Graham Delafield, Ph.D.

228 Duncan Street · San Francisco, CA 94131 · (405) 219-4741 · graham.delafield@gmail.com

I am a developing researcher in the fields of proteomics, bioinformatics, and computer science. Currently I am focused on analytical innovation and computational modeling to aid in the profiling and characterization of the human glycoproteome, performing graduate research at the University of Wisconsin-Madison. Anticipating graduation in March, 2023, I am interested in gaining experience in industrial and governmental settings that allow me to exercise my technical expertise and strong communication and leadership skills.

Employment

Calico

Scientist
  • Developed and implemented platforms for rapid chemoproteomic screening, increasing throughput by >40x.
  • Implemented affinity selection mass spectrometry assays and bioinformatic pipelines to screen rational design peptides against single protein targets of interest.
  • Coordinated with oncology, cell biology, and other internal collaborators to design, iterate, and implement quantitative and discovery-base proteomic assays specific to an area of interest.
July 2023 - Present

Genentech, BAS-O3M

Research Intern
  • Developed custom, full-stack desktop applications to automate and streamline immunogenicity assessment of drug candidates, enabling >99% reduction in analysis time.
  • Engineered custom user interfaces to enable high-throughput analysis of large proteomic datasets, providing a 500-fold increase in data utilization.
  • Constructed analysis pipelines leading to the discovery of constitutive immunogenic signatures that enable reliable quality control in immunopeptidomic workflows.
June 2021 - August 2021

Wisconsin-Alumni Research Foundation

Graduate Ambassador
  • Identified novel scientific intellectual property from with a personal academic network of 300+ graduate students and 50+ principal investigators.
  • Implemented new outreach events, canvas campaigns, and network opportunities aimed towards educating investigators over intellectual propoerty protection, management, and licensing.
  • Augmented the $3 Billion+ WARF portfolio through addition of novel gene edited cell line technologies.
August 2018 - April 2023

Research Experience

Graduate Research Assistant

University of Wisconsin-Madison, PI: Lingjun Li
  • Fabricated and validated PGC-enabled nano separation methodologies that provide up to 40% greater protein, peptide, and glycopeptide identifications.
  • Identified chromatographic conditions most suitable for glycopeptide label-free quantitation, isomeric resolution, and MS-based profiling depth.
  • Utilized DIA-MS to identify 1,245 dysregulated proteins across six diagnostic patterns correlated with early-, mid-, and late-stage prostate cancer.
  • Coupled machine learning with DIA-MS to quantify >9,300 cerebrospinal fluid proteins and elucidate 1,642 putative neurological disease markers across patient cohorts.
  • Engineered and deployed custom web-application based solutions for browsing, filtering, and sharing mass spectrometry data.
  • Performed custom informatic analysis of MALDI-MSI datasets to normalize multiplexed datasets, extract features of interest, and perform machine learning classification.
  • Development of novel online multiplexed analysis of bottom-up, middle-down, and top-down glycoconjugate species utilizing capillary electrophoresis, porous graphitized carbon liquid chromatography, ion mobility spectrometry, and mass spectrometry.
  • Leveraged custom liquid chromatography, capillary electrophoresis, and ion mobility to identify multiple conformations of active biomolecules.
  • Trained and led small research teams of new graduate students and non-expert scientists in the areas of biomolecular analysis, bioinformatic processing, and project development.
  • Maintained, serviced, and assisted in troubleshooting a variety of high-end mass spectrometers from several major vendors (Thermo, Bruker, Agilent).

August 2018 - June 2023

Graduate Research Assistant

University of Oklahoma, PI: Si Wu
  • Developed a three-dimensional method of glycopeptide purification and characterization allowing universal application, unbiased separation, and rapid recognition through the use of HPLC, concurrent fractionation, Mass Spectrometry, and Differential Ion Mobility (FAIMS).
  • Demonstrated correlation between differential ion mobility detection and glycopeptide analytes based on backbone variation, glycan composition, and a combination thereof.
  • Analyzed post translationally modified glycoproteins of control and SLE patient serum immunoglobulin searching for correlations to immune response and glycan features based on our previous glycopeptide purification platform.
August 2016 - May 2018

Honors Undergraduate Research Assistant

University of Oklahoma, PI: Si Wu
  • Conceptualized, designed, and constructed an online affinity capture technique for immunoprecipitation application involving intensive immunoglobulin purification, original apparatus design, and top-down mass spectrometry.
  • · Determined activity of novel biomass degrading enzymes from Great Lakes fungal samples through culturing, secretome extraction, enzymatic assays, concentration determination, electrophoresis, liquid chromatography and mass spectrometry.
August 2015 - May 2016

Education

Doctor of Philosophy

University of Wisconsin-Madison
  • Primary field: Chemistry
  • Division: Analytical Chemistry
  • GPA: 4.0
August 2018 - March 2023

Master of Science

University of Oklahoma
  • Primary field: Chemistry
  • Division: Analytical Chemistry
  • GPA: 3.9
August 2016 - May 2018

Bachelor of Science

University of Oklahoma
  • Major: Biochemistry
  • Minor: Music
  • Honors: Cum Laude
August 2011 - May 2016

Publications

D.G. Delafield, H.N. Miles, T.N. Liu, W.A. Ricke, L. Li. “Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification, Compartment and Process Coverage, and Enables More Reflective Protein-Level Label-Free Quantitation.” Published online October 10, 2023. 10.1021/acs.jproteome.3c00373

D.G. Delafield, H.N. Miles, W.A. Ricke, L. Li (2022). “Higher Temperature Porous Graphitic Carbon Separations Differentially Impact Distinct Glycopeptide Classes.” Journal for the American Society for Mass Spectrometric. Published online November 30, 2022. 10.1021/jasms.2c00249

D.G. Delafield, C. Kaminsky, G. Liu, L. Li. (2022) “High-End Ion Mobility Mass Spectrometry: A Current Review of Analytical Capacity in Omics Applications and Structural Investigations.” Trends in Analytical Chemistry. Published online August 24, 2022. 10.1016/j.trac.2022.116761

D.G. Delafield, H.N. Miles, Y. Liu, W.A. Ricke, L. Li, (2022). "Complementary Proteome and Glycoproteome Access Revealed Through Comparative Analysis of Reversed Phase and Porous Graphitic Carbon Chromatography." Anal. Bioanal. Chem. Published online February 9, 2022. 10.1007/s00216-022-03934-7

D.G. Delafield†, H.N. Miles†, L. Li, (2021). "Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Cancer Biomolecular Analyses in Cancer Research." RSC Chemical Biology. Published online May 15, 2021. 10.1039/D1CB00039J (†Co-first authors)

D.G. Delafield, L. Li, (2020). "Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation." Molecular & Cellular Proteomics. Published online June 23, 2020. 10.1074/mcp.R120.002095

D.G. Delafield, H.N. Miles, W.A. Ricke, L. Li. "Proteomic Fingerprinting of Prostate Cancer Progression Through Library-Free DIA-MS Reveals Systematic and Conserved Pathway Dysregulation." (In Submission) Poster Available

D.G. Delafield†, X. Zhong†, L. Li. "Sample Agnostic Spectral Libraries Enable Quantitation of >9,300 Cerebrospinal Fluid Proteins Across Neurodegenerative Disease Patient Cohorts." (In Submission) († Co-First Authors) Poster Available

D.G. Delafield, H.N. Miles, W.A. Ricke, L. Li. “Six-plex Isobaric Labeling Reveals Glycosylation Dysregulation Across Benign, Metastatic, and Tumorigenic Prostate Cancer.” (In Preparation)

D.G. Delafield, N. Treuttner, H.N. Miles, W.A. Ricke, L. Li. “Capsule Network Retention Time Correction Facilitates Prostatic Tumorigenesis Discovery Through Porous Graphitic Carbon DIA-MS.” (In Preparation)

D.G. Delafield†, X. Zhong†, L. Li. "Enhanced Proteomic Coverage Enabled through BoxCar DIA and Sample Agnostic Spectral Libraries." (In Preparation) († Co-First Authors)

Y. Liu, D.G. Delafield, L. Li "Comprehensive Mass Spectrometric Characterization of Neuropeptidome in Nervous System of the Atlantic Blue Crab, Callinectes sapidus." Analytical Chemistry. (To Be Submitted).

S. Xu, Z. Zhu, D.G. Delafield, M.J. Rigby, G. Lu, L. Puglielli, L. Li, "Spatially and Temporally Probing Distinctive Glycerophospholipid Alteration In Alzheimer's Disease Mouse Brain Via High-Resolution Ion Mobility-Enabled sn-Position-Resolved Lipidomics." In Submission.

S. Xu, Z. Zhu, T.J. Gu, Z. Wang, D.G. Delafield, M.J. Rigby, G. Lu, M. Ma, P. Liu, L. Puglielli, L. Li, "sn-position Resolved Quantification of Aminophospholipids in Alzheimer's Disease Progression by Isotopic N, N-dimethyl leucine Labeling and High-resolution Ion Mobility Mass Spectrometry." In Submission.

M. Ma, Q. Yu, D.G. Delafield, Y. Cui, Z. Li, W. Wu, X. Shi, A. Gutierrez, P.R. Westmark, M. Xu, C.J. Westmark, L. Li (2023) “On-tissue Spatial Proteomics Integrating MALDI-MS Imaging with Shotgun Proteomics Reveals Soy Consumption-induced Biomarkers in a Fragile X Syndrome Mouse Model.” Publishbed online December 18, 2023. 10.1021/acschemneuro.3c00497

Z. Zhu, S. Xu, Z. Wang, D.G. Delafield, M.J. Rigby, G. Lu, T. Gu, P. Liu, M. Ma, L. Puglielli, L. Li, (2023) "Chiral Pair Isobaric Labeling Strategy for Multiplexed Absolute Quantitation (CHRISTMAS) Enabled Quantitatively Probing of Enantiomeric Amino Acids Alteration in Alzheimer's Disease Progression," Analytical Chemistry. Published online November 30, 2023. 10.1021/acs.analchem.3c03847

G. Li, C.K. Jeon, M. Ma, Z. Zheng, Y. Jia, Z. Zheng, D.G. Delafield, G. Lu, E. Romanova, J. Sweedler, B. Ruotolo, L. Li, (2023) "Site-specific Chirality-conferred Structural Compaction Differentially Rescues the Cytotoxicity of Aβ42." Chemical Science. Published online May 8, 2023. 10.1039/D3SC00678F

H. Zhang, D.G. Delafield, L. Li (2023) "Mass spectrometry imaging: the rise of spatially resolved single-cell omics," Nature Methods 20, 327-330. 10.1038/s41592-023-01774-6

Y Shi, Z. Li, B. Wang, Z. Ye, H. Ye, D.G. Delafield, X. Shi, Z. Chen, F. Ma, L. Li (2022) "Enabling Global Analysis of Protein Citrullination and Homocitrullination via Biotin Thiol Tag-Assisted Mass Spectrometry." Analytical Chemistry. Published online December 13, 2022. 10.1021/acs.analchem.2c03844.

N. Wang, N. Wang, S. Yu, H. Zhang, S. Tang, D. Wang, W. Lu, H. Li, D.G. Delafield, Y. Kong, X. Wang, C. Shao, L. Lv, G. Wang, R. Tan, N. Wang, H. Hao, H. Ye (2022) “Cyclic Immonium Ion of Lactyllysine Reveals Widespread Lactylation in the Human Proteome.” Nature Methods. Published online June 28, 2022. 10.1038/s41592-022-01523-1

Z. Li, D. M. Tremmel, F. Ma, Q. Yu, M. Ma, D.G. Delafield, Y. Shi, B. Wang, S. A. Mitchell, A. K. Feeney, V. S. Jain, S. D. Sackett, J. S. Odorico, L. Li (2020) "Proteome-wide and Matrisome-specific Alterations during Human Pancreas Development and Maturation" Nature Communications. Published online February 15, 2021. 10.1038/s41467-021-21261-w

Ruiz, M., Y. Yang, C. A. Lochbaum, D.G. Delafield, J. J. Pignatello, L. Li and J. A. Pedersen (2019). "Peroxymonosulfate Oxidizes Amino Acids in Water without Activation." Environmental Science and Technology. 53, 10845-10854. 10.1021/acs.est.9b01322

Li, G., D.G. Delafield and L. Li (2019). "Improved Structural Elucidation of Peptide Isomers and Their Receptors Using Advanced Ion Mobility-Mass Spectrometry." Trends in Analytical Chemistry. Published online, June 4, 2019, in press. 10.1016/j.trac.2019.05.048

Ma, H., D.G. Delafield, Z. Wang, J. You and S. Wu (2017). "Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP)." Journal of American for Mass Spectrometry. 28, 655-663. 10.1021/jasms.8b05509

Funding

DiLeu-enabled multiplexed quantitation for biomarker discovery and validation in Alzheimer's disease (Renewal)

2R01AG052324-02
  • Funding Awarded: $2,835,460
  • Project Length: 5 years
  • Role: Contributing Author
  • Award Date: May 2023

Creating a region- specific biomolecular atlas of the brain of Alzheimer’s disease

1R01AG078794-01
  • Funding Awarded: $3,780,730
  • Project Length: 5 years
  • Role: Contributing Author
  • Award Date: September 2022

Acquisition of a Dual-Source, High-Performance, Ion Mobility, Quadrupole Time-of-Flight Mass Spectrometry System for Biomedical Research at UW-Madison

1S10OD028473-01A1
  • Funding Awarded: $1,275,704
  • Project Length: 1 year, direct
  • Role: Primary Author
  • Award Date: May 2021

Skills

Proteomics Research
  • High-Throughput Mass Spectrometry
  • Instrumentation: Thermo Elite, Q-Exactive Series | Agilent 6560 IM-QTOF | Bruker timsTOF Pro | Waters Synapt G2
  • Multi-tier Protein Analysis
  • Bottom-up | middle-down | top-down
  • Protein & peptide identification
  • Post-Translational Modification Analysis
  • Glycan & glycopeptide identification
  • Phosphopeptide identification and localization
  • Quantitative Proteomics
  • Isobaric labeling relative quantitation
  • Data-dependent & data-independent acquisition label free quantitation
  • Isotopic incorporation & spike-in absolute quantitation
  • Reaction monitoring relative quantitation
  • High Pressure Liquid Chromatography
  • Nano & Standard Flow | Reversed-phase | Porous graphitic carbon | Ion-Exchange | Size Exclusion
  • Capillary Electrophoresis
  • Custom Bioinformatics and Programming
Programming Languages & Tools
  • C Language

Awards & Certificates

  • Gary Parr Memorial Award for Outstanding Bioanalytical Graduate Research (2023)
  • Luminex Summer Fellowship, Department of Chemistry (2022)
  • Department of Chemistry Research Travel Award (2022)
  • Harold Hay Fellowship, Department of Chemistry (2022)
  • Student Research Travel Award (2019)
  • Honored Instructor Awward (2018)
  • ASMS Travel Grant (2018, 2019)
  • Head Teaching Assistant (2017)
  • Certifcate of Distinction in Teaching (2017, 2018)
  • College of Arts & Sciences Travel Grant (2017)
  • Scott Liang Outstanding Undergraduate Research Award (2016)
  • J. Lee Burke Outstanding Student Achievement Award (2016)
  • Outstanding Senior Man Award (2016)