Label-free mass spectrometry-based proteomics for biomarker discovery and validation in tissues and biofluids

Analyzing spectral count data generated in these studies is, however, not straightforward as commonly used techniques for genomics data analysis are not suitable. We have shown that the beta-binomial test performs favourably in comparison with other methods on several datasets in terms of both true detection rate and false positive rate [2]. This test is now routinely used in all our projects for significance analysis and available for down-load (www.oncoproteomics.nl).