What is mmSearch

mmSearch is a cutting-edge protein database search software designed to revolutionize the identification of peptides and proteins from tandem mass spectrometry (MS/MS) data.

mmSearch uses a mass accuracy sensitive probabilistic scoring model to match tandem mass spectra with theoretical peptide sequences derived from a comprehensive protein database.

Our innovative approach ensures higher sensitivity and specificity in peptide identification, outperforming traditional search algorithms, especially in datasets with high mass accuracy.

Key Advantages of mmSearch

  • Superior sensitivity and specificity, with a false positive rate of just 2%.
  • Unique capability to identify peptides and proteins, including those with disulfide bonds, without the need for chemical reduction or derivatization.
  • Intuitive probability-based statistical scoring model that accurately assesses the significance of peptide and protein matches.

The Science Behind mmSearch

1. Xu H, Freitas MA. MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data. Proteomics. 2009 Mar;9(6):1548-55. doi: 10.1002/pmic.200700322. PMID: 19235167; PMCID: PMC2759086.

2. Xu H, Hsu PH, Zhang L, Tsai MD, Freitas MA. Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry. J Proteome Res. 2010 Jul 2;9(7):3384-93. doi: 10.1021/pr100369y. PMID: 20469931; PMCID: PMC4141472.

3. Xu H, Zhang L, Freitas MA. Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine. J Proteome Res. 2008 Jan;7(1):138-44. doi:10.1021/pr070363z. Epub 2007 Dec 12. PMID: 18072732; PMCID: PMC2749473.

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