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.

About MassMatrix


mmSearch is a database search software package that was developed in the laboratory of Dr. Michael A. Freitas.  

The software was originally created to assist with the analysis of complex PTMs patterns present on histone proteins.  During development of the software, mass spectrometers capable of rapid acquisition of high mass accuracy  LC-MS/MS data sets were becoming commercially available.  High mass accuracy sensitive probabilistic scoring models were developed to better rank peptide and protein matches. The resulting database search engine provided improvements in sensitivity over other similar tools with comparably low false positives when characterizing complex modified proteins.

The Freitas Lab provided the software to the scientific community, from 2007 until 2014.

Additional capabilities were developed by the lead scientist and co inventor Dr. Hua Xu.  These improvements included hierarchical MSn (n>=3) analysis (useful in phosphopeptide analysis) and the direct searching of disulfide or chemical cross-linked peptides.

In 2018, two new products were announced / released…mmMap for rapid interrogation and validation of peptide maps and mmIntact for automating intact mass data analysis workflows.


The MassMatrix team includes the original inventors of MassMatrix and additional folks with expertise and experience in proteomics, data science, software architecture / development and business building.

Below are some of the key leaders of our team.

Michael Freitas, PhD Founder, Scientific Advisor and Board of Directors

Michael Freitas, PhD

Founder, Scientific Advisor and Board of Directors

Michael (Mike) Freitas PhD is an Associate Professor in the Department of Cancer Biology and Genetics at the Ohio State University.  Dr. Freitas has been working in the field of mass spectrometry and proteomics for nearly 30 years and has spent the last part of his career developing and improving mass spectrometry and bioinformatic methods for his research in the fields of cancer proteomics and chromatin biology. He performed his postdoctoral research at the National High Magnetic Field laboratory and his Ph.D. work at Kansas State University.  His research at OSU has focused on development of high sensitivity microproteomic methods and bioinformatics approaches to enable deep proteomic analysis of clinical specimens. He is a recipient of the Camille and Henry Dreyfus New Faculty Award the American Society for Mass Spectrometry Research Award and was nominated as the Ohio State University Innovator of Year.  Dr. Freitas is the Co-director of the OSU Comprehensive Cancer Center’s Proteomics Shared Resource and advisor to the OSU Campus Chemical Instrument Center’s Mass Spectrometry and Proteomics Facility.

Parminder Kaur, PhD Head of Product Development

Parminder Kaur, PhD

Head of Product Development

Parminder Kaur, PhD has over 12 years of experience developing bioinformatic solutions for various aspects of mass spectrometry experiments.

She obtained her PhD from Boston University and worked for eight years at Case Western Reserve University as a Senior Scientist.  

Parminder’s work focuses on developing machine learning, data analytics and visualization methods for turning large scale biological/chemical data into actionable knowledge. Her work includes developing state-of-art experimental and computational methods to increase protein structure resolution using structural mass spectrometry.

Parminder received the University Gold Medal for ranking first in her BS in Computer Engineering.

Robert O’Malley

Technical Advisor / Sr Architect

Mr. O’Malley has over 25 years experience in IT leadership including design, development, project management, architecture, project management, product management and resource management.  As the Application Manager and Solution Architect for a major Bank, he has been responsible for the development, security upgrades and for Architecture of a broad range of Banking systems. He has been the Practice Lead for several disciplines at a large IT consulting firm.

Hall Johnson

Founder and CEO

Senior executive with over 25 years building high-tech ventures with broad experience in business development, strategic partners & alliances, intrapreneurship, operations, financial planning, and management.  Early career years worked in the scientific and engineering computer group for Hewlett-Packard.  A graduate of Rensselaer Polytechnic Institute in Troy, NY with a BS in Engineering.

Carol Clark

Board of Directors

With more than 35 years of IT and management experience, Carol Clark, co-founder of  internet training software company MindLeaders Inc., served as CEO/Chair of the Board of the company from its formation in 1981 until it was acquired in 2007.  Carol is now an active angel investor with Ohio TechAngels, Golden Seeds, Investors Circle and X Squared Angels where she is a founding member.


Xu H, Freitas MA. A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra. BMC Bioinformatics. 2010 Aug 23;11:436. doi: 10.1186/1471-2105-11-436. PubMed PMID: 20731867; PubMed Central PMCID: PMC2939612.

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. PubMed PMID: 20469931; PubMed Central PMCID: PMC4141472.

Xu H, Freitas MA. Automated diagnosis of LC-MS/MS performance. Bioinformatics. 2009 May 15;25(10):1341-3. doi: 10.1093/bioinformatics/btp155. PubMed PMID: 19304874; PubMed Central PMCID: PMC2677746.

Xu H, Wang L, Sallans L, Freitas MA. A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra. Proteomics. 2009 Apr;9(7):1763-70. doi: 10.1002/pmic.200800282. PubMed PMID: 19288523; PubMed Central PMCID: PMC2775432.

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. PubMed PMID: 19235167; PubMed Central PMCID: PMC2759086.

Zhang L, Xu H, Chen CL, Green-Church KB, Freitas MA, Chen YR. Mass spectrometry profiles superoxide-induced intramolecular disulfide in the FMN-binding subunit of mitochondrial Complex I. J Am Soc Mass Spectrom. 2008 Dec;19(12):1875-86. doi: 10.1016/j.jasms.2008.08.004. PubMed PMID: 18789718; PubMed Central PMCID: PMC2614441.

Xu H, Yang L, Freitas MA. A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time. BMC Bioinformatics. 2008 Aug 19;9:347. doi: 10.1186/1471-2105-9-347. PubMed PMID: 18713471; PubMed Central PMCID: PMC2553802.

Xu H, Freitas MA. Monte carlo simulation-based algorithms for analysis of shotgun proteomic data. J Proteome Res. 2008 Jul;7(7):2605-15. doi: 10.1021/pr800002u. PubMed PMID: 18543962; PubMed Central PMCID: PMC2749500.

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. PubMed PMID: 18072732; PubMed Central PMCID: PMC2749473.

Xu H, Freitas MA. A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data. BMC Bioinformatics. 2007 Apr 20;8:133. PubMed PMID: 17448237; PubMed Central PMCID: PMC1876247.


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?