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Getting the software

  • Please download version 1 of this software for LINUX here
  • Please download version 1 of this software for Windows here


msBID is a java package designated for label-free LC-MS based comparative proteomic analysis. There are four modules in the package.

  • Detection of peptide features from MS1.
  • Map identified peptides from MS2 to the features detected from MS1.
  • Alignment of peptide features from multiple LC-MS experiments.
  • Normalize the feature intensities due to systematic variations.
  • The output from msBID can be readily analyzed by BAMarray [1] for selecting the differentially expressed peptides.

Environment to run the software

You need

  • JDK1.6 or Jre1.6 [2]
  • R [3]
  • Perl


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