Inhalt

•  
  Introduction
•  
   Motivation
•  
   Aims and objectives
•  
   Structure of this work
•  
   Related publications
•  
  From genomics to proteomics
•  
   Protein synthesis – from genes to proteins
•  
   Protein turnover: degradation and synthesis
•  
   Mass spectrometry-based proteomics
•  
   A historical view on mass spectrometry
•  
   Mass spectrometry for the identification of proteins
•  
  Fundamentals of mass spectrometry data processing
•  
   Peak detection – profile vs. centroid data
•  
   Resolution and accuracy
•  
   Purpose and function of mass spectrometry in proteomics
•  
   Two-dimensional electrophoresis in combination with matrix-assisted laser desorption/ionization and time-of-flight mass spectrometry
•  
   Protein separation – two-dimensional electrophoresis
•  
   Ionization – matrix-assisted laser desorption/ionization
•  
   Analyzer – time-of-flight
•  
   Protein identification – peptide mass fingerprinting
•  
  Liquid chromatography in combination with electrospray ionization
•  
   Protein separation – liquid chromatography
•  
   Advanced separation – multidimensional protein identification technology
•  
   Ionization – electrospray
•  
   Analyzer – quadrupole
•  
   Analyzer – ion trap
•  
   Fragmentation – collision-induced dissociation
•  
   Protein identification – MS/MS ion search
•  
   Protein quantification
•  
   Stable isotope labeling
•  
   Metabolic labeling using stable isotopes
•  
   Metabolic labeling using amino acids: SILAC
•  
   Chemical tags: ICAT, ICPL, iTRAQ
•  
   Absolute quantification: AQUA
•  
   Special application: analysis of protein turnover
•  
   Two-dimensional electrophoresis
•  
   Label-free approaches
•  
   Shedding light on the importance of mass spectrometry for proteome research
•  
  State of the art in proteomics data analysis
•  
   Data standards in proteomics
•  
   Human Proteome Organization: PSI, MIAPE and MIBBI
•  
   Institute for systems biology
•  
  Data standards for mass spectra
•  
   mzXML
•  
   mzData and mzML
•  
   Ontologies and controlled vocabularies
•  
   Software for protein identification
•  
   Mascot™
•  
   Sequest™
•  
   Evaluation of search results
•  
   Quantitative analysis of isotopically labeled data
•  
   ASAPRatio
•  
   RelEx
•  
   ProRata
•  
   Census
•  
   QN
•  
   QuantiSpec
•  
   MaxQuant
•  
   Data storage and management solutions
•  
  Laboratory information management systems
•  
   ProDB
•  
   CPAS
•  
   MASPECTRAS
•  
   ProSE/Proteios
•  
   Trans-Proteomics pipeline
•  
   Data repositories
•  
   PRIDE – proteomics identifications database
•  
   PeptideAtlas
•  
   Identification, quantification, ... and next?
•  
   Spreadsheet-alike analysis of proteomics data: DAnTE, StatQuant, GProX
•  
   Integration of functional annotation data: PIPE
•  
   An inventory of the current state of proteomics software tools and applications
•  
   Requirements: computational support for quantitative proteome experiments
•  
   Use case analysis
•  
   Data organization and structuring
•  
   Protein identification
•  
   Protein quantification
•  
   Statistical analysis, data mining, and visualization
•  
  Methods for the statistical analysis of quantitative proteomics data
•  
   Detection of differentially regulated proteins
•  
   Up- or down- regulation of an individual protein
•  
   Comparison of multiple-condition proteome data
•  
   Error in hypothesis testing
•  
   Identification of co-regulated proteins
•  
   Measures of similarity between two proteins
•  
   Formal definition of cluster analysis
•  
   Hierarchical cluster analysis
•  
   Single- and Complete-linkage
•  
   Average-linkage
•  
   Centroid-linkage
•  
   Ward-linkage
•  
  Partitioning cluster analysis
•  
   K-means
•  
   Neural-Gas
•  
   Cluster validation
•  
   Calinski-Harabasz
•  
   Index-I
•  
   Davies-Bouldin
•  
   Krzanowski-Lai
•  
   Figure of Merit
•  
   A measure to determine the congruence between clustering results
•  
   Data analysis: more questions than answers
•  
  Implementation of the QuPE system
•  
   System design
•  
  System architecture
•  
   Data access layer
•  
   Object model for mass spectra
•  
   Object model for protein and peptide identifications
•  
   Object model for analysis results
•  
   Object model to structure experiments and related data
•  
  Logic layer
•  
   Job and tools framework
•  
  Presentation layer
•  
   Graphical user interface
•  
   Design and control of the graphical user interface using a model-view-controller pattern
•  
   Algorithms for the analysis of quantitative proteomics data
•  
   Sum quantification approach – simple but powerful
•  
   Utilizing the time
•  
   Pulse chase quantification
•  
  Summary of features of the QuPE system
•  
   Data management: projects and experiments
•  
   Protein identification: peptide mass fingerprinting and MS/MS ion search
•  
   Protein quantification
•  
   Statistical analysis, data mining, and visualization
•  
  Performance and accuracy of protein quantification
•  
   Protein mixtures – fully labeled vs. unlabeled
•  
   Reference measurements
•  
   Accuracy of the sum quantification
•  
   Accuracy of the elution peak quantification
•  
   Protein mixtures – unlabeled vs. partially labeled
•  
   Accuracy of the pulse chase quantification
•  
   Protein quantification: final considerations
•  
  A workflow for the analysis of quantitative proteomics data
•  
  Case studies
•  
   Experimental setups
•  
   Protein identification
•  
   Protein quantification
•  
   Detection of differentially regulated proteins
•  
   Identification of co-regulated proteins
•  
   Similarities and differences between cluster algorithms
•  
   Computational and biological significance of clustering results
•  
   Proposal of a workflow for the analysis of quantitative proteomics experiments
•  
  Discussion and Conclusion
•  
   The rich internet application QuPE
•  
   Algorithms for protein quantification
•  
   A workflow for the analysis of quantitative proteomics experiments
•  
   Further developments of the QuPE system
•  
   Final remarks
•  
   Appendix
•  
  Implementation of the QuPE system – additional information
•  
   Isotopic Distribution Calculation
•  
  Performance and accuracy of protein quantification – additional information
•  
  Reference measurements – additional information
•  
   Configuration of the tool ProRata
•  
   Configuration of the tool Census
•  
  Evaluation of implemented quantification algorithms – additional information
•  
   Accuracy of the elution peak quantification – parameter evaluation
•  
   Analysis of quantitative proteomics data – additional information
•  
   Glossary
•  
   Bibliography