Skip to main content

Paul Piehowski
Proteomics Team Leader

Dr. Paul Piehowski leads a team of researchers on the Biomolecular Pathways team. As an analytical chemist, Piehowski's research is focused on the application of mass spectrometry to biological problems. Since 2009, he has been working with the Integrative Omics group at PNNL to improve reproducibility, sensitivity, and throughput of proteomics measurements. These efforts have resulted in novel capabilities made available to the EMSL user community that have enabled new areas of research in high-throughput proteomics and nanoscale proteomics measurements. 

The high-throughput sample processing pipelines have been applied to support large-scale, clinical proteomics efforts at PNNL, such as The Environmental Determinants of Diabetes in the Young, Proteogenomic Translational Research Center, and Molecular Transducers of Physical Activity Consortium. Most recently, he has adapted this platform to study breath samples from COVID-19 patients to develop signatures of severe COVID infection. During his tenure, he has served in varied roles in this effort from laboratory scientist to principal investigator.

Improvements in measurement sensitivity have culminated in the development of the nanoPOTS platform that can make broad proteomics measurements down to the single-cell level. This sensitivity, combined with PNNL’s custom automated sample analysis, allows the creation of proteome maps with spatial resolution of better than 50 µm.

The development and application of these methodologies have led to many publications in high-impact Nature family and Cell journals. The nanoPOTS platform was a finalist for an R&D 100 Award. His developments have been recognized internally with numerous outstanding performance awards and an exceptional contribution award.

Piehowski received his PhD from Penn State University, carrying out his thesis research developing and applying mass spectrometry imaging techniques for single-cell analysis. His research was supported by the Chemistry Department Braucher fellowship.

Research Interests

  • Improving reproducibility, sensitivity, and throughput of bottom-up proteomics measurements
  • Laboratory automation
  • Imaging mass spectrometry
  • Bioinformatics

Education

  • PhD in Analytical Chemistry, Pennsylvania State University, 2004 – 2009
  • BA in Chemistry, St. John’s University, 1999 – 2003

Awards and Recognition

  • R&D 100 Finalist for “nanoPOTS”, R&D Magazine (2019)
  • Exceptional Contribution Award, PNNL (2011, 2011, 2013, 2014, 2018, 2019)
  • Student Presentation Award, 17th International SIMS Conference (2009)
  • Braucher Fellowship, Chemistry Department, Pennsylvania State University (2008)
  • Student Presentation Award, 20th Annual Workshop on SIMS (2007)

Patents

PD Piehowski, Y Zhu, RT Kelly, KE Burnum-Johnson, RJ Moore. “Methods and systems of proteome analysis and imaging.” US Patent App. 15/993,949.

Publications

2020

Alcazar, O., L. F. Hernandez, E. S. Nakayasu, P. D. Piehowski, C. Ansong, M. H. Abdulreda, and P. Buchwald. 2020. “Longitudinal Proteomics Analysis in the Immediate Microenvironment of Islet Allografts During Progression of Rejection.” Journal of Proteomics 223. https://doi.org/10.1016/j.jprot.2020.103826. 

Clark, D. J., Clinical Proteomic Tumor Analysis Consortium, et al. 2020. “Erratum: Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (Cell (2019) 179(4) (964–983.E31), (S0092867419311237), (10.1016/J.Cell.2019.10.007)).” Cell 180 (1): 207. https://doi.org/10.1016/j.cell.2019.12.026. 

Dou, Y., Clinical Proteomic Tumor Analysis Consortium, et al. 2020. “Proteogenomic Characterization of Endometrial Carcinoma.” Cell 180 (4): 729-748.e26. https://doi.org/10.1016/j.cell.2020.01.026. 

Orwoll, E. S., J. Wiedrick, C. M. Nielson, J. Jacobs, E. S. Baker, P. Piehowski, V. Petyuk, Y. Gao, T. Shi, R. D. Smith, D. C. Bauer, S. R. Cummings, J. Lapidus, and G. for the Osteoporotic Fractures in Men Study Research. 2020. “Proteomic Assessment of Serum Biomarkers of Longevity in Older Men.” Aging Cell. https://doi.org/10.1111/acel.13253. 

Piehowski, P. D., Y. Zhu, L. M. Bramer, K. G. Stratton, R. Zhao, D. J. Orton, R. J. Moore, J. Yuan, H. D. Mitchell, Y. Gao, B. J. M. Webb-Robertson, S. K. Dey, R. T. Kelly, and K. E. Burnum-Johnson. 2020. “Automated Mass Spectrometry Imaging of over 2000 Proteins from Tissue Sections at 100-µm Spatial Resolution.” Nature Communications 11 (1). https://doi.org/10.1038/s41467-019-13858-z. 

Sanford, J. A., Molecular Transducers of Physical Activity Consortium, et al. 2020. “Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise.” Cell 181 (7): 1464-1474. https://doi.org/10.1016/j.cell.2020.06.004. 

Sigdel, T. K., P. D. Piehowski, S. Roy, J. Liberto, J. R. Hansen, A. C. Swensen, R. Zhao, Y. Zhu, P. Rashmi, A. Schroeder, I. Damm, S. Sur, J. Luo, Y. Yang, W. J. Qian, M. M. Sarwal, and the Kidney Precision Medicine Project (KPMP) Consortium. 2020. “Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney.” Frontiers in Medicine 7. https://doi.org/10.3389/fmed.2020.00499. 

Wang, X., A. C. Swensen, T. Zhang, P. D. Piehowski, M. J. Gaffrey, M. E. Monroe, Y. Zhu, H. Dong, and W. J. Qian. 2020. “Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy.” Journal of Proteome Research 19 (4): 1863-1872. https://doi.org/10.1021/acs.jproteome.9b00766. 

Wood-Charlson, E. M., Anubhav, D. Auberry, H. Blanco, M. I. Borkum, Y. E. Corilo, K. W. Davenport, S. Deshpande, R. Devarakonda, M. Drake, W. D. Duncan, M. C. Flynn, D. Hays, B. Hu, M. Huntemann, P. E. Li, M. Lipton, C. C. Lo, D. Millard, K. Miller, P. D. Piehowski, S. Purvine, T. B. K. Reddy, M. Shakya, J. C. Sundaramurthi, P. Vangay, Y. Wei, B. E. Wilson, S. Canon, P. S. G. Chain, K. Fagnan, S. Martin, L. A. McCue, C. J. Mungall, N. J. Mouncey, M. E. Maxon, and E. A. Eloe-Fadrosh. 2020. “The National Microbiome Data Collaborative: Enabling Microbiome Science.” Nature Reviews Microbiology 18 (6): 313-314. https://doi.org/10.1038/s41579-020-0377-0. 

Zhang, T., M. J. Gaffrey, M. E. Monroe, D. G. Thomas, K. K. Weitz, P. D. Piehowski, V. A. Petyuk, R. J. Moore, B. D. Thrall, and W. J. Qian. 2020. “Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling.” Journal of Proteome Research 19 (7): 2863-2872. https://doi.org/10.1021/acs.jproteome.0c00310. 

Zhang, T., M. J. Gaffrey, D. G. Thomas, T. J. Weber, B. M. Hess, K. K. Weitz, P. D. Piehowski, V. A. Petyuk, R. J. Moore, W. J. Qian, and B. D. Thrall. 2020. “A Proteome-Wide Assessment of the Oxidative Stress Paradigm for Metal and Metal-Oxide Nanomaterials in Human Macrophages.” NanoImpact 17. https://doi.org/10.1016/j.impact.2019.100194. 

2019

Arshad, O. A., V. Danna, V. A. Petyuk, P. D. Piehowski, T. Liu, K. D. Rodland, and J. E. McDermott. 2019. “An Integrative Analysis of Tumor Proteomic and Phosphoproteomic Profiles to Examine the Relationships between Kinase Activity and Phosphorylation.” Molecular and Cellular Proteomics 18 (8): S26-S36. https://doi.org/10.1074/mcp.RA119.001540. 

Couvillion, S. P., Y. Zhu, G. Nagy, J. N. Adkins, C. Ansong, R. S. Renslow, P. D. Piehowski, Y. M. Ibrahim, R. T. Kelly, and T. O. Metz. 2019. “New Mass Spectrometry Technologies Contributing Towards Comprehensive and High Throughput Omics Analyses of Single Cells.” Analyst 144 (3): 794-807. https://doi.org/10.1039/c8an01574k. 

Dirice, E., S. Kahraman, D. F. De Jesus, A. El Ouaamari, G. Basile, R. L. Baker, B. Yigit, P. D. Piehowski, M. J. Kim, A. J. Dwyer, R. W. S. Ng, C. Schuster, H. Vethe, T. Martinov, Y. Ishikawa, A. K. K. Teo, R. D. Smith, J. Hu, K. Haskins, T. Serwold, W. J. Qian, B. T. Fife, S. Kissler, and R. N. Kulkarni. 2019. “Increased β-Cell Proliferation before Immune Cell Invasion Prevents Progression of Type 1 Diabetes.” Nature Metabolism 1 (5): 509-518. https://doi.org/10.1038/s42255-019-0061-8. 

Dou, M., C. F. Tsai, P. D. Piehowski, Y. Wang, T. L. Fillmore, R. Zhao, R. J. Moore, P. Zhang, W. J. Qian, R. D. Smith, T. Liu, R. T. Kelly, T. Shi, and Y. Zhu. 2019. “Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables in-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples.” Analytical Chemistry 91 (15): 9707-9715. https://doi.org/10.1021/acs.analchem.9b01248. 

Johnston, G. P., B. Bradel-Tretheway, P. D. Piehowski, H. M. Brewer, B. N. R. Lee, N. T. Usher, J. L. R. Zamora, V. Ortega, E. M. Contreras, J. R. Teuton, J. P. Wendler, K. M. Matz, J. N. Adkins, and H. C. Aguilar. 2019. “Nipah Virus-Like Particle Egress Is Modulated by Cytoskeletal and Vesicular Trafficking Pathways: A Validated Particle Proteomics Analysis.” mSystems 4 (5). https://doi.org/10.1128/mSystems.00194-19. 

Kelly, R., Y. Zhu, Y. Liang, Y. Cong, P. Piehowski, M. Dou, R. Zhao, W. J. Qian, K. Burnum-Johnson, and C. Ansong. 2019. “Single Cell Proteome Mapping of Tissue Heterogeneity Using Microfluidic Nanodroplet Sample Processing and Ultrasensitive Lc-Ms.” Journal of Biomolecular Techniques JBT 30: S61. http://jbt.abrf.org/jbt-static/index.cfm/page/archives/jbt_archive.htm. 

Nagarajan, A., M. Zhou, A. Y. Nguyen, M. Liberton, K. Kedia, T. Shi, P. Piehowski, A. Shukla, T. L. Fillmore, C. Nicora, R. D. Smith, D. W. Koppenaal, J. M. Jacobs, and H. B. Pakrasi. 2019. “Proteomic Insights into Phycobilisome Degradation, a Selective and Tightly Controlled Process in the Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973.” Biomolecules 9 (8). https://doi.org/10.3390/biom9080374. 

Wakasaki, R., K. Matsushita, K. Golgotiu, S. Anderson, M. B. Eiwaz, D. J. Orton, S. J. Han, H. T. Lee, R. D. Smith, K. D. Rodland, P. D. Piehowski, and M. P. Hutchens. 2019. “Glomerular Filtrate Proteins in Acute Cardiorenal Syndrome.” JCI insight 4 (4). https://doi.org/10.1172/jci.insight.122130. 

Xu, K., Y. Liang, P. D. Piehowski, M. Dou, K. C. Schwarz, R. Zhao, R. L. Sontag, R. J. Moore, Y. Zhu, and R. T. Kelly. 2019. “Benchtop-Compatible Sample Processing Workflow for Proteome Profiling of < 100 Mammalian Cells.” Analytical and bioanalytical chemistry 411 (19): 4587-4596. https://doi.org/10.1007/s00216-018-1493-9. 

Yi, L., C. F. Tsai, E. Dirice, A. C. Swensen, J. Chen, T. Shi, M. A. Gritsenko, R. K. Chu, P. D. Piehowski, R. D. Smith, K. D. Rodland, M. A. Atkinson, C. E. Mathews, R. N. Kulkarni, T. Liu, and W. J. Qian. 2019. “Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells.” Analytical Chemistry 91 (9): 5794-5801. https://doi.org/10.1021/acs.analchem.9b00024. 

2018

Dou, M., Y. Zhu, A. Liyu, Y. Liang, J. Chen, P. D. Piehowski, K. Xu, R. Zhao, R. J. Moore, M. A. Atkinson, C. E. Mathews, W. J. Qian, and R. T. Kelly. 2018. “Nanowell-Mediated Two-Dimensional Liquid Chromatography Enables Deep Proteome Profiling of <1000 Mammalian Cells.” Chemical Science 9 (34): 6944-6951. https://doi.org/10.1039/c8sc02680g. 

Kedia, K., J. P. Wendler, E. S. Baker, K. E. Burnum-Johnson, L. G. Jarsberg, K. G. Stratton, A. T. Wright, P. D. Piehowski, M. A. Gritsenko, D. M. Lewinsohn, G. B. Sigal, M. H. Weiner, R. D. Smith, J. M. Jacobs, and P. Nahid. 2018. “Application of Multiplexed Ion Mobility Spectrometry Towards the Identification of Host Protein Signatures of Treatment Effect in Pulmonary Tuberculosis.” Tuberculosis 112: 52-61. https://doi.org/10.1016/j.tube.2018.07.005. 

Matsushita, K., K. Golgotiu, D. J. Orton, R. D. Smith, K. D. Rodland, P. D. Piehowski, and M. P. Hutchens. 2018. “Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy.” Journal of visualized experiments : JoVE (140). https://doi.org/10.3791/58206. 

Olah, M., E. Patrick, A. C. Villani, J. Xu, C. C. White, K. J. Ryan, P. Piehowski, A. Kapasi, P. Nejad, M. Cimpean, S. Connor, C. J. Yung, M. Frangieh, A. McHenry, W. Elyaman, V. Petyuk, J. A. Schneider, D. A. Bennett, P. L. De Jager, and E. M. Bradshaw. 2018. “A Transcriptomic Atlas of Aged Human Microglia.” Nature Communications 9 (1). https://doi.org/10.1038/s41467-018-02926-5. 

Orwoll, E. S., J. Wiedrick, J. Jacobs, E. S. Baker, P. Piehowski, V. Petyuk, Y. Gao, T. Shi, R. D. Smith, D. C. Bauer, S. R. Cummings, C. M. Nielson, J. Lapidus, for the Osteoporotic Fractures in Men Study Research Group. 2018. “High-Throughput Serum Proteomics for the Identification of Protein Biomarkers of Mortality in Older Men.” Aging Cell 17 (2). https://doi.org/10.1111/acel.12717. 

Park, J., P. D. Piehowski, C. Wilkins, M. Zhou, J. Mendoza, G. M. Fujimoto, B. C. Gibbons, J. B. Shaw, Y. Shen, A. K. Shukla, R. J. Moore, T. Liu, V. A. Petyuk, N. Tolić, L. Paša-Tolić, R. D. Smith, S. H. Payne, and S. Kim. 2018. “Author Correction: Informed-Proteomics: Open-Source Software Package for Top-Down Proteomics (Nature Methods (2017) 14 (909-914) Doi: 10.1038/Nmeth.4388).” Nature Methods 15 (7): 554. https://doi.org/10.1038/s41592-018-0040-0. 

Petyuk, V. A., R. Chang, M. Ramirez-Restrepo, N. D. Beckmann, M. Y. R. Henrion, P. D. Piehowski, K. Zhu, S. Wang, J. Clarke, M. J. Huentelman, F. Xie, V. Andreev, A. Engel, T. Guettoche, L. Navarro, P. De Jager, J. A. Schneider, C. M. Morris, I. G. McKeith, R. H. Perry, S. Lovestone, R. L. Woltjer, T. G. Beach, L. I. Sue, G. E. Serrano, A. P. Lieberman, R. L. Albin, I. Ferrer, D. C. Mash, C. M. Hulette, J. F. Ervin, E. M. Reiman, J. A. Hardy, D. A. Bennett, E. Schadt, R. D. Smith, and A. J. Myers. 2018. “The Human Brainome: Network Analysis Identifies HSPA2 as a Novel Alzheimer's Disease Target.” Brain 141 (9): 2721-2739. https://doi.org/10.1093/brain/awy215. 

Piehowski, P. D., V. A. Petyuk, R. L. Sontag, M. A. Gritsenko, K. K. Weitz, T. L. Fillmore, J. Moon, H. Makhlouf, R. F. Chuaqui, E. S. Boja, H. Rodriguez, J. S. H. Lee, R. D. Smith, D. M. Carrick, T. Liu, and K. D. Rodland. 2018. “Residual Tissue Repositories as a Resource for Population-Based Cancer Proteomic Studies.” Clinical Proteomics 15 (1). https://doi.org/10.1186/s12014-018-9202-4. 

Piehowski, P. D., R. Zhao, R. J. Moore, G. Clair, and C. Ansong. 2018. Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially Resolved Tissue Profiling. Methods in Molecular Biology 1788: 269-277. https://doi.org/10.1007/7651_2017_78 

Rodland, K. D., P. Piehowski, and R. D. Smith. 2018. “Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics.” Cancer Journal (United States) 24 (3): 117-121. https://doi.org/10.1097/PPO.0000000000000315. 

Stanfill, B. A., E. S. Nakayasu, L. M. Bramer, A. M. Thompson, C. K. Ansong, T. R. Clauss, M. A. Gritsenko, M. E. Monroe, R. J. Moore, D. J. Orton, P. D. Piehowski, A. A. Schepmoes, R. D. Smith, B. J. M. Webb-Robertson, and T. O. Metz. 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 (9): 1824-1836. https://doi.org/10.1074/mcp.RA118.000648. 

Yu, L., V. A. Petyuk, C. Gaiteri, S. Mostafavi, T. Young-Pearse, R. C. Shah, A. S. Buchman, J. A. Schneider, P. D. Piehowski, R. L. Sontag, T. L. Fillmore, T. Shi, R. D. Smith, P. L. De Jager, and D. A. Bennett. 2018. “Targeted Brain Proteomics Uncover Multiple Pathways to Alzheimer's Dementia.” Annals of Neurology 84 (1): 78-88. https://doi.org/10.1002/ana.25266. 

Zhu, Y., M. Dou, P. D. Piehowski, Y. Liang, F. Wang, R. K. Chu, W. B. Chrisler, J. N. Smith, K. C. Schwarz, Y. Shen, A. K. Shukla, R. J. Moore, R. D. Smith, W. J. Qian, and R. T. Kelly. 2018. “Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets.” Molecular and Cellular Proteomics 17 (9): 1864-1874. https://doi.org/10.1074/mcp.TIR118.000686. 

Zhu, Y., P. D. Piehowski, R. T. Kelly, and W. J. Qian. 2018. “Nanoproteomics Comes of Age.” Expert Review of Proteomics 15 (11): 865-871. https://doi.org/10.1080/14789450.2018.1537787. 

Zhu, Y., P. D. Piehowski, R. Zhao, J. Chen, Y. Shen, R. J. Moore, A. K. Shukla, V. A. Petyuk, M. Campbell-Thompson, C. E. Mathews, R. D. Smith, W. J. Qian, and R. T. Kelly. 2018. “Nanodroplet Processing Platform for Deep and Quantitative Proteome Profiling of 10-100 Mammalian Cells.” Nature Communications 9 (1). https://doi.org/10.1038/s41467-018-03367-w. 

Zhu, Y., R. Zhao, P. D. Piehowski, R. J. Moore, S. Lim, V. J. Orphan, L. Paša-Tolić, W. J. Qian, R. D. Smith, and R. T. Kelly. 2018. “Subnanogram Proteomics: Impact of LC Column Selection, MS Instrumentation and Data Analysis Strategy on Proteome Coverage for Trace Samples.” International Journal of Mass Spectrometry 427: 4-10. https://doi.org/10.1016/j.ijms.2017.08.016. 

2017

Nielson, C. M., J. Wiedrick, J. Shen, J. Jacobs, E. S. Baker, A. Baraff, P. Piehowski, C. G. Lee, A. Baratt, V. Petyuk, S. McWeeney, J. Y. Lim, D. C. Bauer, N. E. Lane, P. M. Cawthon, R. D. Smith, J. Lapidus, E. S. Orwoll, for the Osteoporotic Fractures in Men Study Research Group. 2017. “Identification of Hip BMD Loss and Fracture Risk Markers through Population-Based Serum Proteomics.” Journal of Bone and Mineral Research 32 (7): 1559-1567. https://doi.org/10.1002/jbmr.3125. 

Park, J., P. D. Piehowski, C. Wilkins, M. Zhou, J. Mendoza, G. M. Fujimoto, B. C. Gibbons, J. B. Shaw, Y. Shen, A. K. Shukla, R. J. Moore, T. Liu, V. A. Petyuk, N. Tolić, L. Paša-Tolić, R. D. Smith, S. H. Payne, and S. Kim. 2017. “Informed-Proteomics: Open-Source Software Package for Top-Down Proteomics.” Nature Methods 14 (9): 909-914. https://doi.org/10.1038/nmeth.4388. 

Qiu, J., K. Yu, X. Fei, Y. Liu, E. S. Nakayasu, P. D. Piehowski, J. B. Shaw, K. Puvar, C. Das, X. Liu, and Z. Q. Luo. 2017. “A Unique Deubiquitinase That Deconjugates Phosphoribosyl-Linked Protein Ubiquitination.” Cell Research 27 (7): 865-881. https://doi.org/10.1038/cr.2017.66. 

Shen, Y., N. Tolić, P. D. Piehowski, A. K. Shukla, S. Kim, R. Zhao, Y. Qu, E. Robinson, R. D. Smith, and L. Paša-Tolić. 2017. “High-Resolution Ultrahigh-Pressure Long Column Reversed-Phase Liquid Chromatography for Top-Down Proteomics.” Journal of Chromatography A 1498: 99-110. https://doi.org/10.1016/j.chroma.2017.01.008. 

Smith, J. N., K. J. Tyrrell, J. R. Hansen, D. G. Thomas, T. A. Murphree, A. Shukla, T. Luders, J. M. Madden, Y. Li, A. T. Wright, and P. D. Piehowski. 2017. “Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling.” Analytical Chemistry 89 (24): 13559-13566. https://doi.org/10.1021/acs.analchem.7b03984. 

Yi, L., P. D. Piehowski, T. Shi, R. D. Smith, and W. J. Qian. 2017. “Advances in Microscale Separations Towards Nanoproteomics Applications.” Journal of Chromatography A 1523: 40-48. https://doi.org/10.1016/j.chroma.2017.07.055. 

2016

Clair, G., P. D. Piehowski, T. Nicola, J. A. Kitzmiller, E. L. Huang, E. M. Zink, R. L. Sontag, D. J. Orton, R. J. Moore, J. P. Carson, R. D. Smith, J. A. Whitsett, R. A. Corley, N. Ambalavanan, and C. Ansong. 2016. “Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples.” Scientific Reports 6. https://doi.org/10.1038/srep39223. 

Hasin-Brumshtein, Y., A. H. Khan, F. Hormozdiari, C. Pan, B. W. Parks, V. A. Petyuk, P. D. Piehowski, A. Brümmer, M. Pellegrini, X. Xiao, E. Eskin, R. D. Smith, A. J. Lusis, and D. J. Smith. 2016. “Hypothalamic Transcriptomes of 99 Mouse Strains Reveal Trans eQTL Hotspots, Splicing QTLs and Novel Non-Coding Genes.” eLife 5 (September2016). https://doi.org/10.7554/eLife.15614. 

Huang, E. L., P. D. Piehowski, D. J. Orton, R. J. Moore, W. J. Qian, C. P. Casey, X. Sun, S. K. Dey, K. E. Burnum-Johnson, and R. D. Smith. 2016. “SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities.” Endocrinology 157 (3): 1307-1314. https://doi.org/10.1210/en.2015-1821. 

2015

Aylward, F. O., L. Khadempour, D. M. Tremmel, B. R. McDonald, C. D. Nicora, S. Wu, R. J. Moore, D. J. Orton, M. E. Monroe, P. D. Piehowski, S. O. Purvine, R. D. Smith, M. S. Lipton, K. E. Burnum-Johnson, and C. R. Currie. 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 (8). https://doi.org/10.1371/journal.pone.0134752. 

Aylward, F. O., L. Khadempour, D. M. Tremmel, B. R. McDonald, C. D. Nicora, S. Wu, R. J. Moore, D. J. Orton, M. E. Monroe, P. D. Piehowski, S. O. Purvine, R. D. Smith, M. S. Lipton, K. E. Burnum-Johnson, and C. R. Currie. 2015. “Erratum: 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 (2015) 10:8 (E0134752) (Doi:10.1371/Journal.Pone.0134752)).” PLoS ONE 10 (9). https://doi.org/10.1371/journal.pone.0139151. 

Cha, J., K. E. Burnum-Johnson, A. Bartos, Y. Li, E. S. Baker, S. C. Tilton, B. J. M. Webb-Robertson, P. D. Piehowski, M. E. Monroe, A. G. Jegga, S. Murata, Y. Hirota, and S. K. Dey. 2015. “Muscle Segment Homeobox Genes Direct Embryonic Diapause by Limiting Inflammation in the Uterus.” Journal of Biological Chemistry 290 (24): 15337-15349. https://doi.org/10.1074/jbc.M115.655001. 

Wright, A. T., T. Magnaldo, R. L. Sontag, L. N. Anderson, N. C. Sadler, P. D. Piehowski, Y. Gache, and T. J. Weber. 2015. “Deficient Expression of Aldehyde Dehydrogenase 1a1 Is Consistent with Increased Sensitivity of Gorlin Syndrome Patients to Radiation Carcinogenesis.” Molecular Carcinogenesis 54 (6): 473-484. https://doi.org/10.1002/mc.22115. 

2014

Baker, E. S., K. E. Burnum-Johnson, J. M. Jacobs, D. L. Diamond, R. N. Brown, Y. M. Ibrahim, D. J. Orton, P. D. Piehowski, D. E. Purdy, R. J. Moore, W. F. Danielson, M. E. Monroe, K. L. Crowell, G. W. Slysz, M. A. Gritsenko, J. D. Sandoval, B. L. LaMarche, M. M. Matzke, B. J. M. Webb-Robertson, B. C. Simons, B. J. McMahon, R. Bhattacharya, J. D. Perkins, R. L. Carithers Jr, S. Strom, S. G. Self, M. G. Katze, G. A. Anderson, and R. D. Smith. 2014. “Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry.” Molecular and Cellular Proteomics 13 (4): 1119-1127. https://doi.org/10.1074/mcp.M113.034595. 

Hyung, S. W., P. D. Piehowski, R. J. Moore, D. J. Orton, A. A. Schepmoes, T. R. Clauss, R. K. Chu, T. L. Fillmore, H. Brewer, T. Liu, R. Zhao, and R. D. Smith. 2014. “Microscale Depletion of High Abundance Proteins in Human Biofluids Using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid.” Analytical and bioanalytical chemistry 406 (28): 7117-7125. https://doi.org/10.1007/s00216-014-8058-3. 

2013

Aylward, F. O., K. E. Burnum-Johnson, S. G. Tringe, C. Teiling, D. M. Tremmel, J. A. Moeller, J. J. Scott, K. W. Barry, P. D. Piehowski, C. D. Nicor, S. A. Malfatti, M. E. Monroe, S. O. Purvine, L. A. Goodwin, R. D. Smith, G. M. Weinstock, N. M. Gerardo, G. Suen, M. S. Lipton, and C. R. Currie. 2013. “Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens.” Applied and environmental microbiology 79 (12): 3770-3778. https://doi.org/10.1128/AEM.03833-12. 

Crowell, K. L., E. S. Baker, S. H. Payne, Y. M. Ibrahim, M. E. Monroe, G. W. Slysz, B. L. Lamarche, V. A. Petyuk, P. D. Piehowski, W. F. Danielson Iii, G. A. Anderson, and R. D. Smith. 2013. “Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry.” International Journal of Mass Spectrometry 354-355: 312-317. https://doi.org/10.1016/j.ijms.2013.06.028. 

Piehowski, P. D., V. A. Petyuk, D. J. Orton, F. Xie, R. J. Moore, M. Ramirez-Restrepo, A. Engel, A. P. Lieberman, R. L. Albin, D. G. Camp, R. D. Smith, and A. J. Myers. 2013. “Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis.” Journal of Proteome Research 12 (5): 2128-2137. https://doi.org/10.1021/pr301146m. 

Piehowski, P. D., V. A. Petyuk, J. D. Sandoval, K. E. Burnum, G. R. Kiebel, M. E. Monroe, G. A. Anderson, D. G. Camp, and R. D. Smith. 2013. “STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results.” Proteomics 13 (5): 766-770. https://doi.org/10.1002/pmic.201200096. 

2012

Aylward, F. O., K. E. Burnum, J. J. Scott, G. Suen, S. G. Tringe, S. M. Adams, K. W. Barry, C. D. Nicora, P. D. Piehowski, S. O. Purvine, G. J. Starrett, L. A. Goodwin, R. D. Smith, M. S. Lipton, and C. R. Currie. 2012. “Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-Cutter Ant Fungus Gardens.” ISME Journal 6 (9): 1688-1701. https://doi.org/10.1038/ismej.2012.10. 

2010

Heien, M. L., P. D. Piehowski, N. Winograd, and A. G. Ewing. 2010. Lipid Detection, Identification, and Imaging Single Cells with SIMS. Methods in Molecular Biology 656: 85-97. https://doi.org/10.1007/978-1-60761-746-4_4 

Kurczy, M. E., P. D. Piehowski, C. T. Van Bell, M. L. Heien, N. Winograd, and A. G. Ewing. 2010. “Mass Spectrometry Imaging of Mating Tetrahymena Show That Changes in Cell Morphology Regulate Lipid Domain Formation.” Proceedings of the National Academy of Sciences of the United States of America 107 (7): 2751-2756. https://doi.org/10.1073/pnas.0908101107. 

2009

Piehowski, P. D., A. M. Davey, M. E. Kurczy, E. D. Sheets, N. Winograd, A. G. Ewing, and M. L. Heien. 2009. “Time-of-Flight Secondary Ion Mass Spectrometry Imaging of Subcellular Lipid Heterogeneity: Poisson Counting and Spatial Resolution.” Analytical Chemistry 81 (14): 5593-5602. https://doi.org/10.1021/ac901065s. 

2008

Kurczy, M. E., J. Kozole, S. A. Parry, P. D. Piehowski, N. Winograd, and A. G. Ewing. 2008. “Relative Quantification of Cellular Sections with Molecular Depth Profiling Tof-Sims Imaging.” Applied Surface Science 255 (4): 1158-1161. https://doi.org/10.1016/j.apsusc.2008.05.018. 

Kurczy, M. E., P. D. Piehowski, S. A. Parry, M. Jiang, G. Chen, A. G. Ewing, and N. Winograd. 2008. “Which Is More Important in Bioimaging Sims Experiments-the Sample Preparation or the Nature of the Projectile?” Applied Surface Science 255 (4): 1298-1304. https://doi.org/10.1016/j.apsusc.2008.05.139. 

Piehowski, P. D., A. J. Carado, M. E. Kurczy, S. G. Ostrowski, M. L. Heien, N. Winograd, and A. G. Ewing. 2008. “Ms/Ms Methodology to Improve Subcellular Mapping of Cholesterol Using TOF-SIMS.” Analytical Chemistry 80 (22): 8662-8667. https://doi.org/10.1021/ac801591r. 

Piehowski, P. D., M. E. Kurczy, D. Willingham, S. Parry, M. L. Heien, N. Winograd, and A. G. Ewing. 2008. “Freeze-Etching and Vapor Matrix Deposition for TOF-SIMS Imaging of Single Cells.” Langmuir 24 (15): 7906-7911. https://doi.org/10.1021/la800292e.