Inferring proteolytic processes from mass spectrometry time series data:
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2013
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| Schlagworte: | |
| Online-Zugang: | Volltext Inhaltsverzeichnis |
| Beschreibung: | Nebentitel: Bestimmen proteolytischer Prozesse auf Basis von Massenspektrometrie-Zeitreihen |
| Beschreibung: | XV, 121 S. graph. Darst. |
Internformat
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| 245 | 1 | 0 | |a Inferring proteolytic processes from mass spectrometry time series data |c vorgelegt von Stephan Aiche |
| 246 | 1 | 3 | |a Bestimmen proteolytischer Prozesse auf Basis von Massenspektrometrie-Zeitreihen |
| 264 | 1 | |c 2013 | |
| 300 | |a XV, 121 S. |b graph. Darst. | ||
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Datensatz im Suchindex
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| adam_text | CONTENTS
1 INTRODUCTION 1
1.1 PROTEASES - ESSENTIAL PART OF NATURE S TOOLKIT 1
1.2 GUIDE TO THIS THESIS 5
2 MASS SPECTROMETRY BASED PROTEOMICS - AN INTRODUCTION 7
2.1 SAMPLE PREPARATION 7
2.2 SEPARATION 9
2.2.1 HIGH-PERFORMANCE LIQUID-CHROMATOGRAPHY 9
2.2.2 CAPILLARY ELECTROPHORESIS 9
2.3 MASS SPECTROMETRY 10
2.3.1 ION SOURCES 11
2.3.2 MASS ANALYZERS 12
2.3.3 DETECTORS 13
2.3.4 DATA NOMENCLATURE 13
2.4 ANALYSIS OF LC-MS DATA 18
2.4.1 IDENTIFICATION 18
2.4.2 QUANTIFICATION 20
2.4.3 SUMMARY 23
2.5 OPENMS - AN OPEN-SOURCE FRAMEWORK FOR MASS SPECTROMETRY DATA
ANALYSIS . 23
3 A NEW GROUND TRUTH FOR COMPUTATIONAL MASS SPECTROMETRY 27
3.1 WHY WE NEED A GROUND TRUTH 27
3.2 EXISTING APPROACHES 28
3.3 STRUCTURE OF MSSIMULATOR 28
3.3.1 DIGESTION 29
3.3.2 PEPTIDE SEPARATION 29
3.3.3 ELUTION PROFILE SHAPES 31
3.3.4 FILTERING PEPTIDES BY THEIR DETECTABILITY 33
3.3.5 IONIZATION 33
3.3.6 MODELING PEPTIDE SIGNALS IN THE MASS SPECTRUM 34
VII
HTTP://D-NB.INFO/104425016X
VIII
CONTENTS
3.3.7 TANDEM MS SAMPLING 35
3.3.8 LABELED EXPERIMENTS 36
3.4 OUTPUT OF MSSIMULATOR 37
3.5 BENCHMARKING THE DATA GENERATED WITH MSSIMULATOR 38
3.5.1 COMPARISON OF TWO ESTABLISHED APPROACHES FOR S1LAC QUANTIFICATION
. 39
3.5.2 BENCHMARKING FEATURE DETECTION IN HIGH-RESOLUTION DATA 41
3.6 CONTRIBUTIONS 43
4 MODELING PROTEOLYTIC PROCESSES: THE DEGRADATION GRAPH 45
4.1 EXISTING APPROACHES 46
4.2 DEFINITION OF THE DEGRADATION GRAPH 46
4.3 CONSTRUCTING A DEGRADATION GRAPH 47
4.3.1 IDENTIFICATION OF PEPTIDE SIGNALS 49
4.3.2 VERIFICATION OF THE DEGRADATION GRAPH 49
4.3.3 EXTENSION OF THE DEGRADATION GRAPH 51
4.3.4 HANDLING MORE THEN ONE SEED SEQUENCE 51
4.4 MODELING THE REACTION KINETICS 52
4.4.1 GENERATING A KINETIC MODEL FOR THE DEGRADATION GRAPH 53
4.4.2 TRANSFORMING PEPTIDE CONCENTRATIONS TO SIGNAL INTENSITIES 54
4.4.3 ESTIMATING KINETIC RATE CONSTANTS 56
4.5 STRUCTURE EVALUATION AND OPTIMIZATION 58
4.5.1 EVALUATING DIFFERENT MODELS 59
4.5.2 HEURISTIC SEARCH FOR THE OPTIMAL DEGRADATION GRAPH 61
4.6 RUNNING TIME CONSIDERATIONS 62
4.7 IMPLEMENTATION 64
5 VALIDATION OF DEGRADATION GRAPHS 67
5.1 SIMULATION STUDY 67
5.1.1 EXPERIMENTAL SETUP 68
5.1.2 SIMULATION STUDY 1: VALIDATION USING THE EX VIVO DEGRADATION OF
FIB-
RINOPEPTIDE A (FPA) 68
5.1.3 SIMULATION STUDY 2: COMPLEX DEGRADATION OF HUMAN PLASMA PEPTIDES
70
5.2 EVALUATION ON REAL DATA 73
5.2.1 EXPERIMENTAL SETUP 77
5.2.2 ANALYSIS USING THE DEGRADATION GRAPH APPROACH 78
5.2.3 RESULTS 79
CONTENTS IX
6 COMPUTATIONAL ASPECTS 85
6.1 THE QUASI AD-HOC GRID 86
6.1.1 BUILDING BLOCKS OF THE QUASI AD-HOC GRID 87
6.1.2 QAD GRID DESIGN CONCEPTS 88
6.1.3 THE WORKER CONCEPT 89
6.1.4 EXTENDING THE WORKER IMPLEMENTATION 90
6.2 ENABLING TRANSPORTATION OF MASS DATA IN THE QAD GRID 92
6.3 EMBEDDING THE DEGRADATION GRAPH INTO THE QAD GRID 96
6.4 EMBEDDING MSSIMULATOR IN THE QAD GRID 98
7 CONCLUSION AND FUTURE DIRECTIONS 99
7.1 CONCLUSION 99
7.2 IMPROVING THE GROUND TRUTH 100
7.3 VALIDATION AND EXTENSION OF THE DEGRADATION GRAPH CONCEPT 101
7.4 EXTENDING OUR VIEW ON BIOMARKERS 102
CURRICULUM VITAE 103
BIBLIOGRAPHY 107
|
| any_adam_object | 1 |
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| dewey-full | 572.648 |
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| dewey-ones | 572 - Biochemistry |
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| dewey-search | 572.648 |
| dewey-sort | 3572.648 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
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| spelling | Aiche, Stephan Verfasser (DE-588)1043403655 aut Inferring proteolytic processes from mass spectrometry time series data vorgelegt von Stephan Aiche Bestimmen proteolytischer Prozesse auf Basis von Massenspektrometrie-Zeitreihen 2013 XV, 121 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Nebentitel: Bestimmen proteolytischer Prozesse auf Basis von Massenspektrometrie-Zeitreihen Berlin, Freie Univ., Diss., 2013 (DE-588)4113937-9 Hochschulschrift gnd-content Erscheint auch als Online-Ausgabe urn:nbn:de:kobv:188-fudissthesis000000095370-0 http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000095370 kostenfrei Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026829490&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Aiche, Stephan Inferring proteolytic processes from mass spectrometry time series data |
| subject_GND | (DE-588)4113937-9 |
| title | Inferring proteolytic processes from mass spectrometry time series data |
| title_alt | Bestimmen proteolytischer Prozesse auf Basis von Massenspektrometrie-Zeitreihen |
| title_auth | Inferring proteolytic processes from mass spectrometry time series data |
| title_exact_search | Inferring proteolytic processes from mass spectrometry time series data |
| title_full | Inferring proteolytic processes from mass spectrometry time series data vorgelegt von Stephan Aiche |
| title_fullStr | Inferring proteolytic processes from mass spectrometry time series data vorgelegt von Stephan Aiche |
| title_full_unstemmed | Inferring proteolytic processes from mass spectrometry time series data vorgelegt von Stephan Aiche |
| title_short | Inferring proteolytic processes from mass spectrometry time series data |
| title_sort | inferring proteolytic processes from mass spectrometry time series data |
| topic_facet | Hochschulschrift |
| url | http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000095370 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026829490&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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