OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics

Simulation biologischer Systeme, WSI/ZBIT,Eberhard-Karls-Universitat Tu¨bingen, Sand 14, 72076 T¨ubingen, Germany,oliver.kohlbacher@uni-tuebingen.deAbstract. One of the main goals of proteomics research is the discov-ery of novel diagnostic markers and therapeutic targets. Currently, massspectrometry is the main platform for analyzing complex protein sam-ples. Lately, HPLC/MS-based approaches havegained considerable inter-est due to their larger potential for full automation when compared togel-based techniques. Particularly, multi-dimensional HPLC-MS meth-ods have a great potential as a platform for differential quantification ofproteins in complex mixtures. However, computational methods to ana-lyze these automated analyses at a large scale are yet to be developed.The development of these methods should encompass new methods fordata reduction, data interpretation, data management and visualization.We propose an algorithmic framework for a fully automated differen-tial analysis of HPLC/MS samples, which goes beyond the currentlyestablished pairwise comparison of samples towards a statistically soundanalysis of larger sample numbers. In this short paper we outline theframework in its current state and lay out future plans.Keywords. computational proteomics, quantitativeanalysis, C++,soft-ware framework, mass spectrometry

[1]  Patrick G. A. Pedrioli,et al.  A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. , 2004, Analytical chemistry.

[2]  Knut Reinert,et al.  High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques , 2005, Pacific Symposium on Biocomputing.

[3]  Rolf Apweiler,et al.  Common interchange standards for proteomics data: Public availability of tools and schema. Report on the Proteomic Standards Initiative Workshop, 2nd Annual HUPO Congress, Montreal, Canada, 8–11th October 2003 , 2004, Proteomics.

[4]  Knut Reinert,et al.  Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. , 2006, Journal of proteome research.

[5]  R. Aebersold,et al.  Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. , 2003, Analytical chemistry.

[6]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[7]  J. Yates,et al.  Shotgun Proteomics and Biomarker Discovery , 2002, Disease markers.

[8]  R. Aebersold,et al.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry , 2001, Nature Biotechnology.

[9]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[10]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[11]  Knut Reinert,et al.  Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples , 2005, CompLife.