Data manipulation and modeling with R, Python and Java. Cloud compute servers and data center engineering.


Over 20 years industry experience in LCMS and biomarker discovery. Advanced degrees in Analytical Chemistry and Informatics.


Multiple peer reviewed publications on LCMS and proteomics. Patents in clinical biomarkers.

Jeff Jones Ph.D. Founder

Jeff founded SoCal Bioinformatics Inc. to provide consulting services for proteomic data mining and biomarker discovery. He has been successful in experiment planning, development of data reduction pipeline, and data mining large plasma based LCMS datasets for candidate markers. Previously, he was a major contributor to research and development which culminated in the launch of a colorectal cancer diagnostic CLIA LDT. He has been member of the American Society for Mass Spectrometry since 1996 and currently serves on the International Advisory Board for the The Alliance for Safe Biologic Medicines


  1. A plasma-based protein marker panel for colorectal cancer detection identified by multiplex targeted mass spectrometry J Jones, BE Wilcox, RW Benz, N Babbar, G Boragine, T Burrell, Clinical colorectal cancer 15 (2), 186-194. e13 2016

  2. Discovery and Validation of Plasma-Protein Biomarker Panels for the Detection of Colorectal Cancer and Advanced Adenoma in a Danish Collection of Samples from Patients Referred for Diagnostic Colonoscopy JE Blume, M Wilhelmsen, RW Benz, N Brunner, IJ Christensen, LJ Croner, J Jones, The Journal of Applied Laboratory Medicine: An AACC Publication, jalm-2016

  3. The Discovery and Validation of Blood Plasma Protein-Based Classifier Panels for Colorectal Cancer and Advanced Adenoma using a Combined Mass Spectrometry-and ELISA-based Workflow in Studies Including 1,605 Patient Samples BE Wilcox, RW Benz, LJ Croner, R Dillon, JJ Jones, A Kao, J You, Abstract Accepted for Oral Presentation May 24, 2016 at Digestive Disease Week 2016

  4. A targeted proteomic analysis of the ubiquitin-like modifier nedd8 and associated proteins J Jones, K Wu, Y Yang, C Guerrero, N Nillegoda, ZQ Pan, L Huang Journal of proteome research 7 (3), 1274 2008

  5. Characterizing the phospholipid profiles in mammalian tissues by MALDI FTMS J Jones, S Borgmann, CL Wilkins, RM O'Brien Analytical chemistry 78 (9), 3062-3071 2006

  6. MALDI-FTMS of Whole-Cell bacteria J Jones, MJ Stump, CL Wilkins Identification of Microorganisms by Mass Spectrometry 169, 279 2005

  7. Ionic liquid matrix-induced metastable decay of peptides and oligonucleotides and stabilization of phospholipids in MALDI FTMS analyses J Jones, SMAB Batoy, CL Wilkins, R Liyanage, JO Lay Journal of the American Society for Mass Spectrometry 16 (12), 2000-2008 2005

  8. A comprehensive and comparative analysis for MALDI FTMS lipid and phospholipid profiles from biological samples J Jones, SMAB Batoy, CL Wilkins Computational biology and chemistry 29 (4), 294-302 2005

  9. Strategies and data analysis techniques for lipid and phospholipid chemistry elucidation by intact cell MALDI-FTMS J Jones, MJ Stump, RC Fleming, JO Lay Jr, CL Wilkins Journal of the American Society for Mass Spectrometry 15 (11), 1665-1674 2004

  10. Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach RW Benz, F Castro-Romàn, DJ Tobias, SH White Biophysical Journal, 88, 805-817, 2005.

  11. Investigation of MALDI-TOF and FT-MS Techniques for Analysis of Escherichia coli Whole Cells J Jones, MJ Stump, RC Fleming, JO Lay, CL Wilkins Analytical chemistry 75 (6), 1340-1347 2003

  12. Protein biomarker panels for detecting colorectal cancer and advanced adenoma J Blume, J Jones, R Benz, A Kao, L Croner, R Dillon, J You, B Wilcox,
    US Patent App. 15/094,767

  13. Method for evaluation of presence of or risk of colon tumors J Blume, R Benz, L Croner, R Dillon, AZ Randall, J Jones, H Skor,
    US Patent App. 14/526,181
    US Patent App. 14/526,282
    US Patent App. 14/094,594