays are quite time consuming and do not provide molecular details. A recent paper by (Downard and Morrissey, 2007) introduces a new surveillance approach for screening the structure and antigenicity of the virus. The method is based on creation of MS and MS/MS spectra from the tryptic digest of hemagglutin. The resulting MS fingerprints can be compared to reference fingerprints and by analyzing the MS/MS spectra even the molecular structure and sequence can be determined in a single step.
Chapter 5 Computer Science Grid Strategies Contents 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 103 5.2 The Quasi Ad-hoc (QAD) Grid . . . . . . . . . . . . 111 5.3 QAD Grid Platform Server . . . . . . . . . . . . . . 114 5.4 QAD Grid Worker . . . . . . . . . . . . . . . . . . . . 129 5.5 QAD Grid Platform Services . . . . . . . . . . . . . 138 5.6 QAD Grid Workflows . . . . . . . . . . . . . . . . . . 141 5.7 Related Work . . . . . . . . . . . . . . . . . . . . . . . 146 The previous chapters have introduced new methods for the analysis of mass spectrometry data. The main advantage of our algorithms was increased sensitivity that - unfortunately - introduced more complex computations and increased amount of data. To speed up these calculations we developed a new framework that can split up the analyses tasks and distribute these sub-tasks to compute machines organized in an environment we call the quasi ad-hoc Grid. This framework and its advantages (e.g. over commonly used compute clusters) are described in the following sections. 5.1 Introduction Driven by increasingly complex problems, new technologies and machines producing gigabytes of data each day, today’s science is based on computation power and data analysis as never before. But even as development of computer power and data storage continue to improve exponentially 1 , these resources are failing to keep up with what scientists demand of them. As an example, scientists back in 1990 were happy assembling small parts of DNA sequence information of a chromosome. These days they want to assemble the complete human genome and several physics projects such as CERN’s Large Hadron Collider, produce multiple petabytes of data per year. Of course, current desktop computers are much more powerful than supercomputers in the early 1990s and the storage a PC ships with is comparable with an entire 1990 1 According to Moore’s Law stating that semiconductor power doubles roughly every 18 months. 103
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New Statistical Algorithms for the
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Contents Acknowledgments . . . . .
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New Statistical Algorithms for the
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Extended Abstract English Version M
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German Version Das Gebiet der Prote
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Chapter 1 Introduction and Survey 1
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1.2. GOALS, OBJECTIVES AND TASKS 7
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1.2. GOALS, OBJECTIVES AND TASKS 9
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Chapter 2 Preliminaries 2.1 Topic O
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2.1. TOPIC OVERVIEW 13 Figure 2.1.1
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2.1. TOPIC OVERVIEW 15 completeness
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2.2. AN EXAMPLE 17 (a) Opera A (b)
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2.2. AN EXAMPLE 19 Figure 2.2.6: Tw
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2.2. AN EXAMPLE 21 successes. We ca
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Chapter 3 Mathematical Modeling and
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3.2. INTRODUCTION TO MALDI TOF MS 2
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3.3. PREPROCESSING 31 mix (external
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3.3. PREPROCESSING 33 Figure 3.3.5:
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3.3. PREPROCESSING 35 Figure 3.3.7:
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3.4. HIGHLY SENSITIVE PEAK DETECTIO
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3.5. PEAK DETECTION IN 2D MAPS 43
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3.6. PEAK REGISTRATION (ALIGNMENT)
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Page 89 and 90: 4.3. STUDY RESULTS 83 � kNN (gen.
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6.2. CASE STUDIES 153 6.2 Case Stud
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6.2. CASE STUDIES 155 Figure 6.2.2:
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6.2. CASE STUDIES 157 MASCOT and SE
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6.2. CASE STUDIES 159 The peak pick
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6.2. CASE STUDIES 161 first entry i
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6.2. CASE STUDIES 163 Approach Base
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6.2. CASE STUDIES 165 Figure 6.2.5:
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Chapter 7 Related Work In this chap
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Chapter 8 Conclusion and Future Dir
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8.3. FROM BIOMARKERS TO BIOPRINTS 1
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Appendix A Implementation Details T
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Appendix B Curriculum Vitae Name Ti
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References Aebersold, R. and Mann,
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REFERENCES 179 Breiman, L. (2001).
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REFERENCES 181 Downard, K. M. and M
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REFERENCES 183 Gillette, M. A., Man
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REFERENCES 185 Huyghe, E., Muller,
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REFERENCES 187 Kuijpens, J. L. P.,
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REFERENCES 189 McLachlan, S. M. and
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REFERENCES 191 Platt, J. C. (1999).
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REFERENCES 193 Stone, M. (1974). Cr
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REFERENCES 195 Washburn, M. P., Wol
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