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Project Lead - scProteomics; Senior Proteomics Bioinformatician, Physics
Roukes Group | Caltech | Pasadena CA

Ph.D. Analytical Chemistry
2005 – Univ. Arkansas, Fayetteville AR
Advisor: Prof. Charles L. Wilkins

BS Biochemistry & BS Microbiology
2001 – Cal Poly, San Luis Obispo CA

CURRENT PROJECTS

Single Cell Proteomics
The goal is to create arrays of tiny electrostatic traps to measure the mass and charge of single molecule peptides, which are then grouped together for efficient analysis of a single mammalian cell's proteome.

Researcher | Funding: Wellcome Leap Foundation Delta Tissue
Spatial Proteomics
Building and optimizating an electrostatic trap based mass spectrometry system to enable imaging and identification of proteins with single cell spatial resolution.

Co-PI | Funding: National Institute of Health Director's Transformative Research Award Program
2023 press release
NEMS for the direct in situ observation of drug-target interactions
Using Nanoelectromechanical Systems (NEMS) systems to study the mass and shape of proteins and protein-pharmaceutical complexes in order to discover potential new model interactions.

Co-PI | Funding: Amgen Chem-Bio-Engineering Award
TB Proteomics
Characterizing the in-situ proteomes (1000's of proteins) of both the host and pathogen (Mycobacterium tuberculosis) to provide deeper insights into the molecular responses and highlight possible new theraputic avenues.

Collaboration: Prof. Steyn at AHRI

BIOSKETCH

Currently the Project Lead for Single Cell Proteomics and the Senior Proteomics Bioinformatician for the Roukes Group at Caltech (Pasadena, CA) in the Division of Physics, Mathematics and Astronomy.

Dr. Jeff Jones (Ph.D. ’05) has extensive experience in mass spectrometry instrumentation and cellular biology with over twenty years in proteomics and bioinformatics spanning several patents and publications. In early academic work, Dr. Jones developed and published several approaches using matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) studying intact whole cell microorganisms. His work included novel bioinformatic applications for characterizing the lipid and phospholipid cell components of single cellular bacteria and fungi.

In commercial biotech, he focused on developing proteomic applications for clinical biomarker discovery from liquid biopsies. Using mass spectrometry-based methods, identified a multivariate set of markers from routine plasma collections that are predictive for colorectal cancer. These signatures were translated to CLIA/CAP certified laboratory-developed tests (LDTs) that were offered to the public as a screening step prior to colonoscopy.

Dr. Jones is currently focused on redefining bioinformatic methods for accurately identifying peptide and protein sequences, with a particular emphasis on new developments in ultra-sensitive, single-molecule mass spectrometry. His interests include utilizing techniques from signal processing, information theory, and machine learning in proteomics-based biomarker development.

INTERESTS

Infectious Disease
Developing of proteomic-based signatures derived from infectious disease tissue samples aims to bridge gaps in our comprehension of both host and pathogen responses. We anticipate that insights gained from studying proteomic responses to environmental factors will pave the way for innovative treatment and prevention strategies.


Bioinformatics
In addition, Jeff is dedicatedly exploring novel computational techniques for the identification and quantification of proteomic sequences and peptides. His work primarily concentrates on enhancing the accuracy and precision of data extraction in this domain.
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AFFILIATIONS

American Society For Mass Spectrometry Instructor: Learning R for Mass Spectrometry (paid 2-day short course)

University of Arkansas, Fayetteville AR Data Science Program Technical & Curriculum Advisory Workgroup

PUBLICATIONS

  1. Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer.
    A. Mohanty, A. Nam, S. Srivastava, J. Jones, B. Lomenick, S. S. Singhal, L. Guo, H. Cho, A. Li, A. Behal, T. Mirzapoiazova, E. Massarelli, M. Koczywas, L. D. Arvanitis, T. Walser, V. Villaflor, S. Hamilton, I. Mambetsariev, M. Sattler, M. W. Nasser, M. Jain, S. K. Batra, R. Soldi, S. Sharma, M. Fakih, S. K. Mohanty, A. Mainan, X. Wu, Y. Chen, Y. He, T.-F. Chou, S. Roy, J. Orban, P. Kulkarni, R. Salgia,
    Sci Adv. 9, eade3816 (2023).

  2. Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization.
    J. Jones, E. J. MacKrell, T.-Y. Wang, B. Lomenick, M. L. Roukes, T.-F. Chou,
    BMC Bioinformatics. 24, 239 (2023).

  3. Age-related matrix stiffening epigenetically regulates α-Klotho expression and compromises chondrocyte integrity.
    H. Iijima, G. Gilmer, K. Wang, A. C. Bean, Y. He, H. Lin, W.-Y. Tang, D. Lamont, C. Tai, A. Ito, J. J. Jones, C. Evans, F. Ambrosio,
    Nat. Commun. 14, 18 (2023).

  4. MTCH2 is a mitochondrial outer membrane protein insertase.
    A. Guna, T. A. Stevens, A. J. Inglis, J. M. Replogle, T. K. Esantsi, G. Muthukumar, K. C. L. Shaffer, M. L. Wang, A. N. Pogson, J. J. Jones, B. Lomenick, T.-F. Chou, J. S. Weissman, R. M. Voorhees,
    Science. 378, 317–322 (2022).

  5. Surface cysteines could protect the SARS-CoV-2 main protease from oxidative damage.
    R. Ravanfar, Y. Sheng, M. Shahgholi, B. Lomenick, J. Jones, T.-F. Chou, H. B. Gray, J. R. Winkler,
    J. Inorg. Biochem. 234, 111886 (2022).

  6. System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity.
    C.-I. Yang, Z. Zhu, J. J. Jones, B. Lomenick, T.-F. Chou, S.-O. Shan,
    iScience. 25, 104756 (2022).

  7. Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa.
    M. Spero, J. Jones, B. Lomenick, S. Zareian, T. Chou,
    J. Cyst. Fibros. (2021).

  8. 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.
    J. E. Blume, M. Wilhelmsen, R. W. Benz, N. Brünner, I. J. Christensen, L. J. Croner, R. Dillon, T. Hillig, J. J. Jones, L. N. Jørgensen, A. Kao, M. Klaerke, S. Laurberg, M. R. Madsen, K. T. Nielsen, J. Vilandt, B. E. Wilcox, J. You, H. J. Nielsen,
    J Appl Lab Med. 1, 181–193 (2016).

  9. A Plasma-Based Protein Marker Panel for Colorectal Cancer Detection Identified by Multiplex Targeted Mass Spectrometry.
    J. J. Jones, B. E. Wilcox, R. W. Benz, N. Babbar, G. Boragine, T. Burrell, E. B. Christie, L. J. Croner, P. Cun, R. Dillon, S. N. Kairs, A. Kao, R. Preston, S. R. Schreckengaust, H. Skor, W. F. Smith, J. You, W. D. Hillis, D. B. Agus, J. E. Blume,
    Clin. Colorectal Cancer. 15, 186–194.e13 (2016).

  10. Lipid and phospholipid profiling of biological samples using MALDI Fourier transform mass spectrometry.
    S. M. A. B. Batoy, S. Borgmann, K. Flick, J. Griffith, J. J. Jones, V. Saraswathi, A. H. Hasty, P. Kaiser, C. L. Wilkins,
    Lipids. 44, 367–371 (2009).

  11. A targeted proteomic analysis of the ubiquitin-like modifier nedd8 and associated proteins.
    J. Jones, K. Wu, Y. Yang, C. Guerrero, N. Nillegoda, Z.-Q. Pan, L. Huang,
    J. Proteome Res. 7, 1274–1287 (2008).

  12. Characterization of the yeast proteasome interaction network by qtax-based tag-team mass spectrometry and protein interaction network analysis.
    C. Guerrero, T. Milenkovic, N. Przulj, J. J. Jones, P. Kaiser,
    Proc. Natl. Acad. Sci. U. S. A. (2008).

  13. Characterizing the phospholipid profiles in mammalian tissues by MALDI FTMS.
    J. J. Jones, S. Borgmann, C. L. Wilkins, R. M. O’Brien,
    Anal. Chem. 78, 3062–3071 (2006).

  14. Ionic liquid matrix-induced metastable decay of peptides and oligonucleotides and stabilization of phospholipids in MALDI FTMS analyses.
    J. J. Jones, S. M. A. B. Batoy, C. L. Wilkins, R. Liyanage, J. O. Lay Jr,
    J. Am. Soc. Mass Spectrom. 16, 2000–2008 (2005).

  15. Real-time monitoring of recombinant bacterial proteins by mass spectrometry.
    J. J. Jones, C. L. Wilkins, Y. Cai, R. R. Beitle, R. Liyanage, J. O. Lay Jr,
    Biotechnol. Prog. 21, 1754–1758 (2005).

  16. A comprehensive and comparative analysis for MALDI FTMS lipid and phospholipid profiles from biological samples.
    J. J. Jones, S. M. A. B. Batoy, C. L. Wilkins,
    Comput. Biol. Chem. 29, 294–302 (2005).

  17. Real‐time monitoring of recombinant bacterial proteins by mass spectrometry.
    J. J. Jones, C. L. Wilkins, Y. Cai, R. R. Beitle,
    Biotechnology (2005).

  18. Strategies and data analysis techniques for lipid and phospholipid chemistry elucidation by intact cell MALDI-FTMS.
    J. J. Jones, M. J. Stump, R. C. Fleming, J. O. Lay Jr, C. L. Wilkins,
    J. Am. Soc. Mass Spectrom. 15, 1665–1674 (2004).

  19. Use of double-depleted 13C and 15N culture media for analysis of whole cell bacteria by MALDI time-of-flight and Fourier transform mass spectrometry.
    M. J. Stump, J. J. Jones, R. C. Fleming, J. O. Lay Jr, C. L. Wilkins,
    J. Am. Soc. Mass Spectrom. 14, 1306–1314 (2003).

  20. Investigation of MALDI-TOF and FT-MS techniques for analysis of Escherichia coli whole cells.
    J. J. Jones, M. J. Stump, R. C. Fleming, J. O. Lay Jr, C. L. Wilkins,
    Anal. Chem. 75, 1340–1347 (2003).

  21. Matrix-assisted laser desorption mass spectrometry.
    M. J. Stump, R. C. Fleming, W. H. Gong, J. Jones, C. L. Wilkins,
    Appl. Spectrosc. Rev. 3, 275-303 (2002)

PATENTS

  1. Tandem Identification Engine. US Patent App. US11592448B2 (2021)
    J. Jones, W. F. Smith
  2. Automated sample workflow gating and data analysis. US Patent App. US20210063410A1 (2021)
    B. Wilcox, L. Croner, J. Blume, R. Benz
  3. Marker analysis for quality control and disease detection. US Patent App. US20200188907A1 (2020)
    B. Wilcox, R. Benz, J. Jones, J. Blume
  4. Biomarker Database Generation and Use. US Patent App. US20190113520A1 (2019)
    J. Blume, R. Benz, J. Jones, W. F. Smith, P. Cun
  5. Mass Spectrometric Data Analysis Workflow. US Patent App. US20190130994A1 (2019)
    D. Ruderman, J. Jones, R. Benz
  6. Protein biomarker panels for detecting colorectal cancer and advanced adenoma. US Patent App. US20170370937A1 (2017)
    J. Blume, J. Jones, R. Benz, A. Kao, L. Croner
  7. Method for evaluation of presence of or risk of colon tumors. Patent WO2014085826A2 (2014)
    J. Blume, B. Ryan, L. Croner, R. Dillon, A. Randall, J. Jones, H. Skor

SOFTWARE

  1. tidyproteomics: An S3 data object and analytical framework for common quantitative proteomic analyses.

  2. msfastar: A tool for calculating peptide sequence and fragment masses integrating Rust code and libraries to improve computational efficiencies.

  3. mspredictr: An lightweight R package for parsing FASTA protein databases files into an R usable list or data.frame. Utilizing simple regular expressions and Rust code to improve computational efficiencies.

  4. A Pre-computed Probabilistic Molecular Search Engine for Tandem Mass Spectrometry Proteomics. bioRxiv (2020), p. 2020.02.06.937870.