title: Bioinformatics support for high-throughput proteomics.
abstract: In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteome data. The rapid advancement of this technique in combination with other methods used in proteomics results in an increasing number of high-throughput projects. This leads to an increasing amount of data that needs to be archived and analyzed. To cope with the need for automated data conversion, storage, and analysis in the field of proteomics, the open source system ProDB was developed. The system handles data conversion from different mass spectrometer software, automates data analysis, and allows the annotation of MS spectra (e.g. assign gene names, store data on protein modifications). The system is based on an extensible relational database to store the mass spectra together with the experimental setup. It also provides a graphical user interface (GUI) for managing the experimental steps which led to the MS data. Furthermore, it allows the integration of genome and proteome data. Data from an ongoing experiment was used to compare manual and automated analysis. First tests showed that the automation resulted in a significant saving of time. Furthermore, the quality and interpretability of the results was improved in all cases.
authors.affiliation: Center for Genome Research, Bielefeld University, D-33594 Bielefeld, Germany. andreas.wilke@genetik.uni-bielefeld.de
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilke
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Michael
authors.initials: M
authors.lastname: Dondrup
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Andrea T
authors.initials: AT
authors.lastname: Hüser
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kespohl
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Martina
authors.initials: M
authors.lastname: Mahne
authors.forename: Alice
authors.initials: A
authors.lastname: McHardy
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D012371:Robotics / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome