• Significant contributions to securing competitive grant awards of over $3M in direct costs.
• Responsible for hiring and leading a team of bioinformatics software developers.
• Interfaced with users, gathered requirements, developed mockups/plans, wrote code.
• Authored three and co-authored four peer-reviewed articles on analysis of mass spectrometry data with a focus on developing algorithms for biomarker discovery by LC-MS. In particular: developed and published (1, 2) an algorithm based on linear regression for interpreting ¹⁸O labeled differential proteomics data.
• Developed open source, object-oriented library (libmprc) in C++ & R for analyzing terabyte-scale high-resolution mass spectrometry datasets. Includes FT-ICR transient processing, peak picking, isotope cluster detection (THRASH, ¹⁸O labeling), artifact removal, statistics, etc. Used in support of research on Pancreatic & Ovarian Cancer, Diabetes, others.
• Managed/developed protein identification workflow system using Java Servlets, Google Web Toolkit, Java Messaging Service, Groovy scripting language, Hibernate/Oracle that combines statistical algorithms (Peptide/Protein Prophet) with a facile Web 2.0 interface, custom visualizations and DRMAA/Grid Engine parallel queuing.
• Developed 3D OpenGL LC-MS chromatogram visualization tool used for quality control.

• Led Sequel’s informatics efforts and developed strategy. Managed software developers.
• Designed, built and deployed a complex, client-server software system for analyzing and visualizing mass spectrometry data resulting from Sequel's proprietary genotyping process in 18 months with two people. (~100,000 lines of code in C++, Java, and Perl)
• Designed an easy to use, fast, threaded user interface for viewing spectra and implemented in Java Swing and CORBA. Sophisticated caching architecture; novel visualization algorithms.
• Implemented templated object persistence/query interface using Objectivity object database.
• Performed competitive review of genotyping products and contributed to a technical development plan; both were used in securing second round financing.

• Twice awarded support from the Merck foundation for original research.
• Developed a modular C++ version of an existing lisp tool for determining protein homology using sparse Nuclear Magnetic Resonance (NMR) data.

• Led a team of volunteer peer educators and leaders to develop and run a series of Fraternity new member education programs that set a precedent for effectiveness and participation.

• Developed, in perl, a Scribe to Standard Generalized Markup Language (SGML) translation system that eliminated cumbersome and costly manual translation of documentation sets.

• Developed a set of web-based tools in perl that discovered hundreds of previously unknown errors in online documentation for the Performer product.
• A full time staff member was trained and tasked to continue my work.

A method for automatically interpreting mass spectra of ¹⁸O labeled isotopic clusters. Mason CJ, Therneau TM, Eckel-Passow JE, Johnson KL, Oberg AL, Olson JE, Nair KS, Muddiman DC, and Bergen HR III. Molecular and Cellular Proteomics 2007, 6:305-318.

Regression analysis for comparing protein samples with ¹⁶O/¹⁸O stable-isotope labeled mass spectrometry. Eckel-Passow JE, Oberg AL, Therneau TM, Mason CJ, Mahoney DW, Johnson KL, Olson JE and Bergen HR III. Bioinformatics 2006 22(22):2739-2745.

Reproducibility of Retention Time using a Splitless nanoLC Coupled to an ESI-FTICR Mass Spectrometer. Mason CJ, Johnson KL, Muddiman DC. Journal of Biomolecular Techniques 2005 16:414-422.

Analysis of the Low Molecular Weight Fraction of Serum by LC-DualESI-FT-ICR Mass Spectrometry: Precision of Retention Time, Mass, and Amplitude. Johnson KL, Mason CJ, Muddiman DC, Eckel JE. Analytical Chemistry 2004 Sep 1;76(17):5097-103. (co-first author)

Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry. Hawkridge AM, Nepomuceno AI, Lovik SL, Mason CJ, Muddiman DC. Rapid Commununications in Mass Spectrometry 2005;19(7):915-8.

Utility of Accurate Monoisotopic Mass Measurements to Confidently Identify Lambda Exonuclease Generated Single-Stranded Amplicons Containing 7-Deaza Analogs by Electrospray Ionization FT-ICR Mass Spectrometry. J.L. Frahm, C.J. Mason, and D.C. Muddiman. International Journal of Mass Spectrometry 2004, 234, 79-87.

Detection of genetic variants of transthyretin by liquid chromatography-dual electrospray ionization fourier-transform ion-cyclotron-resonance mass spectrometry. Nepomuceno AI, Mason CJ, Muddiman DC, Bergen HR 3rd, Zeldenrust SR. Clinical Chemistry 2004 Sep;50(9):1535-43.

Detection of cystic fibrosis mutations by peptide mass signature genotyping. Malehorn DE, Telmer CA, McEwen SB, An J, Kinsey AD, Retchless AC, Mason C, Vieta WM, Jarvik JW. Clinical Chemistry 2003 Aug;49(8):1318-30.

Introduction to Mass Spectrometry Based Proteomics. Christopher J Mason. Invited Presentation. Winona College Bioinformatics program. April 2007.

Introduction to Mass Spectrometry Based Proteomics. Christopher J Mason. Invited Presentation. Eastern North American Region/International Biometric Society. March 2007.

RAAMS: An algorithm for automatically interpreting mass spectra of ¹⁸O labeled isotopic clusters. Mason CJ; Eckel-Passow JE; Johnson KL; Therneau TM; Oberg AL; Muddiman DC; Bergen, HR III. Poster. American Society for Mass Spectrometry, 2006.

Informatics Techniques for Biomarker Discovery in Serum using LC-FT-ICR Mass Spectrometry. Mason CJ; Hawkridge AM; Muddiman DC; Johnson KL; Oberg AL. Oral Presentation. American Society for Mass Spectrometry, 2004.