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Sven Nahnsen, Alfred Nordheim, and Oliver Kohlbacher (2009)

A geometric matching approach improves throughput and accurary in DIGE based proteomics

In: Proceedings of the sixth International Workshop on Computational Systems Biology (WCSB 2009), pp. 123-126, Tampere International Center for Signal Processing, WCSB 2009. #48.

Two-Dimensional Difference In Gel Electrophoresis (2DDIGE) is a powerful tool in quantitative proteomics. However, the matching of replication experiments remains very labor-intensive and hard to automate. We present a novel geometric approach based on landmarks - unambiguously identified proteins - for inter-gel matching where we transform the pairwise gel matching problem into a maximum weight matching problem. We then apply network flow algorithms to solve this problem optimally. The approach automatically selects proteins that are reproducibly regulated across several experiments without manual intervention. In a case study our method outperformed common commercially available tools. Source code is available upon request from the authors.