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(Please note, msBID evolved from the older MSAnalyzer project.)

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


After you download the tar ball, please look at the README.txt inside the package carefully for setting up the program and commands to run the program and some example input and output were also included in the package.


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