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Getting the software

Please download this software from the Sashimi Site.


The SpecArray software suite generates a peptide vs. sample expression array from a set of LC-MS data, obtained by analyzing peptide samples under identical LC-MS settings. The SpecArray software suite include several closely integrated programs:

  • Pep3D: Generate 2D gel type images from LC-MS data (Note: Pep3D is also integrated into the TPP)
  • mzxml2dat: Denoise and centroidize LC-MS data in mzXML file format and convert them into binary file format
  • PepList: Extract a list of peptide features from LC-MS data
  • PepMatch: Align peptide features of different samples
  • PepArray: Generate a peptide vs. sample expression array


X-J Li, E.C. Yi, C.J. Kemp, H. Zhang, and R. Aebersold, Molecular & Cellular Proteomics 4: 1328-1340, 2005.

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