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Matthew Monroe, Ph.D.


Matthew Monroe
Matthew Monroe

Dr. Monroe's research involves development of algorithms and software for custom and automated analysis of proteomics and bioinformatics data, including managing, summarizing, and mining 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.

His efforts at PNNL have involved automating existing LC-MS peak matching software, collaborating with the development team to incorporate the software into PRISM. In addition, he developed algorithms for estimating the abundance of proteins given the observed peptide abundances, creating a framework for automatically generating these values and reporting them to researchers, along with peptide and protein observations. He is currently in charge of administering, optimizing, and expanding a large collection of Sql Server databases used to process and organize data from the AMT tag process. Dr. Monroe is a key participant in the team of developers in charge of implementing algorithms and new processing paradigms for the ever increasing volumes of data.


  • Ph.D., Analytical Chemistry, University of North Carolina, Chapel Hill, 2002
  • B.S., Chemistry, University of Wyoming, 1997

Honors and Awards

  • Francis P. Venable Fellowship, 1997 -1998
  • R. Owen Asplund Award for Outstanding Academic Performance, 1996
  • Experimental Program to Stimulate Competitive Research (EPSCoR) Summer Fellowship Recipient, 1995 & 1996
  • College of Arts and Sciences Independent Study Fellowship, 1994

Selected Publications

Norbeck AD, ME Monroe, JN Adkins, KK Anderson, DS Daly, RD Smith. 2005. "The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes." Journal of the American Society for Mass Spectrometry 16(8): 1239-1249.

Qian W, T Liu, ME Monroe, EF Strittmatter, JM Jacobs, LJ Kangas, K Petritis, DG Camp II, and RD Smith. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research 4(1):53-62.

Adkins JN, ME Monroe, KJ Auberry, Y Shen, JM Jacobs, DG Camp II, F Vitzthum, KD Rodland, RC Zangar, RD Smith, and JG Pounds. 2005. "A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy." Proteomics 5(13): 3454-3466.

Jacobs JM, ME Monroe, W Qian, Y Shen, GA Anderson, and RD Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240(3):195-212.

Anderson KK, ME Monroe, and DS Daly. 2004. "Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations." In Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04), eds. Faramarz Valafar and Homayoun Valafar, pp. 151-156.

Contact Information

Systems Biology at PNNL

Research & Capabilities