EXPERTISE

Dr. Monroe’s research involves development of algorithms and software for custom and automated analysis of proteomics and bioinformatics data, including managing and summarizing the large volumes of data generated. His areas of expertise include microcolumn liquid chromatography, LC-MS/MS of peptides and proteins using Q-TOF mass spectrometry, and analytical instrumentation design and automation. Dr. Monroe has over 15 years of programming experience, specializing in software design using Visual Basic .NET, LabView, and relational databases including Microsoft SQL Server and Microsoft Access.

EDUCATION

University of North Carolina at Chapel Hill

• Ph.D. Analytical Chemistry, 3.76 GPA equivalent, December 2002
• Doctoral Thesis Advisor: Dr. James W. Jorgenson

University of Wyoming, Laramie, WY

• ACS Certified B.S. in Chemistry, With Honors, 4.0 GPA, May 1997

Laramie Senior H.S., Laramie, WY

• Valedictorian, 4.0 GPA, May 1993

PROFESSIONAL EXPERIENCE

Senior Research Scientist, 2003-present
Post doctoral associate, 2002-2003

• Pacific Northwest National Laboratory; Richland, WA
  Dr. Richard D. Smith, advisor
• Wrote custom software for data mining applications.

Undergraduate Chemistry Research Assistant, 1994-1997

• University of Wyoming, Chemistry Department; Laramie, WY
  Dr. Patrick Sullivan, advisor
• Investigated the photochemical effects of halocarbon pollutants on the natural iron cycle of freshwaters.

Office Assistant, 1993-1997

• University of Wyoming, Speech Pathology/Audiology Dept.; Laramie, WY
  Claoma Woodall, supervisor
• Specialized in writing customized computer applications and Access databases, computer maintenance, and computer instruction.

SKILLS

Chemistry Laboratory Research Techniques and Instrumentation

• Mass Spectrometry: LC-ESI-TOF MS and Q-TOF MS/MS
• Microcolumn Liquid Chromatography
• Proteomics
• Instrumentation design, integration, and automation including machining

Computer Skills

• 15 years programming experience
  
  • VB.NET, Visual Basic 6, Visual Basic for Applications, and VB Script
    Examples of Visual Basic 6 applications written:
    • Molecular Weight Calculator to assist scientists in computing molecular weights of compounds, performing mole/mass conversions, and searching for unknown compounds given a molecular weight or percent composition data
    • MassLynx Data Analyzer to assist in searching for clusters of ions in electrospray mass spectra based on mass, charge, and intensity, followed by matching of ions to those expected based on theoretical proteolysis
    • Dart Scorekeeper to keep track of Cricket, 301, and golf games; includes player statistics tracking
    • HTML Photo Gallery Cataloger to automatically create a navigatable photo gallery of all pictures (.Jpg files) in a given directory tree; includes thumbnail creation
    • Basketball Tourney to help organize an NCAA basketball tournament pool; includes html output of statistics for all contestants
    • MakeBat, a command-line program for automating file maintenance
    • Personal Calculator, a user-configurable, simple calculator
    • File Conglomerator, a program to group large numbers of text files into conglomerate files
  • LabView (National Instruments)
    Examples of Labview applications written:
    • Peak Finder program for automated identification of Gaussian shaped peaks and computation of peak capacity in a chromatogram
    • Stripchart Recorder XP (cowritten with Keith Fadgen) for real-time configurable, multi-channel data acquisition
    • Dual Syringe Ultra High Pressure Liquid Chromatography Control program
    • Electrospray Needle Laser Puller Control program
    • Gradient Profile Modelling program
    • Imaging Mass Spectrometer control program
  • SQL Server Administration and Database Architecture
  • • HTML, Active server pages, SQL, Javascript, Microsoft Internet Information Services
    Web sites designed:
    • Univ. of North Carolina Jorgenson Group web site
    • Univ. of Wyoming Speech-Language Pathology and Audiology (Now Division of Communication Disorders)
    • Univ. of Wyoming School of Physical and Health Education
    • Univ. of Wyoming Sullivan Group home page
    • My own pages
  • C and C++, including MS Visual C++/MFC, Perl
  • Wavemetrics Igor Pro
• Microsoft Office power user, including Access database design
  Examples of Access Applications written:
  • Visa Orders database for tracking orders placed using a group purchasing card
  • Database to organize current students in the Univ. of Wyoming SPPA Dept.
  • Database to organize and rank students applying for the UW SPPA Graduate Program
  • Database to track repair/manufacture jobs and current inventory of the UW Glass Shop
• Windows 9x/NT/00/XP / Unix / Macintosh / Internet
• Assembling, Troubleshooting, and Maintaining Systems, including Win 2000/2003 Administration

DOCTORAL THESIS RESEARCH

Instrumentation and Application Development Involving Microcolumn Liquid Chromatography Coupled to Time-of-Flight Mass Spectrometry

• Developed a protocol for isolation and purification of small peptides and hormones in human blood serum and blood plasma using solid phase extraction and size exclusion chromatography.
• Developed a method to separate, digest, and identify the isolated peptides and hormones using microcolumn LC/ESI-MS and LC/ESI-MS/MS in conjunction with custom analysis software.
• Collaborated with Kamlesh Patel to automate operation and data collection from a dual-syringe UHPLC system utilizing laser-induced-fluorescence and ESI-MS detection. Currently interfacing system with Q-TOF MS/MS to obtain high resolution, multi-dimensional separations.
• Completed numerous software design projects including a MassLynx Data Analyzer (VB), Molecular Weight Calculator (VB), Peak Capacity Finder (LabView), Stripchart Recorder-type data acquisition package (LabView), and automated mass spectral data analysis package (Igor Pro).
• Designed and constructed a software controlled, CO₂ laser–based capillary puller for automated, reproducible pulling of electrospray needles.
• Trained various co-workers in the use and maintenance of mass spectrometry systems.

TEACHING EXPERIENCE

• Graduate Level Electronics Lab, 1998; UNC Chemistry Department, Dr. Wightman
• Introductory Chemistry Lab, 1997; UNC Chemistry Department, Dr. Jicha, supervisor
• Undergraduate Chemistry Majors Lab, 1997; UW Chemistry Department, Dr. Harris, supervisor
• Undergraduate Chemistry Lab, 1996; UW Chemistry Department, Dr. Lew Noe, supervisor

AFFILIATIONS & AWARDS

• American Chemical Society Member since 1993
• Francis P. Venable Fellowship, 1997-1998
• Phi Beta Kappa membership, 1997
• American Chemical Society Student Affiliate, President, 1996-1997
• R. Owen Asplund Award for Outstanding Academic Performance, 1996
• Summer EPSCoR Fellowship Recipient, 1995 & 1996
• Barry M. Goldwater Scholarship Recipient, 1995-1997
• College of A&S Independent Study Fellowship, 1994
• Outstanding Freshman Chemistry Major Award, 1994
• UW Western Thunder Marching Band Member, 1993-1996
• Dean's or Provost's lists for 4.0 GPA, 1993-1997
• UW Trustee's Academic Scholarship Recipient (tuition, room, and board), 1993-1997

PUBLICATIONS

• "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements," J.M. Jacobs, M.E. Monroe, W. Qian, Y. Shen, G.A. Anderson, and R.D. Smith, Intl. J. of Mass Spectrometry, 240 (3), 195-212 (2004).
• "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome", S.M. Varnum, D.N. Streblow, M.E. Monroe, P. Smith, K.J. Auberry, L. Pasa-Tolic, D. Wang, D.G Camp, K. Rodland, S. Wiley, W. Britt, T. Shenk, R.D. Smith, and J.A. Nelson. Journal of Virology, 78 (20), 10960-10966 (2004).
• "Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations.", K.K. Anderson, M.E. Monroe, and D.S. Daly. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04), ed. Faramarz Valafar and Homayoun Valafar, pp. 151-156 (2004).
• "Integrative analysis of the mitochondrial proteome in yeast," H. Prokisch, C. Scharfe, D.G. Camp II, W. Xiao, L. David, C. Andreoli, M.E. Monroe, R.J. Moore, M.A. Gritsenko, C. Kozany, K.K. Hixson, H.M. Mottaz, H. Zischka, M. Ueffing, Z.S. Herman, R.W. Davis, T. Meitinger, P.J. Oefner, R.D. Smith, and L.M. Steinmetz, PLoS Biology, 2 (6), 795-804 (2004).
• "Multidimensional proteome analysis of human mammary epithelial cells," J.M. Jacobs, H.M. Mottaz, L. Yu, D.J. Anderson, R. J. Moore, W. U. Chen, K.J. Auberry, E.F. Strittmatter, M.E. Monroe, B.D. Thrall, D.G. Camp II, and R.D. Smith, J. Proteome Research, 3 (1), 68-75 (2004).
• "The AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis," M.S. Lipton, M.F. Romine, M.E. Monroe, D.A. Elias, L. Pasa-Tolic, G.A. Anderson, D.J. Anderson, J.K. Fredrickson, K.K. Hixson, C.D. Masselon, H.M. Mottaz, N. Tolic, and R.D. Smith. Book chapter in Microbial Proteomics. (2004).
• "The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes," A.D. Norbeck, M.E. Monroe, J.N. Adkins, K.K. Anderson, D.S. Daly, R.D. Smith. J. Am. Soc. Mass Spectrom., 16 (8), 1239-1249 (2005).
• "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using mass spectrometry," W. Qian, J. M. Jacobs, D.G. Camp II, M.E. Monroe, R.J. Moore, M.A. Gritsenko, S.E. Calvano, S.F. Lowry, W. Xiao, L.L. Moldawer, R.W. Davis, R.G. Tompkins, and R.D. Smith, Proteomics, in press (2005).
• "Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome," T. Liu, W. Qian, U. Chen, J.M. Jacobs, R.J. Moore, D.J. Anderson, M.A. Gritsenko, M.E. Monroe, B.D. Thrall, D.G. Camp II, and R.D. Smith, Proteomics, in press (2005).
• "Identification of shed proteins from chinese hamster ovary cells: Application of statistical confidence using human and mouse protein databases," M. Ahram, E.F. Strittmatter, M.E. Monroe, J.N. Adkins, J.C. Hunter, J.H. Miller, and D.L. Springer, Proteomics, 5 (7), 1815-1826 (2005).
• "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics," D.A. Elias, M.E. Monroe, M.J. Marshall, M.F. Romine, A.S. Belieav, J.K. Fredrickson, G.A. Anderson, R.D. Smith, and M.S. Lipton. 2005. Proteomics, 5 (12), 3120-3130.
• "A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy," J.N. Adkins, M.E. Monroe, K.J. Auberry, Y. Shen, J.M. Jacobs, D.G. Camp II, F. Vitzthum, K.D. Rodland, R.C. Zangar, R.D. Smith, and J.G. Pounds. Proteomics, 5 (13), 3454-3466 (2005).
• "Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations," E. Kolker, A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates, III, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje, Proc. Natl. Acad. Sci., in press (2005).
• "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome", W. Qian, T. Liu, M.E. Monroe, E.F. Strittmatter, J.M. Jacobs, L.J. Kangas, K. Petritis, D.G. Camp II, and R.D. Smith, J. Proteome Research, 4 (1), 53-62 (2005).
• "Global Whole-Cell FTICR Mass Spectrometric Proteomics Analysis of the Heat Shock Response in the Radioresistant Bacterium Deinococcus radiodurans," A.K. Schmid, M.S. Lipton, H. Mottaz, M.E. Monroe, R.D. Smith, and M.E. Lidstrom, J. Proteome Research, 4 (3), 709-718 (2005).
• "Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach," W. Qian, M.E. Monroe, T. Liu, J.M. Jacobs, G.A. Anderson, Y, Shen, R.J. Moore, D.J. Anderson, R. Zhang, S.E. Calvano, S.F. Lowry, W. Xiao, L.L. Moldawer, R.W. Davis, R.G. Tompkins, D.G. Camp, II, and R.D. Smith. Molecular & Cellular Proteomics, 4 (5), 700-709 (2005).
• "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry," T. Liu, W. Qian, M.A. Gritsenko, D.G. Camp II, M.E. Monroe, R.J. Moore, and R.D. Smith, Journal of Proteome Research, 4 (6), 2070-2080 (2005).
• "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach," J.D. Zimmer, M.E. Monroe, W.J. Qian, R.D. Smith. Mass Spectrometry Reviews, DOI 10.1002/mas.20071 (2006).
• "PRISM: A Data Management System for High-Throughput Proteomics," G.R. Kiebel, K.J. Auberry, N. Jaitly, D.A. Clark, M.E. Monroe, E.S. Peterson, N. Tolic, G.A. Anderson, and R.D. Smith. Proteomics, DOI 10.1002/pmic.200500500 (2006).

POSTERS

• Zhang, H.; Monroe, M.E.; Jorgenson, J.W. Analytical Chemistry, in preparation.
• 25th International Symposium on Capillary Chromatography & Electrophoresis, May 2002 (poster and lecture), Riva del Garde, Italy
• Pittsburgh Conference 2002, Celebrating Diversity in Analytical Chemistry (poster), New Orleans, LA
• 24th International Symposium on Capillary Chromatography & Electrophoresis, May 2001 (poster), Las Vegas, NV
• Triangle Chromatography Discussion Group Symposium, May 2001 (poster), Raleigh, NC
• Triangle Chromatography Discussion Group Symposium, May 2000 (poster with Kamlesh Patel), Raleigh, NC
• Triangle Chromatography Discussion Group Symposium, May 1999 (poster with Luke Tolley), Raleigh, NC

PRESENTATIONS

• 2004: Anderson KK, ME Monroe, and DS Daly. "Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Data." Presented by ME Monroe at The 2004 International MultiConference in Computer Science & Computer Engineering, Las Vegas, NV. (paper and lecture)
• 2002: Monroe ME, JC Link, and JW Jorgenson. "Combined Ultra-High Pressure µLC and MS of Peptides from Complex Mixtures." Presented by ME Monroe at the 25th Intl. Symp. on Capillary Chromatography & Electrophoresis.
• 1999: Research seminar discussing overview of personal graduate research, 1999
• 1998: Literature seminar covering procedures and instrumentation used in Proteomics, 1998
• 1997: Research proposal for graduate-level Inorganic Mechanisms class, 1997
• 1997: Summary of research for the Honor's Program Senior Roundtables, 1997
• 1996: Summary of summer research for Inorganic Group Seminar, 1996
• 1996: Research proposal for graduate-level Photochemistry class, 1996
• 1995: Summary of research for REU seminar, 1995
• 1995: Summary of summer research for Inorganic Group Seminar, 1995
• 1994: Summary of summer research for Inorganic Group Seminar, 1994

INTERESTS

In addition to programming, I enjoy cross country skiing, performing vocal and instrumental music, and attending all varieties of cultural programs.

REFERENCES

Dr. James Jorgenson, UNC
Dr. R. Mark Wightman, UNC
Dr. Gary Glish, UNC
Dr. Linda Spremulli, UNC
Dr. Patrick Sullivan, UW
Dr. Suzanne Harris, UW
Claoma Woodall, UW

This resume is available on-line at http://www.alchemistmatt.com/resume/resume.html Included are links to many of the people listed on this resume, plus screen shots and working versions of the programs and databases I have written.

An abbreviated, two page, Microsoft Word format of this resume is available for printing.

Back to my home page.

These pages are mirrored at http://www.alchemistmatt.com/ and http:/www.geocities.com/alchemistmatt/.

Last updated March 7, 2006