Responding to Data Analysis and Evaluation Challenges in Mass Spectrometry-Based Methods for High-Throughput Proteomics

Technology implemented in proteomics studies has recently been scrutinized for its effectiveness. As reported in a recent Nature Methods paper, questions have been raised about sample preparation, sample handling, data analysis, and data evaluation with the latter two being highlighted most. This article presents a new data management method that is specifically designed to handle the large amounts of data produced in proteomics studies. Experimental methods and data are presented from a recent study conducting proteomics profiling of Schizosaccharomyces pombe (S. pombe) (published in Methods) to demonstrate the effectiveness of the data management solution. The results demonstrate enhanced data search speeds as well as effective data analysis.