mmSearch – MassMatrix’s LC-MS/MS Database Search Engine

“MassMatrix [mmSearch] offers unique core functionality…low false discovery rate and high performance with modern high resolution instruments…that makes it an ideal analytical engine for protein characterization workflows.”
Director, Protein Analytics, Top 10 Pharmaceutical Company

 mmSearch Unique Features

  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 (see below) 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: mmSearch 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.

mmSearch 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

XMapper Heat Map of Crosslink Peptides


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?