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BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information from multiple technical replicates of the same sample to identify peaks detected consistently in given sample. BigRedBin then places peaks into bins of a given size to allow the data to be analysed using their preferred software e.g. PCA.

Getting and Using BigRedBin

BigRedBin needs to be downloaded and installed on a UNIX/Linux based computer running the Apache web server. This isn't as complicated as it may seem and I encourage you to try following the installation instructions and let me know if you run into any major problems.

Problems with Mass Spectrometry Data

Data obtained from mass spectrometry machines is problematic for several reasons:

  • There are a large number of noisy peaks present in all runs
  • Real peaks shift in m/z values between different samples
  • Real peaks have different intensity values between technical replicates

BigRedBin to the Rescue

BigRedBin makes attempts to address these issues by:

  • Reduce the amount of noise to uncover peaks with small intensities
  • Through the use of internal lockmass peaks, align peaks in different samples so they are comparable in further analyses
  • Identifying "real" peaks by assessing the distribution of m/z and intensity values for peaks in technical replicates
  • Binning peaks such that the same compound in different sample falls into the same bin - making subsequent analyses easier