MassMatrix Search Engine 2018-04-18T17:21:45+00:00


MassMatrix delivers protein bioinformatic solutions that accelerate advances in science to improve people’s lives. With an innovative approach tailored to meet the unique needs of research organizations and pharmaceutical companies, MassMatrix combines advanced algorithms and a user-focused experience to help scientists gain accurate insights from biological data, resulting in fewer false discoveries and increased productivity.

 Features & Unique Aspects

  1. Mass Accuracy Sensitive Probabilistic Scoring Model: Pure statistical models that are sensitive to high mass accuracy. The mass accuracy sensitive models  provide better discrimination between true and false positives for high mass accuracy LC-MS/MS data collected on modern mass spectrometers.
  2. Automated Disulfide Linkage and Chemical Cross-Linkage Searching: Proteins and peptides with disulfide bonds or chemical cross linking can be directly identified without chemical reduction and/or other derivatization.  Our unique XMapper algorithm scores disulfide bonds and chemical crosslinks by aggregating peptide matches. XMapper provides a quick and reliable way to compare disulfide bonds or crosslink identifications within and across searches.
  3. PTM search: MassMatrix provides high sensitivity and specificity for the identification and site localization of post-translational modifications on proteins and peptides.
  4. Hierarchical MSn (n>2) spectral data base searching for peptide: Hierarchical search improves confidence of peptides with neutral losses, such as phosphopeptides. This algorithm can be applied to peptides that are difficult to identify by MS2 only, e.g. peptides with multiple phosphorylations.

Minimum System Requirements

  • 64-bit computer running Windows 7 or higher
  • 2 processors (additional processors needed for more instances)
  • 8 GB of RAM;  >8 GB recommended
  • 200 GB of disk space


Interested in improving your peptide mapping or proteomic workflow?
Need to characterize complex post translational modifications patterns?
Want to do a better job identifying and quantifying disulphide bonds or cross links?