Motivation

After conducting proteome wet lab experiments, it may be noticed that the gathered data and information is somehow cluttered and distributed across several places: Details of the experimental setup are recorded in a laboratory book, mass spectrometry datasets are stored in some folder on a local hard disk, and lists of identified peptides and proteins are saved someplace else. To summarize, the relevant data belonging to one experiment are often not organised in a common fashion. In addition, techniques like stable isotope labelling yield quantitative information, implying the necessity of the application of further statistical tests and data mining approaches. We introduce our software QuPE as a repository and algorithmic framework to store and analyse mass spectrometry based quantitative proteome experiments.

Design and Implementation

QuPE is implemented in Java and based on the Spring framework, which provides a centralized, automated configuration and wiring of the individual parts of the system. Our J2EE-compliant application is deployable on any Java application server. Following the three tier architecture model, the system is separated into a data access, bussines logic, and presentation layer. The user interface of the software is implemented using the Echo2 web framework. With the help of an Ajax-based rendering engine, this approach combines the advantages of a web-based solution with those of a desktop application. On the one hand, the application is hosted as a service and provided over the internet. This eliminates the need for installation and simplifies software maintenance and support. On the other hand, the interactivity and responsiveness of a desktop application are retained. We used an in-house developed software tool to build the bridge between our object-oriented data model and a relational database management system. JavaO2DBI utilises Hibernate to create the data access layer of QuPE consisting of the appropriate POJO and DAO classes as well as the corresponding mapping files. Hibernate in combination with the Spring framework provides transaction management and encapsulates database access.

Job and Tools Concept

QuPE provides an easily extensible and configurable job concept. Using XML, jobs consisting of one or more tools can be defined, where input and output types provided by the implementation of a tool determine the data a job is executed with. Due to specific interfaces, tools can announce their need for an interactive configuration. The job and tool concept allows the integration of routines written in R, a programming language, specifically designed for mathematical and statistical purposes.

Features

  • Webrowser-based application using Web 2.0 technologies
  • Extensive capabilities to securely store and organise experiments and complete projects (fine-grained application-based security, GPMS)
  • Import of mass spectrometry data: mzData, mzXML, the Mascot generic format
  • Data model adapted to suggestions made by the HUPO proteomics standards initiative (PSI)
  • Integrated Mascot search engine, import of search results, e.g. as DTASelect-filter
  • Framework supporting analysis of quantitative proteomics data, including:
    • Quantification of stable-isotope labelled samples (15N, 13C, SILAC)
    • Significance tests, analysis of variance
    • Principal component analysis
    • Cluster analysis + validation: Hierarchical cluster analysis, K-means, Neuralgas