%PDF-1.4 % 4 0 obj << /S /GoTo /D (toc.0) >> endobj 7 0 obj (Contents) endobj 8 0 obj << /S /GoTo /D (chapter.1) >> endobj 11 0 obj (1 Introduction) endobj 12 0 obj << /S /GoTo /D (section.1.1) >> endobj 15 0 obj (1.1 Motivation) endobj 16 0 obj << /S /GoTo /D (section.1.2) >> endobj 19 0 obj (1.2 LC-MS/MS Proteomics) endobj 20 0 obj << /S /GoTo /D (section.1.3) >> endobj 23 0 obj (1.3 The Protein Inference Problem) endobj 24 0 obj << /S /GoTo /D (section.1.4) >> endobj 27 0 obj (1.4 Contributions of this Thesis) endobj 28 0 obj << /S /GoTo /D (chapter.2) >> endobj 31 0 obj (2 Experimental Background) endobj 32 0 obj << /S /GoTo /D (section.2.1) >> endobj 35 0 obj (2.1 Sample Preparation) endobj 36 0 obj << /S /GoTo /D (section.2.2) >> endobj 39 0 obj (2.2 Liquid Chromatography) endobj 40 0 obj << /S /GoTo /D (section.2.3) >> endobj 43 0 obj (2.3 Ionisation Methods) endobj 44 0 obj << /S /GoTo /D (section.2.4) >> endobj 47 0 obj (2.4 Mass Spectrometers) endobj 48 0 obj << /S /GoTo /D (chapter.3) >> endobj 51 0 obj (3 Computational Background) endobj 52 0 obj << /S /GoTo /D (section.3.1) >> endobj 55 0 obj (3.1 LC-MS/MS Data Interpretation) endobj 56 0 obj << /S /GoTo /D (section.3.2) >> endobj 59 0 obj (3.2 Estimating the Quality of Identifications) endobj 60 0 obj << /S /GoTo /D (section.3.3) >> endobj 63 0 obj (3.3 Protein Databases) endobj 64 0 obj << /S /GoTo /D (section.3.4) >> endobj 67 0 obj (3.4 Specifications of the Terminology for Protein Ambiguity Groups, Sub-Groups and Clusters) endobj 68 0 obj << /S /GoTo /D (section.3.5) >> endobj 71 0 obj (3.5 The Proteomics Standards Initiative of the Human Proteome Organization) endobj 72 0 obj << /S /GoTo /D (chapter.4) >> endobj 75 0 obj (4 Analysis of the Uniqueness of Peptides and Proteins) endobj 76 0 obj << /S /GoTo /D (section.4.1) >> endobj 79 0 obj (4.1 In Silico Digestion of UniProtKB Databases) endobj 80 0 obj << /S /GoTo /D (section.4.2) >> endobj 83 0 obj (4.2 Peptide and Protein Uniqueness in Example Datasets) endobj 84 0 obj << /S /GoTo /D (chapter.5) >> endobj 87 0 obj (5 Assessment of Protein Inference Methods) endobj 88 0 obj << /S /GoTo /D (section.5.1) >> endobj 91 0 obj (5.1 Description of the Benchmark Datasets) endobj 92 0 obj << /S /GoTo /D (section.5.2) >> endobj 95 0 obj (5.2 Assessment of PIA) endobj 96 0 obj << /S /GoTo /D (section.5.3) >> endobj 99 0 obj (5.3 Assessment of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics) endobj 100 0 obj << /S /GoTo /D (section.5.4) >> endobj 103 0 obj (5.4 Advanced Application Example: Protein Isoform Detection) endobj 104 0 obj << /S /GoTo /D (chapter.6) >> endobj 107 0 obj (6 PIA - Protein Inference Algorithms) endobj 108 0 obj << /S /GoTo /D (section.6.1) >> endobj 111 0 obj (6.1 Design Goals) endobj 112 0 obj << /S /GoTo /D (section.6.2) >> endobj 115 0 obj (6.2 Basic Concepts) endobj 116 0 obj << /S /GoTo /D (section.6.3) >> endobj 119 0 obj (6.3 Frontends for PIA) endobj 120 0 obj << /S /GoTo /D (section.6.4) >> endobj 123 0 obj (6.4 Technical Details of the Implementation) endobj 124 0 obj << /S /GoTo /D (chapter.7) >> endobj 127 0 obj (7 Conclusion and Outlook) endobj 128 0 obj << /S /GoTo /D (section*.79) >> endobj 131 0 obj (Bibliography) endobj 132 0 obj << /S /GoTo /D (appendix.A) >> endobj 135 0 obj (A Abbreviations) endobj 136 0 obj << /S /GoTo /D (appendix.B) >> endobj 139 0 obj (B Contributions) endobj 140 0 obj << /S /GoTo /D (appendix.C) >> endobj 143 0 obj (C List of publications) endobj 144 0 obj << /S /GoTo /D (appendix.D) >> endobj 147 0 obj (D Supporting Tables) endobj 148 0 obj << /S /GoTo /D (appendix.E) >> endobj 151 0 obj (E Supporting Figures) endobj 152 0 obj << /S /GoTo /D (appendix.F) >> endobj 155 0 obj (F Additional Material) endobj 156 0 obj << /S /GoTo /D [157 0 R /Fit] >> endobj 159 0 obj << /Length 536 /Filter /FlateDecode >> stream xڕSMs0WhPe$NN;)9=ȶ5m+pė^@v߾vA<WnM ,hN@y 890G9(^UmFȈ simk^[?g2Q@(oU*+?6]Ń?oz'sPNݿԌD)zk*[Ymm.ުwQPޙq>CFe]5%D5HjE 6 gB(>zT&f!O}7AU2/臭rG1,]g:oc