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Fundamental and Computational Sciences Directorate

Staff information

Vladislav Petyuk

Computational Biology
Data Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

PNNL Publications


  • Dou Y., L. Katsnelson, M.A. Gritsenko, Y. Hu, B. Reva, R. Hong, and Y. Wang, et al. 2023. "Proteogenomic insights suggest druggable pathways in endometrial carcinoma." Cancer Cell 41, no. 9:1586-1605.e15. PNNL-SA-177735. doi:10.1016/j.ccell.2023.07.007
  • Fulcher J.M., A.C. Swensen, Y. Chen, B. Verchere, V.A. Petyuk, and W. Qian. 2023. "Top-Down Proteomics of Mouse Islets With Beta Cell CPE Deletion Reveals Molecular Details in Prohormone Processing." Endocrinology 164, no. 12:Art. No. bqad160. PNNL-SA-188096. doi:10.1210/endocr/bqad160
  • Madda R., V.A. Petyuk, Y. Wang, T. Shi, C. Shriver, K.D. Rodland, and T. Liu. 2023. "Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection." In Serum/Plasma Proteomics: Methods and Protocols. Methods in Moleculary Biology, edited by D.W. Greening and R.J. Simpson. 579-592. New York, New York:Humana. PNNL-ACT-SA-10675. doi:10.1007/978-1-0716-2978-9_33
  • Martin E.A., J.M. Fulcher, M. Zhou, M.E. Monroe, and V.A. Petyuk. 2023. "TopPICR: a companion R package for top-down proteomics data analysis." Journal of Proteome Research 22, no. 2:399-409. PNNL-SA-177756. doi:10.1021/acs.jproteome.2c00570
  • Park J., F. Yu, J.M. Fulcher, S.M. Williams, K.M. Engbrecht, R.J. Moore, and G. Clair, et al. 2023. "Evaluating linear ion trap for MS3-based multiplexed single-cell proteomics." Analytical Chemistry 95, no. 3:1888-1898. PNNL-SA-176981. doi:10.1021/acs.analchem.2c03739


  • Kapasi A., L. Yu, V.A. Petyuk, K. Arfanakis, D.A. Bennett, and J.A. Schneider. 2022. "Association of small vessel disease with tau pathology." Acta Neuropathologica 2022, no. 143:349-362. PNNL-SA-177136. doi:10.1007/s00401-021-02397-x
  • Reyes B.C., I. Ortero-Muras, and V.A. Petyuk. 2022. "A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws." BMC Bioinformatics 23, no. 1:Art. No. 1. PNNL-SA-167099. doi:10.1186/s12859-021-04477-x
  • Sanford J.A., Y. Wang, J.R. Hansen, M.A. Gritsenko, K.K. Weitz, T.J. Sagendorf, and C.E. Tognon, et al. 2022. "Evaluation of differential peptide loading on tandem mass tag-based proteomic and phosphoproteomic data quality." Journal of the American Society for Mass Spectrometry 33, no. 1:17-30. PNNL-SA-155168. doi:10.1021/jasms.1c00169
  • Xu G., T.D. Grimes, T.B. Grayson, J. Chen, L.A. Thielen, H.M. Tse, and P. Li, et al. 2022. "Exploratory Study Reveals Far Reaching Systemic and Cellular Effects of Verapamil Treatment in Subjects with Type 1 Diabetes." Nature Communications 13. PNNL-SA-160227. doi:10.1038/s41467-022-28826-3
  • Yu L., Y. Hsieh, R.V. Pearse, Y. Wang, V.A. Petyuk, J.A. Schneider, and A. Buchman, et al. 2022. "Association of AK4 Protein From Stem Cell-Derived Neurons With Cognitive Reserve: An Autopsy Study." Neurology 99, no. 20:E2264 - E2274. PNNL-SA-177139. doi:10.1212/WNL.0000000000201120


  • Jiang W., B. Wen, K. Li, W. Zeng, F. Leprevost, J. Moon, and V.A. Petyuk, et al. 2021. "Deep learning-derived evaluation metrics enable effective benchmarking of computational tools for phosphopeptide identification." Molecular & Cellular Proteomics. MCP 20. PNNL-SA-167275. doi:10.1016/j.mcpro.2021.100171
  • Mahoney E.R., L. Dumitrescu, A.M. Moore, F.E. Cambronero, P.L. De Jager, M.I. Koran, and V.A. Petyuk, et al. 2021. "Brain expression of the vascular endothelial growth factor gene family in cognitive aging and alzheimer’s disease." Molecular Psychiatry 26, no. 3:888-896. PNNL-SA-147565. doi:10.1038/s41380-019-0458-5
  • Petyuk V.A., L. Yu, H.M. Olson, F. Yu, G. Clair, W. Qian, and J.M. Shulman, et al. 2021. "Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss." Journal of Proteome Research 20, no. 5:2266-2282. PNNL-SA-153429. doi:10.1021/acs.jproteome.0c00747
  • Wang L., A. Karpova, M.A. Gritsenko, J.E. Kyle, S. Cao, Y. Li, and D. Rykunov, et al. 2021. "Proteogenomic and Metabolomic Characterization of Human Glioblastoma." Cancer Cell 39, no. 4:509-528.e20. PNNL-SA-151124. doi:10.1016/j.ccell.2021.01.006


  • 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
  • Johnson E., E.B. Dammer, D.M. Duong, L. Ping, M. Zhou, Y. Yin, and L.A. Higginbotham, et al. 2020. "Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation." Nature Medicine 26, no. 5:769-780. PNNL-SA-156646. doi:10.1038/s41591-020-0815-6
  • Killinger B.J., V.A. Petyuk, and A.T. Wright. 2020. "Detecting differential protein abundance by combining peptide level P-values." Molecular Omics 16, no. 6:554-562. PNNL-SA-144005. doi:10.1039/d0mo00045k
  • Lee J., T. Shi, V.A. Petyuk, A.A. Schepmoes, T.L. Fillmore, Y. Wang, and W.A. Cardoni, et al. 2020. "Detection of head and neck cancer based on longitudinal changes in serum protein abundance." Cancer Epidemiology, Biomarkers and Prevention 29, no. 8:1665-1672. PNNL-ACT-SA-10471. doi:10.1158/1055-9965.EPI-20-0192
  • 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
  • Orwoll E.S., J. Wiedrick, C. Nielson, J.M. Jacobs, E.S. Baker, P.D. Piehowski, and V.A. Petyuk, et al. 2020. "Proteomic assessment of serum biomarkers of longevity in older men." Aging Cell 19, no. 11:Article No. e13253. PNNL-SA-155940. doi:10.1111/acel.13253
  • Petralia F., N. Tignor, B. Reva, M. Koptyra, S. Chowdhury, D. Rykunov, and A. Krek, et al. 2020. "Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer." Cell 183, no. 7:1962-1985. PNNL-SA-155153. doi:10.1016/j.cell.2020.10.044
  • Reyes B.C., I. Ortero-Muras, M.T. Shuen, A.M. Tartakovsky, and V.A. Petyuk. 2020. "CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks." Bioinformatics 36, no. 12:3922-3924. PNNL-SA-148872. doi:10.1093/bioinformatics/btaa241
  • Sanford J.A., C.D. Nogiec, M.E. Lindholm, J.N. Adkins, D. Amar, S. Dasari, and J.K. Drugan, et al. 2020. "Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise." Cell 181, no. 7:1464-1474. PNNL-SA-155782. doi:10.1016/j.cell.2020.06.004
  • Yang H., C. White, H. Klein, L. Yu, C. Gaiteri, Y. Ma, and D. Felsky, et al. 2020. "Genetics of gene expression in the aging human brain reveal TDP-43 proteinopathy pathophysiology." Neuron 107, no. 3:496-508.e6. PNNL-SA-156655. doi:10.1016/j.neuron.2020.05.010
  • Zhang T., M.J. Gaffrey, D.G. Thomas, T.J. Weber, B.M. Hess, K.K. Weitz, and P.D. Piehowski, et al. 2020. "A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages." NanoImpact 17. PNNL-SA-147217. doi:10.1016/j.impact.2019.100194
  • 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


  • Arshad O.A., V.G. 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 & Cellular Proteomics 18, no. 8 suppl 1:S26-S36. PNNL-SA-145629. doi:10.1074/mcp.RA119.001540
  • Buchman A., L. Yu, V.A. Petyuk, C. Gaiteri, S. Tasaki, K.D. Blizinsky, and J.A. Schneider, et al. 2019. "Cognition may link cortical IGFBP5 levels with motor function in older adults." PLoS One 14, no. 8:Article No. e0220968. PNNL-SA-147561. doi:10.1371/journal.pone.0220968
  • Capuano A.W., R.S. Wilson, W.G. Honer, V.A. Petyuk, S.E. Leurgons, L. Yu, and J.R. Gatchel, et al. 2019. "Brain IGFBP-5 modifies the relation of depressive symptoms to decline in cognition in older persons." Journal of Affective Disorders 250. PNNL-SA-147567. doi:10.1016/j.jad.2019.03.051
  • Cuesta R., M.A. Gritsenko, V.A. Petyuk, A.K. Shukla, C. Tsai, T. Liu, and J.E. McDermott, et al. 2019. "Phosphoproteome Analysis Reveals Estrogen-ER pathway as a modulator of mTOR activity via DEPTOR." Molecular & Cellular Proteomics 18, no. 8:1607-1618. PNNL-SA-145628. doi:10.1074/mcp.RA119.001506
  • Felsky D., T. Roostaei, K. Nho, S.L. Risacher, E. Bradshaw, V.A. Petyuk, and J.A. Schneider, et al. 2019. "Neuropathological correlates and genetic architecture of microglial activation in elderly human brain." Nature Communications 10, no. 1:Article No. 409. PNNL-SA-147570. doi:10.1038/s41467-018-08279-3
  • Kim N., L. Yu, R. Dawe, V.A. Petyuk, C. Gaiteri, P.L. De Jager, and J.A. Schneider, et al. 2019. "Microstructural changes in the brain mediate the association of AK4, IGFBP5, HSPB2, and ITPK1 with cognitive decline." Neurobiology of Aging 84. PNNL-SA-147569. doi:10.1016/j.neurobiolaging.2019.07.013
  • Nagy G., K. Kedia, I.K. Attah, V. Garimella, Y.M. Ibrahim, V.A. Petyuk, and R.D. Smith. 2019. "Separation of ß-Amyloid Tryptic Peptide Species with Isomerized and Racemized L-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations." Analytical Chemistry 91, no. 7:4374-4380. PNNL-SA-138885. doi:10.1021/acs.analchem.8b04696
  • Ojelade S.A., T.V. Lee, N. Giagtzoglou, L. Yu, B. Ugur, Y. Li, and L. Duraine, et al. 2019. "cindr, the Drosophila Homolog of the CD2AP Alzheimer's Disease Risk Gene, Is Required for Synaptic Transmission and Proteostasis." Cell Reports 28, no. 7:1799-1813.e5. PNNL-SA-147440. doi:10.1016/j.celrep.2019.07.041
  • Stevens S., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNWD-SA-10567. doi:10.1007/s12975-018-0670-7
  • Stevens S.L., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia That Is Associated With Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNNL-SA-153569. doi:10.1007/s12975-018-0670-7
  • Tasaki S., C. Gaiteri, V.A. Petyuk, K.D. Blizinsky, P.L. De Jager, A. Buchman, and D.A. Bennett. 2019. "Genetic risk for Alzheimer's dementia predicts motor deficits through multi-omic systems in older adults." Translational Psychiatry 9. PNNL-SA-148783. doi:10.1038/s41398-019-0577-4
  • Vasaikar S., C. Huang, X. Wang, V.A. Petyuk, S. Savage, B. Wen, and Y. Dou, et al. 2019. "Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities." Cell 177, no. 4:1035-1049. PNNL-SA-137631. doi:10.1016/j.cell.2019.03.030
  • Yu L., V.A. Petyuk, S. Tasaki, P.A. Boyle, C. Gaiteri, J.A. Schneider, and P.L. De Jager, et al. 2019. "Association of Cortical ß-Amyloid Protein in the Absence of Insoluble Deposits With Alzheimer Disease." JAMA Neurology 76, no. 7:818-826. PNNL-SA-147568. doi:10.1001/jamaneurol.2019.0834


  • 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
  • Moghieb A.M., G. Clair, H.D. Mitchell, J. Kitzmiller, E.M. Zink, Y. Kim, and V.A. Petyuk, et al. 2018. "Time-resolved Proteome Profiling of Normal Lung Development." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 1:L11-L24. PNNL-SA-127218. doi:10.1152/ajplung.00316.2017
  • Olah M., E. Patrick, A. Villani, J. Xu, C. White, K. Ryan, and P.D. Piehowski, et al. 2018. "A transcriptomic atlas of aged human microglia." Nature Communications 9, no. 1:Article No. 539. PNNL-SA-134273. doi:10.1038/s41467-018-02926-5
  • Orwoll E.S., J. Wiedrick, J.M. Jacobs, E.M. Baker, P.D. Piehowski, V.A. Petyuk, and Y. Gao, et al. 2018. "High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men." Aging Cell 17, no. 2:Article No. e12717. PNNL-SA-131443. doi:10.1111/acel.12717
  • Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2018. "Author Correction: Informed-Proteomics: open-source software package for top-down proteomics." Nature Methods 15. PNNL-SA-162101. doi:10.1038/s41592-018-0040-0
  • Petyuk V.A., R.R. Chang, M. Ramirez Restrepo, N.B. Bechmann, M.Y. Henrion, P.D. Piehowski, and K. Zhu, et al. 2018. "The human brainome: network analysis identifies HSPA2 as a novel Alzheimer’s disease target." Brain 141, no. 9:2721-2739. PNNL-SA-133886. doi:10.1093/brain/awy215
  • Piehowski P.D., V.A. Petyuk, R.L. Sontag, M.A. Gritsenko, K.K. Weitz, T.L. Fillmore, and J.S. Moon, et al. 2018. "Residual tissue repositories as a resource for population-based cancer proteomic studies." Clinical Proteomics 15. PNNL-SA-130920. doi:10.1186/s12014-018-9202-4
  • Yu L., V.A. Petyuk, C. Gaiteri, S. Mostafavi, T. Young-Pearse, R.C. Shah, and A. Buchman, et al. 2018. "Targeted Brain Proteomics Uncover Multiple Pathways to Alzheimer’s Dementia." Annals of Neurology 84, no. 1:78-88. PNNL-SA-136156. doi:10.1002/ana.25266
  • Zhu Y., P.D. Piehowski, R. Zhao, J. Chen, Y. Shen, R.J. Moore, and A.K. Shukla, et al. 2018. "Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells." Nature Communications 9, no. 1:882. PNNL-SA-125235. doi:10.1038/s41467-018-03367-w


  • Dhondt I., V.A. Petyuk, S. Bauer, H.M. Brewer, R.D. Smith, G.G. Depuydt, and B.P. Braeckman. 2017. "Changes of Protein Turnover in Aging Caenorhabditis elegans." Molecular & Cellular Proteomics 16, no. 9:1621-1633. PNNL-SA-129634. doi:10.1074/mcp.RA117.000049
  • Gwinn K., K.K. David, C.R. Swanson-Fischer, R.L. Albin, C. Hillaire-Clarke, B. Sieber, and C. Lungu, et al. 2017. "Parkinson’s disease biomarkers: perspective from the NINDS Parkinson’s Disease Biomarkers Program." Biomarkers in Medicine 11, no. 6:451-473. PNNL-SA-129861. doi:10.2217/bmm-2016-0370
  • Lobanov A.V., S.M. Heaphy, A.A. Turanov, M.V. Gerashchenko, S. Pucciarelli, R.R. Devaraj, and F. Xie, et al. 2017. "Position-dependent termination and widespread obligatory frameshifting in Euplotes translation." Nature Structural & Molecular Biology 24, no. 1:61-68. PNNL-SA-123907. doi:10.1038/nsmb.3330
  • Nielson C., J. Wiedrick, J. Shen, J.M. Jacobs, E.M. Baker, A. Baraff, and P.D. Piehowski, et al. 2017. "Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics." Journal of Bone and Mineral Research 32, no. 7:1559-1567. PNNL-SA-111322. doi:10.1002/jbmr.3125
  • Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14, no. 9:909-914. PNNL-SA-120171. doi:10.1038/nmeth.4388
  • 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." Journal of Pathology 243, no. 1:78-88. PNNL-SA-119241. doi:10.1002/path.4929
  • Zheng X., L. Deng, E.M. Baker, Y.M. Ibrahim, V.A. Petyuk, and R.D. Smith. 2017. "Distinguishing D- and L-Aspartic and Isoaspartic Acids in Amyloid ß Peptides with Ultrahigh Resolution Ion Mobility Spectrometry." Chemical Communications 53, no. 56:7913-7916. PNNL-SA-124064. doi:10.1039/C7CC03321D


  • Dhondt I., V.A. Petyuk, H. Cai, L. Vandemeulebroucke, A. Vierstraete, R.D. Smith, and G.G. Depuydt, et al. 2016. "FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans." Cell Reports 16, no. 11:3028-3040. PNNL-SA-121059. doi:10.1016/j.celrep.2016.07.088
  • Hasin-Brumshtein Y., A.H. Khan, F. Hormozdiari, C. Pan, B. Parks, V.A. Petyuk, and P.D. Piehowski, et al. 2016. "Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes." eLife 2016, no. 5:e15614. PNNL-SA-120999. doi:10.7554/eLife.15614
  • Hatakeyama H., S.Y. Wu, Y.A. Lyons, S. Pradeep, W. Wang, Q. Huang, and K.A. Court, et al. 2016. "Role of CTGF in Sensitivity to Hyperthermia in Ovarian and Uterine Cancers." Cell Reports 17, no. 6:1621-1631. PNNL-SA-120868. doi:10.1016/j.celrep.2016.10.020
  • Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891
  • Tabb D.L., X. Wang, S.A. Carr, K. Clauser, P. Mertins, M.C. Chambers, and J.D. Holman, et al. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15, no. 3:691-706. PNNL-SA-113210. doi:10.1021/acs.jproteome.5b00859
  • 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


  • Rosenthal L.S., D. Drake, R. Alcalay, D. Babcock, D. Bowman, A. Chen-Plotkin, and T.M. Dawson, et al. 2015. "The NINDS Parkinson’s Disease Biomarkers Program." Movement Disorders 31, no. 6:915-923. PNNL-SA-110383. doi:10.1002/mds.26438
  • Vrablik T.L., V.A. Petyuk, E.M. Larson, R.D. Smith, and J. Watts. 2015. "Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identi?cation of ACS-4 as a lipid droplet-associated protein." Biochimica and Biophysica Acta. Molecular and Cell Biology of Lipids. 1851, no. 10:1337-1345. PNNL-SA-108157. doi:10.1016/j.bbalip.2015.06.004
  • 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


  • Depuydt G.G., F. Xie, V.A. Petyuk, A. Smolders, H.M. Brewer, D.G. Camp, and R.D. Smith, et al. 2014. "LC-MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism." Journal of Proteome Research 13, no. 4:1938-1956. PNNL-SA-86677. doi:10.1021/pr401081b
  • He J., X. Sun, T. Shi, A.A. Schepmoes, T.L. Fillmore, V.A. Petyuk, and F. Xie, et al. 2014. "Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer." Molecular Oncology 8, no. 7:1169-1180. PNNL-SA-97917. doi:10.1016/j.molonc.2014.02.004
  • Martin J.L., P.A. Yates, R. Soysa, J.F. Alfaro, F. Yang, K.E. Burnum-Johnson, and V.A. Petyuk, et al. 2014. "Metabolic Reprogramming During Purine Stress in the Protozoan Pathogen Leishmania donovani." PLoS Pathogens 10, no. 2:e1003938. PNNL-SA-96975. doi:10.1371/journal.ppat.1003938
  • Mertins P., F. Yang, T. Liu, D. Mani, V.A. Petyuk, M. Gillette, and K. Clauser, et al. 2014. "Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels." Molecular & Cellular Proteomics 13, no. 7:1690-1704. PNNL-SA-98702. doi:10.1074/mcp.M113.036392
  • 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
  • Xiong Y., S.T. Coradetti, X. Li, M.A. Gritsenko, T.R. Clauss, V.A. Petyuk, and D.G. Camp, et al. 2014. "The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation." Fungal Genetics and Biology : FG & B 72. PNNL-SA-103196. doi:10.1016/j.fgb.2014.05.005


  • 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
  • Depuydt G.G., F. Xie, V.A. Petyuk, N. Shanmugam, A. Smolders, I. Dhondt, and H.M. Brewer, et al. 2013. "Reduced insulin/Insulin-like Growth Factor-1signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans." Molecular and Cellular Proteomics 12, no. 12:3624-3639. PNNL-SA-98548. doi:10.1074/mcp.M113.027383
  • 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, D.J. Orton, F. Xie, R.J. Moore, M. Ramirez Restrepo, and A. Engel, et al. 2013. "Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis." Journal of Proteome Research 12, no. 5:2128-2137. PNNL-SA-92104. doi:10.1021/pr301146m
  • 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
  • Zhou J., R.K. Krovvidi, Y. Gao, H. Gao, B.O. Petritis, A. De, and C. Miller-Graziano, et al. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7, no. 7-8:571-583. PNWD-SA-9434. doi:10.1002/prca.201200109


  • Andreev V.P., V.A. Petyuk, H.M. Brewer, Y. Karpievitch, F. Xie, J. Clarke, and D.G. Camp, et al. 2012. "Label-Free Quantitative LC-MS Proteomics of Alzheimer’s Disease and Normally Aged Human Brains." Journal of Proteome Research 11, no. 6:3053-3067. PNNL-SA-90452. doi:10.1021/pr3001546
  • Baker E.S., T. Liu, V.A. Petyuk, K.E. Burnum-Johnson, Y.M. Ibrahim, G.A. Anderson, and R.D. Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4. PNNL-SA-86783. doi:10.1186/gm364


  • Ghazalpour A., B. Bennett, V.A. Petyuk, L. Orazco, R. Hagopian, I. Mungrue, and C.R. Farber, et al. 2011. "Comparative Analysis of Proteome and Transcriptome Variation in Mouse." PLoS Genetics 7, no. 6:Article No. e1001393. PNWD-SA-9360. doi:10.1371/journal.pgen.1001393
  • Xie F., T. Liu, W. Qian, V.A. Petyuk, and R.D. Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry 286, no. 29:25443-25449. PNNL-SA-76123.
  • 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.


  • 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
  • Petyuk V.A., W. Qian, R.D. Smith, and D.J. Smith. 2010. "Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry." Methods 50, no. 2:77-84. PNNL-SA-68829.
  • 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


  • Park C.C., V.A. Petyuk, W. Qian, R.D. Smith, and D.J. Smith. 2009. "Dual spatial maps of transcript and protein abundance in the mouse brain." Expert Review of Proteomics 6, no. 3:243-249. PNWD-SA-8709.
  • 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.


  • Chin M.H., W. Qian, H. Wang, V.A. Petyuk, J.S. Bloom, D.M. Sforza, and G. Lacan, et al. 2008. "Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease." Journal of Proteome Research 7, no. 2:666-677. PNNL-SA-58152. doi:10.1021/pr070546l
  • 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
  • Polpitiya A.D., W. Qian, N. Jaitly, V.A. Petyuk, J.N. Adkins, D.G. Camp, and G.A. Anderson, et al. 2008. "DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24, no. 13:1556-1558. PNNL-SA-58107. doi:10.1093/bioinformatics/btn217
  • 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. Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry">doi:10.1002/rcm.3703Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry


  • Chin M.H., A.B. Geng, A.H. Khan, W. Qian, V.A. Petyuk, J. Boline, and S. Levy, et al. 2007. "A genome-scale map of expression for a mouse brain section obtained using voxelation." Physiological Genomics 30, no. 3:313-321. PNWD-SA-7823.
  • 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


  • 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.
  • 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
  • Wang H.H., W. Qian, M.H. Chin, V.A. Petyuk, R.C. Barry, T. Liu, and M.A. Gritsenko, et al. 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5, no. 2:361-369. PNNL-SA-46752.

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