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Fundamental and Computational Sciences Directorate

Staff information

Tujin Shi

Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

PNNL Publications


  • Dakup P.P., S. Feng, T. Shi, J.M. Jacobs, H. Wiley, and W. Qian. 2023. "Targeted quantification of protein phosphorylation and its contributions towards mathematical modeling of signaling pathways." Molecules 28, no. 3:Art. No. 1143. PNNL-SA-179947. doi:10.3390/molecules28031143
  • 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
  • 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
  • Tsai C., Y. Wang, C. Hsu, R. Kitata, R.K. Chu, M. Velickovic, and R. Zhao, et al. 2023. "A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics." Communications Biology 6, no. 1:Art. No. 70. PNNL-SA-171979. doi:10.1101/2022.04.12.488038


  • El-Shennawy L., A.D. Hoffman, N.K. Dashzeveg, K.M. McAndrews, P.J. Mehl, D. Cornish, and Z. Yu, et al. 2022. "Circulating ACE2-expressing Extracellular Vesicles Block Broad Strains of SARS-CoV-2." Nature Communications 13, no. 1:Art. No. 405. PNNL-SA-169658. doi:10.1038/s41467-021-27893-2
  • Ramos E.K., C. Tsai, Y. Jia, Y. Cao, M. Manu, R. Taftaf, and A.D. Hoffman, et al. 2022. "Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity." eLife 11. PNNL-SA-177252. doi:10.7554/eLife.82669
  • Xu Z., B. Peng, R. Kitata, C.D. Nicora, K.K. Weitz, Y. Pu, and T. Shi, et al. 2022. "Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis." Biotechnology for Biofuels and Bioproducts 15, no. 1:Art. No. 117. PNNL-SA-172168. doi:10.1186/s13068-022-02214-x


  • Jarsberg L.G., K. Kedia, T.G. Wendler, A.T. Wright, P.D. Piehowski, M.A. Gritsenko, and T. Shi, et al. 2021. "Nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis differ by geographic region." PLOS ONE 16, no. 5:Article No. e0250586. PNNL-SA-156554. doi:10.1371/journal.pone.0250586
  • Joshi S.K., T. Nechiporuk, D. Bottomly, P.D. Piehowski, J. Reisz, J. Pittsenbarger, and A. Kaempf, et al. 2021. "The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistance." Cancer Cell 39, no. 7:999-1014. PNNL-SA-161620. doi:10.1016/j.ccell.2021.06.003
  • Martin K.D., T. Zhang, T. Lin, A.N. Habowski, R. Zhao, C. Tsai, and W.B. Chrisler, et al. 2021. "Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells." Journal of Proteome Research 20, no. 9:4452-4461. PNNL-SA-160823. doi:10.1021/acs.jproteome.1c00403
  • Swensen A.C., J. He, A.C. Fang, Y. Ye, C.D. Nicora, T. Shi, and A.Y. Liu, et al. 2021. "A comprehensive urine proteome database generated from patients with various renal conditions and prostate cancer." Frontiers in Medicine 8. PNNL-SA-152473. doi:10.3389/fmed.2021.548212
  • Tsai C., J. Smith, D.S. Eiger, K.D. Martin, T. Liu, R.D. Smith, and T. Shi, et al. 2021. "Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides." In Shotgun Proteomics: Methods and Protocols. Methods in Molecular Biology, edited by M. Carrera and J. Mateos. 247-257. New York, New York:Humana Press. PNNL-SA-153327. doi:10.1007/978-1-0716-1178-4_16
  • Tsai C., P. Zhang, D. Scholten, K.D. Martin, Y. Wang, R. Zhao, and W.B. Chrisler, et al. 2021. "Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics." Communications Biology 4, no. 1:265. PNNL-SA-150656. doi:10.1038/s42003-021-01797-9


  • Gao Y., Y. Wang, Y. Chen, H. Wang, D. Young, T. Shi, and Y. Song, et al. 2020. "Proteomic Tissue-based Classifier for Early Prediction of Prostate Cancer Progression." Cancers 12, no. 5:1268. PNNL-SA-149705. doi:10.3390/cancers12051268
  • Gerosa L., C. Chidley, F. Frohlich, G. Sanchez, S.K. Lim, J. Muhlich, and J. Chen, et al. 2020. "Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells." Cell Systems 11, no. 5:478-494.e9. PNNL-SA-156751. doi:10.1016/j.cels.2020.10.002
  • Habowski A.N., J.L. Flesher, J.M. Bates, C. Tsai, K.D. Martin, R. Zhao, and A.K. Ganesan, et al. 2020. "Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt." Communications Biology 3. PNNL-SA-153928. doi:10.1038/s42003-020-01181-z
  • Kagan J., R.L. Moritz, R. Mazurchuk, J. Lee, P. Kharchenko, O. Rozenblatt-Rosen, and E. Ruppin, et al. 2020. "National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions." Journal of Proteome Research 19, no. 5:1900-1912. PNNL-SA-152101. doi:10.1021/acs.jproteome.0c00021
  • 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
  • Li M., R. Li, Y. Gao, C.T. Resch, W. Qian, T. Shi, and L. Shi, et al. 2020. "Nitrate bioreduction dynamics in hyporheic zone sediments under cyclic changes of chemical compositions." Journal of Hydrology 585. PNNL-SA-152190. doi:10.1016/j.jhydrol.2020.124836
  • Martin K.D., T. Zhang, P. Zhang, W.B. Chrisler, T.L. Fillmore, F. Liu, and T. Liu, et al. 2020. "Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells." Journal of Visualized Experiments (JoVE). PNNL-SA-153959. doi:10.3791/61797
  • 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
  • Tan Z., J. Zhu, P.M. Stemmer, L. Sun, Z. Yang, K.D. Martin, and M.J. Gaffrey, et al. 2020. "Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line." Journal of Proteome Research 19, no. 4:1635-1646. PNNL-SA-153237. doi:10.1021/acs.jproteome.9b00840
  • Tsai C., R. Zhao, S.M. Williams, R.J. Moore, K.D. Schultz, W.B. Chrisler, and L. Pasa Tolic, et al. 2020. "An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics." Molecular & Cellular Proteomics 19, no. 5:828-838. PNNL-SA-149183. doi:10.1074/mcp.RA119.001857
  • Wang Y., T. Shi, S. Srivastava, J. Kagan, T. Liu, and K.D. Rodland. 2020. "Proteomic Analysis of Exosomes for Discovery of Protein Biomarkers for Prostate and Bladder Cancer." Cancers 12, no. 9:2335. PNNL-SA-154352. doi:10.3390/cancers12092335


  • Dou M., C. Tsai, P.D. Piehowski, Y. Wang, T.L. Fillmore, R. Zhao, and R.J. Moore, et al. 2019. "Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples." Analytical Chemistry 91, no. 15:9707-9715. PNNL-SA-141437. doi:10.1021/acs.analchem.9b01248
  • Dou M., G. Clair, C. Tsai, K. Xu, W.B. Chrisler, R.L. Sontag, and R. Zhao, et al. 2019. "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform." Analytical Chemistry 91, no. 20:13119-13127. PNNL-SA-146297. doi:10.1021/acs.analchem.9b03349
  • Moghieb A.M., L. Tesfay, S. Nie, M.A. Gritsenko, T.L. Fillmore, J.M. Jacobs, and R.D. Smith, et al. 2019. "A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification." Scientific Reports 9, no. 1:Article No. 7264. PNNL-SA-138022. doi:10.1038/s41598-019-43756-9
  • Nagarajan A., M. Zhou, A.Y. Nguyen, M.L. Liberton, K. Kedia, T. Shi, and P.D. Piehowski, et al. 2019. "Proteomic insights into phycobilisome degradation, a selective and tightly controlled process in the fast growing cyanobacterium Synechococcus elongatus UTEX 2973." Biomolecules 9, no. 8:Article Number 374. PNNL-SA-146394. doi:10.3390/biom9080374
  • Tsai C., J.S. Smith, K. Krajewski, R. Zhao, A.M. Moghieb, C.D. Nicora, and X. Xiong, et al. 2019. "Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides." Analytical Chemistry 91, no. 18:11606-11613. PNNL-SA-142808. doi:10.1021/acs.analchem.9b01814
  • Wu H., L. Yi, R. Wojcik, T. Shi, and K. Tang. 2019. "A Separation Voltage Polarity Switching Method for Higher Sample Loading Capacity and Better Separation Resolution in Transient Capillary Isotachophoresis Separation." Analyst 144, no. 2:454-462. PNNL-SA-135251. doi:10.1039/C8AN01779D
  • Yi L., C. Tsai, E. Dirice, A.C. Swensen, J. Chen, T. Shi, and M.A. Gritsenko, et al. 2019. "Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells." Analytical Chemistry 91, no. 9:5794-5801. PNNL-SA-140381. doi:10.1021/acs.analchem.9b00024
  • Zhang P., M.J. Gaffrey, Y. Zhu, W.B. Chrisler, T.L. Fillmore, L. Yi, and C.D. Nicora, et al. 2019. "Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells." Analytical Chemistry 91, no. 2:1441-1451. PNNL-SA-138130. doi:10.1021/acs.analchem.8b04258


  • Chouinard C.D., G. Nagy, I.K. Webb, T. Shi, E.M. Baker, S.A. Prost, and T. Liu, et al. 2018. "Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry." Analytical Chemistry 90, no. 18:10889-10896. PNNL-SA-135107. doi:10.1021/acs.analchem.8b02397
  • 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
  • Shi T., M.J. Gaffrey, T.L. Fillmore, C.D. Nicora, L. Yi, P. Zhang, and A.K. Shukla, et al. 2018. "Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells." Communications Biology 1, no. 1:Article No. 103. PNNL-SA-130600. doi:10.1038/s42003-018-0107-6
  • Yi L., T. Shi, M.A. Gritsenko, C. Chan, T.L. Fillmore, B.M. Hess, and A.C. Swensen, et al. 2018. "Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway." Analytical Chemistry 90, no. 8:5256-5263. PNNL-SA-131519. doi:10.1021/acs.analchem.8b00071
  • 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


  • Nie S., T. Shi, T.L. Fillmore, A.A. Schepmoes, H.M. Brewer, Y. Gao, and E. Song, et al. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89, no. 17:9139-9146. PNNL-SA-126297. doi:10.1021/acs.analchem.7b01878
  • Shi T., S. Quek, Y. Gao, C.D. Nicora, S. Nie, T.L. Fillmore, and T. Liu, et al. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8, no. 60:101887-101898. PNNL-SA-128413. doi:10.18632/oncotarget.21710
  • Song E., Y. Gao, C. Wu, T. Shi, S. Nie, T.L. Fillmore, and A.A. Schepmoes, et al. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer." Scientific Data. PNNL-SA-122408. doi:10.1038/sdata.2017.91
  • Wang H., C.E. Barbieri, J. He, Y. Gao, T. Shi, C. Wu, and A.A. Schepmoes, et al. 2017. "Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics." Journal of Translational Medicine 15. PNNL-SA-125993. doi:10.1186/s12967-017-1276-7
  • Yi L., P.D. Piehowski, T. Shi, R.D. Smith, and W. Qian. 2017. "Advances in Microscale Separations towards Nanoproteomics Applications." Journal of Chromatography A 1523. PNNL-SA-125498. doi:10.1016/j.chroma.2017.07.055


  • 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 & Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
  • Hoofnagle A.N., J.R. Whiteaker, S.A. Carr, E. Kuhn, T. Liu, S.A. Massoni, and S.N. Thomas, et al. 2016. "Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays." Clinical Chemistry 62, no. 1:48-69. PNNL-SA-113208. doi:10.1373/clinchem.2015.250563
  • Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations." Journal of Clinical Endocrinology and Metabolism 101, no. 5:2226-2234. PNNL-SA-120076. doi:10.1210/jc.2016-1104
  • Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations." The New England Journal of Medicine 374, no. 17:1695-1696. PNNL-SA-108708. doi:10.1056/NEJMc1513502
  • Shi T., E. Song, S. Nie, K.D. Rodland, T. Liu, W. Qian, and R.D. Smith. 2016. "Advances in targeted proteomics and applications to biomedical research." Proteomics 16, no. 15-16:2160-2182. PNNL-SA-120776. doi:10.1002/pmic.201500449
  • 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
  • Sigdel T.K., Y. Gao, J. He, A. Wang, C.D. Nicora, T.L. Fillmore, and T. Shi, et al. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury." Kidney International 89, no. 6:1244-1252. PNNL-SA-115293. doi:10.1016/j.kint.2015.12.049
  • Wang H., T. Shi, W. Qian, T. Liu, J. Kagan, S. Srivastava, and R.D. Smith, et al. 2016. "The Clinical Impact of Recent Advances in LC-MS for Cancer Biomarker Discovery and Verification." Expert Review of Proteomics 13, no. 1:99-114. PNNL-SA-113659. doi:10.1586/14789450.2016.1122529


  • He J., A.A. Schepmoes, T. Shi, C. Wu, T.L. Fillmore, Y. Gao, and R.D. Smith, et al. 2015. "Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods." Journal of Translational Medicine 13. PNNL-SA-107827. doi:10.1186/s12967-015-0418-z


  • 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
  • Shi T., Y. Gao, M.J. Gaffrey, C.D. Nicora, T.L. Fillmore, W.B. Chrisler, and M.A. Gritsenko, et al. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87, no. 2:1103-1110. PNNL-SA-103421. doi:10.1021/ac503797x
  • Shi T., Y. Gao, S. Quek, T.L. Fillmore, C.D. Nicora, D. Su, and R. Zhao, et al. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13, no. 2:875-882. PNWD-SA-10119. doi:10.1021/pr400912c
  • Wu C., T. Shi, J.N. Brown, J. He, Y. Gao, T.L. Fillmore, and A.K. Shukla, et al. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13, no. 10:4479-87. PNNL-SA-102906. doi:10.1021/pr500500d


  • Shi T., and W. Qian. 2013. "Antibody-free PRISM-SRM for multiplexed protein quantification: Is this the new competition for immunoassays in bioanalysis?." Bioanalysis 5, no. 3:267-269. PNNL-SA-92465. doi:10.4155/bio.12.336
  • Shi T., T.L. Fillmore, Y. Gao, R. Zhao, J. He, A.A. Schepmoes, and C.D. Nicora, et al. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85, no. 19:9196-9203. PNNL-SA-96700. doi:10.1021/ac402105s
  • Shi T., X. Sun, Y. Gao, T.L. Fillmore, A.A. Schepmoes, R. Zhao, and J. He, et al. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12, no. 7:3353-3361. PNNL-SA-92544. doi:10.1021/pr400178v
  • 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


  • Liu T., M. Hossain, A.A. Schepmoes, T.L. Fillmore, L.J. Sokoll, S.R. Kronewitter, and G. Izmirlian, et al. 2012. "Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests." Journal of Proteomics 75, no. 15:4747-4757. PNNL-SA-83777. doi:10.1016/j.jprot.2012.01.035
  • Shi T., D. Su, T. Liu, K. Tang, D.G. Camp, W. Qian, and R.D. Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics 12, no. 8:1074-1092. PNNL-SA-82133. doi:10.1002/pmic.201100436
  • Shi T., J. Zhou, M.A. Gritsenko, M. Hossain, D.G. Camp, R.D. Smith, and W. Qian. 2012. "IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery." Methods 56, no. 2:246-253. PNNL-SA-80317. doi:10.1016/j.ymeth.2011.09.001
  • Shi T., T.L. Fillmore, X. Sun, R. Zhao, A.A. Schepmoes, M. Hossain, and F. Xie, et al. 2012. "Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America 109, no. 38:15395-15400. PNNL-SA-83776. doi:10.1073/pnas.1204366109
  • Zhou J., G.P. Dann, T. Shi, L. Wang, X. Gao, D. Su, and C.D. Nicora, et al. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84, no. 6:2862-2867. PNNL-SA-84751. doi:10.1021/ac203394r

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