Exploring science is typically characterized by a lot of puzzles, frustrations or even failures. This weblog is mainly intended to record my working, thinking and knowledge acquisitions. I expect that some reflection would refresh my mind from time to time, and motivate me to move further, and hopefully give me a better view about even changing the landscape of bioinformatics.
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Thursday, February 3, 2011
mzServer: Web-based Programmatic Access for Mass Spectrometry Data Analysis
Continued progress towards systematic generation of large-scale and comprehensive proteomics data in the context of biomedical research will create project-level data sets of unprecedented size and ultimately overwhelm current practices for results validation that are based on distribution of native or surrogate mass spectrometry files. Moreover, the majority of proteomics studies leverage discovery-mode MS/MS analyses, rendering associated data-reduction efforts incomplete at best, and essentially ensuring future demand for re-analysis of data as new biological and technical information become available. Based on these observations, we propose to move beyond the sharing of interpreted spectra, or even the distribution of data at the individual file or project level, to a system much like that used in high-energy physics and astronomy, whereby raw data are made programmatically accessible at the site of acquisition. Towards this end we have developed a web-based server (mzServer), which exposes our common API (mzAPI) through very intuitive (RESTful) URLs and provides remote data access and analysis capabilities to the research community. Our prototype mzServer provides a model for lab-based and community-wide data access and analysis. A live instance of the mzServer can be accessed directly at: http://blais.dfci.harvard.edu/mzServer/ The data associated with this manuscript may be downloaded from the ProteomeCommons.org Tranche network using the following hash: 6g+QpUvlpxc6PM/M9t/49h0PMLwA7dTCgpwyUqfciXEyZpLun7QzPz8E+LDDJfZzBf1lGKe7t1OkXbmomzTEy70Av/kAAAAAAAAYtg== In addition, the data are available here: http://ec2-50-16-31-157.compute-1.amazonaws.com/