November 30, 2009

QUPE – For Mass Spectrometry based Quantitative Proteomics Research

Filed under: Bioinformatics,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 4:22 am
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Mass spectrometry (MS) is an indispensable technique for the fast analysis of proteins and peptides in complex biological samples. One key problem with the quantitative mass spectrometric analysis of peptides and proteins, however, is the fact that the sensitivity of MS instruments is peptide-dependent, leading to an unclear relationship between the observed peak intensity and the peptide concentration in the sample. Various labeling techniques have been developed to circumvent this problem, but are very expensive and time-consuming. A reliable prediction of peptide-specific sensitivies could provide a peptide-specific correction factor, which would be valuable for label-free absolute quantitation.

QUPE is an itegrated platform for storage and analysis of quantitative proteomics data, implemented in JAVA. Its is a repository and an algorithmic framework to store and analyse mass spectrometry based quantitative proteome experiments.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. Below are listed the various features of QUPE:

– 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 mzData as well as mzXML
– Data model adapted to suggestions made by the HUPO proteomics standards initiative (PSI)
– Mascot integration, Import of DTASelect results
– Framework supporting analysis of quantitative proteomics data, including: – Quantification of stable-isotope labelled samples
– Significance tests, analysis of variance
– Principal component analysis

QUPE is hosted here: