Analysis of large-scale MS data sets: the dramas and the delights

Abstract The biotechnology and pharmaceutical industries are faced with the serious challenge of consolidating the enormous quantities of data that have been generated from high-throughput proteomic applications. The bottleneck of data validation and placement of the information obtained into sound biological context urgently needs to be addressed. Here, we review the issues that arise when analysing large quantities of data generated by liquid chromatography mass spectrometry, offer potential solutions for data management and predict the future direction of large-scale data analysis by mass spectrometry.