Computational Scientist
Computational Scientist


Matt Monroe's research involves the development of algorithms and software for custom and automated analysis of proteomics and bioinformatics data, including managing, summarizing, and mining large volumes of data generated by mass spectrometry-based proteomic analysis. His areas of expertise include microcolumn liquid chromatography, liquid chromatography-mass spectrometry (LC-MS) of peptides and proteins using Quadrupole Time-of-Flight and ion trap mass spectrometry, and analytical instrumentation design and automation. 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 Access.

His efforts at PNNL have involved automating existing LC-MS peak matching software, collaborating with development teams to incorporate the software into PRISM, and expanding the software to support new data processing developments. In addition, he has developed numerous utility applications to aid researchers in transforming and interpreting proteomics data (applications and source code are available at He is currently the lead developer for administering, optimizing, and expanding a large collection of SQL Server databases used to process and organize data from the accurate mass and time tag process, and he is a key participant in a team of developers who are implementing algorithms and new processing paradigms for the ever-increasing volumes of data.

Research Interest

  • Proteomics
  • Bioinformatics
  • Software engineering
  • Database architecture


  • PhD in Analytical Chemistry, University of North Carolina, 2002
  • BS in Chemistry, University of Wyoming, 1997

Affiliations and Professional Service

  • Analytical Chemistry Society

Awards and Recognitions

  • Francis P. Venable Fellowship (1997, 1998)
  • R. Owen Asplund Award for Outstanding Academic Performance (1996)
  • Summer EPSCoR Fellowship Recipient (1995, 1996)



  • Dou Y., E. Kawaler, D.C. Zhou, M.A. Gritsenko, C. Huang, L. Blumenberg, and A. Karpova, et al. 2020. "Proteogenomic Characterization of Endometrial Carcinoma." Cell 180, no. 4:729-748.e26. PNNL-SA-147326. doi:10.1016/j.cell.2020.01.026
  • McDermott J.E., O.A. Arshad, V.A. Petyuk, Y. Fu, M.A. Gritsenko, T.R. Clauss, and R.J. Moore, et al. 2020. "Proteogenomic characterization of ovarian HGSC implicates mitotic kinases, replication stress in observed chromosomal instability." Cell Reports Medicine 1, no. 1:Article No. 100004. PNNL-SA-145681. doi:10.1016/j.xcrm.2020.100004
  • Wang X., A.C. Swensen, T. Zhang, P.D. Piehowski, M.J. Gaffrey, M.E. Monroe, and Y. Zhu, et al. 2020. "Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-search Delta Score Strategy." Journal of Proteome Research 19, no. 4:1863-1872. PNNL-SA-149222. doi:10.1021/acs.jproteome.9b00766
  • Zhang T., M.J. Gaffrey, M.E. Monroe, D.G. Thomas, K.K. Weitz, P.D. Piehowski, and V.A. Petyuk, et al. 2020. "Block design with common reference samples enables robust large-scale label-free quantitative proteome profiling." Journal of Proteome Research 19, no. 7:2863-2872. PNNL-SA-151164. doi:10.1021/acs.jproteome.0c00310


  • Clair G., S.M. Reehl, K.G. Stratton, M.E. Monroe, M. Tfaily, C.K. Ansong, and J.E. Kyle. 2019. "Lipid Mini-On: Mining and ontology tool for enrichment analysis of lipidomic data." Bioinformatics 35, no. 21:4507-4508. PNNL-SA-142630. doi:10.1093/bioinformatics/btz250
  • Wojcik R., G. Nagy, I.K. Attah, I.K. Webb, V. Garimella, K.K. Weitz, and A.L. Hollerbach, et al. 2019. "SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes." Analytical Chemistry 91, no. 18:11952-11962. PNNL-SA-147394. doi:10.1021/acs.analchem.9b02808


  • Bilbao Pena A., B.C. Gibbons, G.W. Slysz, K.L. Crowell, M.E. Monroe, Y.M. Ibrahim, and R.D. Smith, et al. 2018. "An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies." International Journal of Mass Spectrometry 427. PNNL-SA-126312. doi:10.1016/j.ijms.2017.11.003
  • Menachery V.D., A. Schafer, K.E. Burnum-Johnson, H.D. Mitchell, A.J. Eisfeld-Fenney, K.B. Walters, and C.D. Nicora, et al. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115, no. 5:E1012-E1021. PNNL-SA-126254. doi:10.1073/pnas.1706928115
  • Mertins P., L.C. Tang, K. Krug, D.J. Clark, M.A. Gritsenko, L. Chen, and K. Clauser, et al. 2018. "Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry." Nature Protocols 13, no. 7:1632-1661. PNNL-SA-137930. doi:10.1038/s41596-018-0006-9
  • Orton D.J., M.M. Tfaily, R.J. Moore, B.L. Lamarche, X. Zheng, T.L. Fillmore, and R.K. Chu, et al. 2018. "A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements." Analytical Chemistry 90, no. 1:737-744. PNNL-SA-128111. doi:10.1021/acs.analchem.7b02986
  • Stanfill B.A., E.S. Nakayasu, L.M. Bramer, A.M. Thompson, C.K. Ansong, T. Clauss, and M.A. Gritsenko, et al. 2018. "Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data." Molecular and Cellular Proteomics 17, no. 9:1824-1836. PNNL-SA-129934. doi:10.1074/mcp.RA118.000648


  • Eisfeld A.J., P. Halfmann, J.P. Wendler, J.E. Kyle, K.E. Burnum-Johnson, Z. Peralta, and T. Maemura, et al. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22, no. 6:817-829. PNNL-SA-120881. doi:10.1016/j.chom.2017.10.011
  • Kyle J.E., C.P. Casey, K.G. Stratton, E.M. Zink, Y. Kim, X. Zheng, and M.E. Monroe, et al. 2017. "Comparing Identified and Statistically Significant Lipids and Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies." Rapid Communications in Mass Spectrometry 31, no. 5:447-456. PNNL-SA-121197. doi:10.1002/rcm.7808
  • Ma J., C.P. Casey, X. Zheng, Y.M. Ibrahim, C.S. Wilkins, R.S. Renslow, and D.G. Thomas, et al. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33, no. 17:2715-2722. PNNL-SA-122828. doi:10.1093/bioinformatics/btx305
  • Wang S., F. Yang, V.A. Petyuk, A.K. Shukla, M.E. Monroe, M.A. Gritsenko, and K.D. Rodland, et al. 2017. "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease." The Journal of Pathology 243, no. 1:78-88. PNNL-SA-119241. doi:10.1002/path.4929
  • Zheng X., R. Wojcik, X. Zhang, Y.M. Ibrahim, K.E. Burnum-Johnson, D.J. Orton, and M.E. Monroe, et al. 2017. "Coupling Front-end Separations, Ion Mobility Spectrometry, and Mass Spectrometry for Enhanced Multidimensional Biological and Environmental Analyses." Annual Review of Analytical Chemistry 10. PNNL-SA-121198. doi:10.1146/annurev-anchem-061516-045212


  • Burnum-Johnson K.E., S. Nie, C.P. Casey, M.E. Monroe, D.J. Orton, Y.M. Ibrahim, and M.A. Gritsenko, et al. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
  • Khadempour L., K.E. Burnum-Johnson, E.S. Baker, C.D. Nicora, B.M. Webb-Robertson, R.A. White, and M.E. Monroe, et al. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25, no. 22:5795-5805. PNNL-SA-113016. doi:10.1111/mec.13872
  • Kyle J.E., X. Zhang, K.K. Weitz, M.E. Monroe, Y.M. Ibrahim, R.J. Moore, and J. Cha, et al. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst 141, no. 5:1649-1659. PNNL-SA-111991. doi:10.1039/C5AN02062J
  • Sadler N.C., H.C. Bernstein, M.R. Melnicki, M.A. Charania, E.A. Hill, L.N. Anderson, and M.E. Monroe, et al. 2016. "Dinitrogenase Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. ATCC 51142." Applied Environmental Microbiology 82, no. 24:7227-7235. PNNL-SA-113160. doi:10.1128/AEM.02098-16
  • Zhang H., T. Liu, Z. Zhang, S.H. Payne, B. Zhang, J.E. McDermott, and J. Zhou, et al. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166, no. 3:755-765. PNNL-SA-107151. doi:10.1016/j.cell.2016.05.069
  • Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002


  • Aylward F.O., L. Khadempour, D. Tremmel, B.R. McDonald, C.D. Nicora, S. Wu, and R.J. Moore, et al. 2015. "Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants." PLoS One 10, no. 8:e0134752. PNNL-SA-108498. doi:10.1371/journal.pone.0134752
  • Baker E.S., K.E. Burnum-Johnson, Y.M. Ibrahim, D.J. Orton, M.E. Monroe, R.T. Kelly, and R.J. Moore, et al. 2015. "Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations." Proteomics 15, no. 16:2766-2776. PNNL-SA-107785. doi:10.1002/pmic.201500048
  • Cha J., K.E. Burnum-Johnson, A. Bartos, Y. Li, E.S. Baker, S.C. Tilton, and B.M. Webb-Robertson, et al. 2015. "Muscle segment homeobox genes direct embryonic diapause by limiting inflammation in the uterus." Journal of Biological Chemistry 290, no. 24:15337-15349. PNNL-SA-107786. doi:10.1074/jbc.M115.655001
  • Gibbons B.C., M.C. Chambers, M.E. Monroe, D.L. Tabb, and S.H. Payne. 2015. "Correcting systematic bias and instrument measurement drift with mzRefinery." Bioinformatics 31, no. 23:3838-3840. PNNL-SA-108198. doi:10.1093/bioinformatics/btv437
  • Payne S.H., M.E. Monroe, C.C. Overall, G.R. Kiebel, M.G. Degan, B.C. Gibbons, and G.M. Fujimoto, et al. 2015. "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity." Scientific Data 2. PNNL-SA-108944. doi:10.1038/sdata.2015.41
  • Wu C., M.E. Monroe, Z. Xu, G.W. Slysz, S.H. Payne, K.D. Rodland, and T. Liu, et al. 2015. "An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics." Journal of the American Society for Mass Spectrometry 26, no. 12:2002-2008. PNNL-SA-108032. doi:10.1007/s13361-015-1169-z
  • Xu Z., C. Wu, F. Xie, G.W. Slysz, N. Tolic, M.E. Monroe, and V.A. Petyuk, et al. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14, no. 1:422-433. PNNL-SA-103951. doi:10.1021/pr500840w
  • Zhang X., Y.M. Ibrahim, T. Chen, J.E. Kyle, R.V. Norheim, M.E. Monroe, and R.D. Smith, et al. 2015. "Enhancing Biological Analyses with Three Dimensional Field Asymmetric Ion Mobility, Low Field Drift Time Ion Mobility and Mass Spectrometry (µFAIMS/IMS-MS) Separations." Analyst 140. PNNL-SA-110080. doi:10.1039/c5an00897b


  • Aevermann B., B.E. Pickett, S. Kumar, E.B. Klem, S. Agnihothram, P.S. Askovich, and A. Bankhead, et al. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1. PNNL-SA-101269. doi:10.1038/sdata.2014.33
  • Amidan B.G., D.J. Orton, B.L. Lamarche, M.E. Monroe, R.J. Moore, A.M. Venzin, and R.D. Smith, et al. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research 13, no. 4:2215-2222. PNNL-SA-97216. doi:10.1021/pr401143e
  • Baker E.S., K.E. Burnum-Johnson, J.M. Jacobs, D.L. Diamond, R.N. Brown, Y.M. Ibrahim, and D.J. Orton, et al. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13, no. 4:1119-1127. PNNL-SA-90826. doi:10.1074/mcp.M113.034595
  • Fujimoto G.M., M.E. Monroe, L.M. Rodriguez, C. Wu, B. MacLean, R.D. Smith, and M. MacCoss, et al. 2014. "Accounting for population variation in targeted proteomics." Journal of Proteome Research 13, no. 1:321-323. PNNL-SA-99100. doi:10.1021/pr4011052
  • Guo J., A.Y. Nguyen, Z. Dai, D. Su, M.J. Gaffrey, R.J. Moore, and J.M. Jacobs, et al. 2014. "Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-Specific Redox Proteomics." Molecular & Cellular Proteomics. MCP 13, no. 12:3270-3285. PNNL-SA-100244. doi:10.1074/mcp.M114.041160
  • Kolker E., V. Ozdemir, L. Martens, W.S. Hancock, G.A. Anderson, N. Anderson, and S. Aynacioglu, et al. 2014. "Towards more transparent and reproducible omics studies through a common metadata checklist and data publications." OMICS. A Journal of Integrative Biology 18, no. 1:10-14. PNNL-SA-99616. doi:10.1089/omi.2013.0149
  • Kronewitter S.R., G.W. Slysz, I. Marginean, C.D. Hagler, B.L. Lamarche, R. Zhao, and M.Y. Harris, et al. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86, no. 13:6268-6276. PNNL-SA-100272. doi:10.1021/ac501492f
  • Nakayasu E.S., S. Wu, M.A. Sydor, A.K. Shukla, K.K. Weitz, R.J. Moore, and K.K. Hixson, et al. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014. PNNL-SA-96571. doi:10.1155/2014/730725
  • Prost S.A., K.L. Crowell, E.S. Baker, Y.M. Ibrahim, B.H. Clowers, M.E. Monroe, and G.A. Anderson, et al. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry 25, no. 12:2020-2027. PNNL-SA-100086. doi:10.1007/s13361-014-0895-y
  • Zhang Q., M.M. Matzke, A.A. Schepmoes, R.J. Moore, B.M. Webb-Robertson, Z. Hu, and M.E. Monroe, et al. 2014. "High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model." PLoS One 9, no. 3:Article No. e92332. PNNL-SA-98075. doi:10.1371/journal.pone.0092332


  • Aryal U.K., S.J. Callister, S. Mishra, X. Zhang, J.I. Shutthanandan, T.E. Angel, and A.K. Shukla, et al. 2013. "Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production." Applied and Environmental Microbiology 79, no. 4:1070-1077. PNNL-SA-90813. doi:10.1128/AEM.02864-12
  • Aylward F.O., K.E. Burnum-Johnson, S.G. Tringe, C. Teiling, D. Tremmel, J. Moeller, and J.J. Scott, et al. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79, no. 12:3770-3778. PNNL-SA-92750. doi:10.1128/AEM.03833-12
  • Crowell K.L., E.S. Baker, S.H. Payne, Y.M. Ibrahim, M.E. Monroe, G.W. Slysz, and B.L. Lamarche, et al. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355. PNNL-SA-95461. doi:10.1016/j.ijms.2013.06.028
  • Crowell K.L., G.W. Slysz, E.S. Baker, B.L. Lamarche, M.E. Monroe, Y.M. Ibrahim, and S.H. Payne, et al. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29, no. 21:2804-2805. PNNL-SA-95214. doi:10.1093/bioinformatics/btt465
  • Kim J., M.E. Monroe, D.G. Camp, R.D. Smith, and W. Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics." Journal of Proteome Research 12, no. 2:910-916. PNNL-SA-91081. doi:10.1021/pr300955f
  • Lamarche B.L., K.L. Crowell, N. Jaitly, V.A. Petyuk, A.R. Shah, A.D. Polpitiya, and J.D. Sandoval, et al. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14. PNNL-SA-89778. doi:10.1186/1471-2105-14-49
  • Nakayasu E.S., R. Tempel, X.A. Cambronne, V.A. Petyuk, M.B. Jones, M.A. Gritsenko, and M.E. Monroe, et al. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12, no. 11:3297-3309. PNNL-SA-93942. doi:10.1074/mcp.M113.029850
  • Nakayasu E.S., R.N. Brown, C. Ansong, M.A. Sydor, S. Imtiaz, C. Mihai, and R.L. Sontag, et al. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12, no. 8:2136-2147. PNNL-SA-88392. doi:10.1074/mcp.M112.026138
  • Piehowski P.D., V.A. Petyuk, J.D. Sandoval, K.E. Burnum, G.R. Kiebel, M.E. Monroe, and G.A. Anderson, et al. 2013. "STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results." Proteomics 13, no. 5:766-770. PNNL-SA-86051. doi:10.1002/pmic.201200096
  • Su D., A.K. Shukla, B. Chen, J. Kim, E.S. Nakayasu, Y. Qu, and U.K. Aryal, et al. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57. PNNL-SA-89035. doi:10.1016/j.freeradbiomed.2012.12.010
  • Wang D., S. Dasari, M.C. Chambers, J.D. Holman, K. Chen, D. Liebler, and D.J. Orton, et al. 2013. "Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates." Genomics, Proteomics & Bioinformatics 11, no. 2:86-95. PNNL-SA-98549. doi:10.1016/j.gpb.2012.11.004
  • Wu S., R.N. Brown, S.H. Payne, D. Meng, R. Zhao, N. Tolic, and L. Cao, et al. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans." International Journal of Proteomics 2013. PNNL-SA-91327. doi:10.1155/2013/279590


  • Alfaro J.F., C. Gong, M.E. Monroe, J.T. Aldrich, T.R. Clauss, S.O. Purvine, and Z. Wang, et al. 2012. "Tandem Mass Spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets." Proceedings of the National Academy of Sciences of the United States of America 109, no. 19:7280-7285. PNNL-SA-84997. doi:10.1073/pnas.1200425109
  • Burnum K.E., Y. Hirota, E.S. Baker, M. Yoshie, Y.M. Ibrahim, M.E. Monroe, and G.A. Anderson, et al. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153, no. 9:4568-4579. PNNL-SA-87211. doi:10.1210/en.2012-1335
  • Diamond D.L., A. Krasnoselski, K.E. Burnum, M.E. Monroe, B.M. Webb-Robertson, J.E. McDermott, and M.M. Yeh, et al. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56, no. 1:28-38. PNWD-SA-9552. doi:10.1002/hep.25649
  • Marginean I., S.R. Kronewitter, R.J. Moore, G.W. Slysz, M.E. Monroe, G.A. Anderson, and K. Tang, et al. 2012. "Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure." Analytical Chemistry 84, no. 21:9208-9213. PNNL-SA-89077. doi:10.1021/ac301961u
  • Merkley E.D., B.J. Anderson, J.H. Park, S.M. Belchik, L. Shi, M.E. Monroe, and R.D. Smith, et al. 2012. "Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography-Mass Spectrometry, and Database Searching." Journal of Proteome Research 11, no. 12:6147-6158. PNNL-SA-89362. doi:10.1021/pr3007914
  • Rutledge A.C., M.B. Jones, S. Chauhan, S.O. Purvine, J. Sanford, M.E. Monroe, and H.M. Brewer, et al. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7, no. 3:Article No. E33903. PNNL-SA-79961. doi:10.1371/journal.pone.0033903
  • Wang L., U.K. Aryal, Z. Dai, A.C. Mason, M.E. Monroe, Z. Tian, and J. Zhou, et al. 2012. "Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry." Journal of Proteome Research 11, no. 1:143-56. PNNL-SA-82556. doi:10.1021/pr200916k


  • Ansong C., N. Tolic, S.O. Purvine, S. Porwollik, M.B. Jones, H. Yoon, and S.H. Payne, et al. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12. PNNL-SA-77195. doi:10.1186/1471-2164-12-433
  • Aryal U.K., J. Stockel, R.K. Krovvidi, M.A. Gritsenko, M.E. Monroe, R.J. Moore, and D.W. Koppenaal, et al. 2011. "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles." BMC Systems Biology 5. PNNL-SA-81418. doi:10.1186/1752-0509-5-194
  • Frank A.M., M.E. Monroe, A.R. Shah, J.J. Carver, N. Bandeira, R.J. Moore, and G.A. Anderson, et al. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8, no. 7:587-591. PNNL-SA-79495. doi:10.1038/nmeth.1609
  • Stanley J.R., J.N. Adkins, G.W. Slysz, M.E. Monroe, S.O. Purvine, Y.V. Karpievitch, and G.A. Anderson, et al. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83, no. 16:6135-6140. PNNL-SA-72379. doi:10.1021/ac2009806
  • Wang Y., F. Yang, M.A. Gritsenko, Y. Wang, T.R. Clauss, T. Liu, and Y. Shen, et al. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11, no. 10:2019-2026. PNNL-SA-75439. doi:10.1002/pmic.201000722
  • Wang Y., F. Yang, Y. Fu, X. Huang, W. Wang, X. Jiang, and M.A. Gritsenko, et al. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286, no. 20:18190-18201. PNNL-SA-79165.
  • Zhang H., F. Yang, W. Qian, R.N. Brown, Y. Wang, E.D. Merkley, and J.H. Park, et al. 2011. "Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83, no. 19:7260-7268. PNNL-SA-77198. doi:10.1021/ac2000829
  • Zhang Q., M.E. Monroe, A.A. Schepmoes, T.R. Clauss, M.A. Gritsenko, D. Meng, and V.A. Petyuk, et al. 2011. "Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects." Journal of Proteome Research 10, no. 7:3076-3088. PNNL-SA-77801.


  • Auberry K.J., G.R. Kiebel, M.E. Monroe, J.N. Adkins, G.A. Anderson, and R.D. Smith. 2010. " A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3, no. 1:1-4. PNNL-SA-75729.
  • Ham B.M., H. Jayachandran, F. Yang, N. Jaitly, A.D. Polpitiya, M.E. Monroe, and L. Wang, et al. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." Journal of Proteome Research 9, no. 2:945-953. PNNL-SA-69020. doi:10.1021/pr9008207
  • Jung H., S.O. Purvine, H. Kim, V.A. Petyuk, S. Hyung, M.E. Monroe, and D. Mun, et al. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82, no. 20:8510-8518. PNNL-SA-74157. doi:10.1021/ac101388b
  • Qian W., B.O. Petritis, A. Kaushal, C.C. Finnerty, M.G. Jescheke, M.E. Monroe, and R.J. Moore, et al. 2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled “Universal” Reference-based Quantitative Proteomics." Journal of Proteome Research 9, no. 9:4779-4789. PNWD-SA-9014.
  • Shah A.R., J.L. Davidson, M.E. Monroe, A.M. Mayampurath, W.F. Danielson, Y. Shi, and A.C. Robinson, et al. 2010. "An efficient data format for mass spectrometry based proteomics." Journal of the American Society for Mass Spectrometry 21, no. 10:1784-1788. PNNL-SA-69363. doi:10.1016/j.jasms.2010.06.014
  • Shah A.R., J.N. Adkins, D.J. Baxter, W.R. Cannon, D. Chavarr�a-Miranda, S. Choudhury, and I. Gorton, et al. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, edited by M Zelkowitz. 1-70. San Diego, California:Academic Press Inc. PNNL-SA-67358.
  • Shah A.R., K. Agarwal, E.S. Baker, M. Singhal, A.M. Mayampurath, Y.M. Ibrahim, and L.J. Kangas, et al. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry." Bioinformatics 26, no. 13:1601-1607. PNWD-SA-8802. doi:10.1093/bioinformatics/btq245
  • Shah A.R., N. Jaitly, N. Zuljevic, M.E. Monroe, A.V. Liyu, A.D. Polpitiya, and J.N. Adkins, et al. 2010. "An architecture for real time data acquisition and online signal processing for high throughput tandem mass spectrometry." In 5th IEEE International Conference on e-Science, 88 - 93. Piscataway, New Jersey:IEEE. PNNL-SA-67849. doi:10.1109/e-Science.2009.21
  • Yang F., K.M. Waters, J.H. Miller, M.A. Gritsenko, R. Zhao, X. Du, and E.A. Livesay, et al. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5, no. 11:e14152. PNNL-SA-73768. doi:10.1371/journal.pone.0014152
  • Zhang H., R.N. Brown, W. Qian, M.E. Monroe, S.O. Purvine, R.J. Moore, and M.A. Gritsenko, et al. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9, no. 5:2160-2169. PNNL-SA-67314.
  • Zhang X., J. Zhou, M.H. Chin, A.A. Schepmoes, V.A. Petyuk, K.K. Weitz, and B.O. Petritis, et al. 2010. "Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model." Journal of Proteome Research 9, no. 3:1496-1509. PNNL-SA-67444. doi:10.1021/pr901024z
  • Zhang X., M.E. Monroe, B. Chen, M.H. Chin, T.H. Heibeck, A.A. Schepmoes, and F. Yang, et al. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9, no. 6:1199-1208. PNNL-SA-65899.
  • Zhou J., A.A. Schepmoes, X. Zhang, R.J. Moore, M.E. Monroe, J. Lee, and D.G. Camp, et al. 2010. "Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences." Journal of Proteome Research 9, no. 11:5698-5704. PNNL-SA-74147. doi:10.1021/pr100508p


  • Heibeck T.H., S. Ding, L.K. Opresko, R. Zhao, A.A. Schepmoes, F. Yang, and A.V. Tolmachev, et al. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8, no. 8:3852-3861. PNNL-SA-63993.
  • Kim W., M.W. Silby, S.O. Purvine, J.S. Nicoll, K.K. Hixson, M.E. Monroe, and C.D. Nicora, et al. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4, no. 12:Article Number: e8455. PNNL-SA-68830. doi:10.1371/journal.pone.0008455
  • Petyuk V.A., A.M. Mayampurath, M.E. Monroe, A.D. Polpitiya, S.O. Purvine, G.A. Anderson, and D.G. Camp, et al. 2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3. PNNL-SA-62317. doi:10.1074/mcp.M900217-MCP200
  • Qian W., T. Liu, V.A. Petyuk, M.A. Gritsenko, B.O. Petritis, A.D. Polpitiya, and A. Kaushal, et al. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled “Universal” Reference Sample." Journal of Proteome Research 8, no. 1:290-299. PNNL-SA-57317.
  • Yang F., S. Wu, D.L. Stenoien, R. Zhao, M.E. Monroe, M.A. Gritsenko, and S.O. Purvine, et al. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81, no. 10:4137-4143. PNNL-SA-63701. doi:10.1021/ac802605m


  • Callister S.J., L.A. McCue, J.E. Turse, M.E. Monroe, K.J. Auberry, R.D. Smith, and J.N. Adkins, et al. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3, no. 2:e1542. PNNL-SA-58389. doi:10.1371/journal.pone.0001542
  • Daly D.S., K.K. Anderson, E.A. Panisko, S.O. Purvine, R. Fang, M.E. Monroe, and S.E. Baker. 2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7, no. 3:1209-1217. PNNL-SA-57824. doi:10.1021/pr070441i
  • Ding J., C.M. Sorensen, N. Jaitly, H. Jiang, D.J. Orton, M.E. Monroe, and R.J. Moore, et al. 2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." Journal of Chromatography B 871, no. 2:243-252. PNNL-SA-58868. doi:10.1016/j.jchromb.2008.04.040
  • Ding S., Y. Wang, J.M. Jacobs, W. Qian, F. Yang, A.V. Tolmachev, and X. Du, et al. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 18O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7, no. 10:4215-24. PNNL-SA-52241. doi:10.1021/pr7007785
  • Du X., F. Yang, N.P. Manes, D.L. Stenoien, M.E. Monroe, J.N. Adkins, and D.J. States, et al. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications." Journal of Proteome Research 7, no. 6:2195-2203. PNNL-SA-56421. doi:10.1021/pr070510t
  • Ham B.M., F. Yang, H. Jayachandran, N. Jaitly, M.E. Monroe, M.A. Gritsenko, and E.A. Livesay, et al. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7, no. 6:2215-2221. PNWD-SA-7904.
  • Lopez-Ferrer D., T.H. Heibeck, K. Petritis, K.K. Hixson, W. Qian, M.E. Monroe, and A.M. Mayampurath, et al. 2008. "Rapid Sample Processing For LC-MS Based Quantitative Proteomics Using High Intensity Focused Ultrasounds." Journal of Proteome Research 7, no. 9:3860-3867. PNNL-SA-59400. doi:10.1021/pr800161x
  • Manes N.P., R.D. Estep, H.M. Mottaz, R.J. Moore, T.R. Clauss, M.E. Monroe, and X. Du, et al. 2008. "Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions." Journal of Proteome Research 3. PNNL-SA-54048. doi:10.1021/pr070432+
  • Mayampurath A.M., N. Jaitly, S.O. Purvine, M.E. Monroe, K.J. Auberry, J.N. Adkins, and R.D. Smith. 2008. "DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra." Bioinformatics 24, no. 7:1021-1023. PNNL-SA-56275. doi:10.1093/bioinformatics/btn063
  • Metz T.O., W. Qian, J.M. Jacobs, M.A. Gritsenko, R.J. Moore, A.D. Polpitiya, and M.E. Monroe, et al. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset." Journal of Proteome Research 7, no. 2:698-707. PNNL-SA-56533. doi:10.1021/pr700606w
  • Monroe M.E., J.L. Shaw, D.S. Daly, J.N. Adkins, and R.D. Smith. 2008. "MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features." Computational Biology and Chemistry 32, no. 3:215-217. PNNL-SA-52621. doi:10.1016/j.compbiolchem.2008.02.006
  • Petyuk V.A., N. Jaitly, R.J. Moore, J. Ding, T.O. Metz, K. Tang, and M.E. Monroe, et al. 2008. "Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics using Regression Models and a priori Partial Knowledge of the Sample Content." Analytical Chemistry 80, no. 3:693-706. PNNL-SA-56693. doi:10.1021/ac701863d
  • Petyuk V.A., W. Qian, C. Hinault, M.A. Gritsenko, M. Singhal, M.E. Monroe, and D.G. Camp, et al. 2008. "Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues." Journal of Proteome Research 7, no. 8:3114-3126. PNNL-SA-58155. doi:10.1021/pr800205b
  • Tolmachev A.V., M.E. Monroe, S.O. Purvine, R.J. Moore, N. Jaitly, J.N. Adkins, and G.A. Anderson, et al. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments." Analytical Chemistry 80, no. 22:8514-8525. PNNL-SA-61186. doi:10.1021/ac801376g
  • Wegener K.M., E.A. Welsh, L.E. Thornton, N.S. Keren, J.M. Jacobs, K.K. Hixson, and M.E. Monroe, et al. 2008. "High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex." Journal of Biological Chemistry 283, no. 41:27829-27837. PNNL-SA-57538. doi:10.1074/jbc.M803918200
  • Zhang Q., V.A. Petyuk, A.A. Schepmoes, D.J. Orton, M.E. Monroe, F. Yang, and R.D. Smith, et al. 2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22, no. 19:3027-3034. PNNL-SA-61116. doi:10.1002/rcm.3703


  • Baker S.E., C.F. Wend, A.D. Martinez, J.K. Magnuson, E.A. Panisko, Z. Dai, and K.S. Bruno, et al. 2007. "Genome and Proteome Analysis of Industrial Fungi." In Exploitation of Fungi, edited by GD Robson, P van West and G Gadd. 3-9. New York, New York:Cambridge University Press. PNNL-SA-51617. doi:10.1017/CBO9780511902451.002
  • Chan E.Y., W. Qian, D.L. Diamond, T. Liu, M.A. Gritsenko, M.E. Monroe, and D.G. Camp, et al. 2007. "Quantitative analysis of human immunodeficiency virus type 1-infected CD4(+) cell proteome: Dysregulated cell cycle progression and nuclear transport coincide with robust virus production." Journal of Virology 81, no. 14:7571-7583. PNWD-SA-7667.
  • Manes N.P., J.K. Gustin, J. Rue, H.M. Mottaz, S.O. Purvine, A.D. Norbeck, and M.E. Monroe, et al. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6, no. 4:717-727. PNNL-SA-50929. doi:10.1074/mcp.M600282-MCP200
  • Monroe M.E., N. Tolic, N. Jaitly, J.L. Shaw, J.N. Adkins, and R.D. Smith. 2007. "VIPER: an advanced software package to support high-throughput LC-MS peptide identification." Bioinformatics 23, no. 15- August 2007:2021-2023. PNNL-SA-52622. doi:10.1093/bioinformatics/btm281
  • Petyuk V.A., W. Qian, M.H. Chin, H.H. Wang, E.A. Livesay, M.E. Monroe, and J.N. Adkins, et al. 2007. "Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry." Genome Research 17, no. 3:328-336. PNNL-SA-49342. doi:10.1101/gr.5799207
  • Yang F., N. Jaitly, H. Jayachandran, Q. Lou, M.E. Monroe, X. Du, and M.A. Gritsenko, et al. 2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research 6, no. 11:4489-4497. PNNL-SA-52332. doi:10.1021/pr070068e


  • Anderson K.K., M.E. Monroe, and D.S. Daly. 2006. "Estimating Probabilities of Peptide Database Identifications to LC-FTICR-MS Observations." Proteome Science 4, no. 1:1-11. PNNL-SA-46729. doi:10.1186/1477-5956-4-1
  • Callister S.J., C.D. Nicora, X. Zeng, J. Roh, M. Dominguez, C. Tavano, and M.E. Monroe, et al. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67, no. 3:424-436. PNNL-SA-46423. doi:10.1016/j.mimet.2006.04.021
  • Elias D.A., M.E. Monroe, R.D. Smith, J.K. Fredrickson, and M.S. Lipton. 2006. "Confirmation of the Expression of a Large Set of Conserved Hypothetical Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 66, no. 2:223-233. PNNL-SA-45416.
  • Fang R., D.A. Elias, M.E. Monroe, Y. Shen, M. McIntosh, P. Wang, and C.D. Goddard, et al. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5, no. 4:714-725. PNNL-SA-47983. doi:10.1074/mcp.M500301-MCP200
  • Jaitly N., M.E. Monroe, V.A. Petyuk, T.R. Clauss, J.N. Adkins, and R.D. Smith. 2006. "Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline." Analytical Chemistry 78, no. 21:7397-7409. PNNL-SA-48693.
  • Kiebel G.R., K.J. Auberry, N. Jaitly, D. Clark, M.E. Monroe, E.S. Peterson, and N. Tolic, et al. 2006. "PRISM: A Data Management System for High-Throughput Proteomics." Proteomics 6, no. 6:1783-1790. PNNL-SA-45753. doi:10.1002/pmic.200500500
  • Lipton M.S., M.F. Romine, M.E. Monroe, D.A. Elias, L. Pasa-Tolic, G.A. Anderson, and D.J. Anderson, et al. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis." In Microbial Proteomics, Methods of Biochemical Analysis, edited by I. Humphery-Smith and M. Hecker. 113-134. Hoboken, New Jersey:John Wiley & Sons, Inc. PNNL-SA-42692.
  • Liu T., W. Qian, M.A. Gritsenko, W. Xiao, L.L. Moldawer, A. Kaushal, and M.E. Monroe, et al. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome." Molecular & Cellular Proteomics. MCP 5, no. 10:1899-1913. PNWD-SA-7271. doi:10.1074/mcp.M600068-MCP200
  • Norbeck A.D., S.J. Callister, M.E. Monroe, N. Jaitly, D.A. Elias, M.S. Lipton, and R.D. Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods 67, no. 3:473-486. PNNL-SA-46770. doi:10.1016/j.mimet.2006.04.024
  • Norbeck A.D., S.J. Callister, M.E. Monroe, N. Jaitly, D.A. Elias, M.S. Lipton, and R.D. Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods 67, no. 3:473-486. PNNL-SA-47555.
  • Petritis K., L.J. Kangas, B. Yan, M.E. Monroe, E.F. Strittmatter, W. Qian, and J.N. Adkins, et al. 2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78, no. 14:5026-5039. PNNL-SA-50263. doi:10.1021/ac060143p
  • Tolmachev A.V., M.E. Monroe, N. Jaitly, V.A. Petyuk, J.N. Adkins, and R.D. Smith. 2006. "Mass Measurement Accuracy In Analyses Of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78, no. 24:8374-8385. PNNL-SA-49340. doi:10.1021/ac0606251
  • Yang F., D.L. Stenoien, E.F. Strittmatter, J. Wang, L. Ding, M.S. Lipton, and M.E. Monroe, et al. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation." Journal of Proteome Research 5, no. 5:1252-1260. PNNL-SA-46275.
  • Zimmer J.S., M.E. Monroe, W. Qian, and R.D. Smith. 2006. "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach." Mass Spectrometry Reviews 25, no. 3:450-482. PNNL-SA-43136.


  • Adkins J.N., M.E. Monroe, K.J. Auberry, Y. Shen, J.M. Jacobs, D.G. Camp, and F. Vitzthum, et al. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5, no. 13:3454-3466. PNWD-SA-6982. doi:10.1002/pmic.200401333
  • Ahram M., E.F. Strittmatter, M.E. Monroe, J.N. Adkins, J.C. Hunter, J.H. Miller, and D.L. Springer. 2005. "Identification of shed proteins from Chinese hamster ovary cells: Application of statistical confidence using human and mouse protein databases." Proteomics 5, no. 7:1815-1826. PNNL-SA-42491.
  • Elias D.A., M.E. Monroe, M.J. Marshall, M.F. Romine, A.S. Beliaev, J.K. Fredrickson, and G.A. Anderson, et al. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5, no. 12:3120-3130. PNNL-SA-42041. doi:10.1002/pmic.200401140
  • Jacobs J.M., M.E. Monroe, W. Qian, Y. Shen, G.A. Anderson, and R.D. Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240, no. 3:195-212. PNNL-SA-42919.
  • Kolker E., A.F. Picone, M.Y. Galperin, M.F. Romine, R. Higdon, K.S. Makarova, and N. Kolker, et al. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102, no. 6:2099-2104. PNNL-SA-43139.
  • Liu T., W. Qian, M.A. Gritsenko, D.G. Camp, M.E. Monroe, R.J. Moore, and R.D. Smith. 2005. "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry." Journal of Proteome Research 4, no. 6:2070-2080. PNNL-SA-44967.
  • Liu T., W. Qian, W.U. Chen, J.M. Jacobs, R.J. Moore, D.J. Anderson, and M.A. Gritsenko, et al. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5, no. 5:1263-1273. PNNL-SA-42468.
  • Norbeck A.D., M.E. Monroe, J.N. Adkins, K.K. Anderson, D.S. Daly, and R.D. 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, no. 8:1239-1249. PNNL-SA-44395.
  • Qian W., J.M. Jacobs, D.G. Camp, M.E. Monroe, R.J. Moore, M.A. Gritsenko, and S.E. Calvano, et al. 2005. "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry." Proteomics 5, no. 2:572-584. PNNL-SA-40692. doi:10.1002/pmic.200400942
  • Qian W., M.E. Monroe, T. Liu, J.M. Jacobs, G.A. Anderson, Y. Shen, and R.J. Moore, et al. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4, no. 5:700-709. PNNL-SA-44302.
  • Qian W., T. Liu, M.E. Monroe, E.F. Strittmatter, J.M. Jacobs, L.J. Kangas, and K. Petritis, et al. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research 4, no. 1:53-62. PNNL-SA-42815.
  • Schmid A.K., M.S. Lipton, H.M. Mottaz, M.E. Monroe, R.D. Smith, and M.E. Lidstrom. 2005. "Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans." Journal of Proteome Research 4, no. 3:709-718. PNNL-SA-44177.


  • Anderson K.K., M.E. Monroe, and D.S. 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), edited by Faramarz Valafar and Homayoun Valafar, 151-156. Las Vegas, Nevada:CSREA Press. PNNL-SA-42106.
  • Jacobs J.M., H.M. Mottaz, L. Yu, D.J. Anderson, R.J. Moore, W.U. Chen, and K.J. Auberry, et al. 2004. "Multidimensional Proteome Analysis of Human Mammary Epithelial Cells." Journal of Proteome Research 3, no. 1:68-75. PNWD-SA-6087.
  • Prokisch H., C.M. Scharfe, D.G. Camp, W. Xiao, L. David, C. Andreoli, and M.E. Monroe, et al. 2004. "Integrative Analysis of the Mitochondrial Proteome in Yeast." PLoS Biology 2, no. 6:0795-0804. PNWD-SA-6619.
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