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Biological Sciences Staff information

Anil Shukla

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

PNNL Publications


  • Dautel SE, JE Kyle, GCD Clair, RL Sontag, KK Weitz, AK Shukla, SN Nguyen, YM Kim, EM Zink, T Luders, C Frevert, SA Gharib, J Laskin, JP Carson, TO Metz, RA Corley, and CK Ansong. 2017. "Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung." Scientific Reports 7:Article No. 40555.  doi:10.1038/srep40555
  • Eisfeld AJ, P Halfmann, JP Wendler, JE Kyle, KE Burnum-Johnson, Z Peralta, T Maemura, KB Walters, T Watanabe, S Fukuyama, M Yamashita, JM Jacobs, YM Kim, CP Casey, KG Stratton, BJM Webb-Robertson, MA Gritsenko, ME Monroe, KK Weitz, AK Shukla, M Tian, G Neumann, JL Reed, H van Bakel, TO Metz, RD Smith, KM Waters, A N'jai, F Sahr, and Y Kawaoka. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22(6):817-829.  doi:10.1016/j.chom.2017.10.011
  • Park JK, PD Piehowski, CS Wilkins, M Zhou, JA Mendoza, GM Fujimoto, BC Gibbons, JB Shaw, Y Shen, AK Shukla, RJ Moore, T Liu, VA Petyuk, N Tolic, L Pasa Tolic, RD Smith, SH Payne, and S Kim. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14(9):909-914.  doi:10.1038/nmeth.4388
  • Shen Y, N Tolic, PD Piehowski, AK Shukla, S Kim, R Zhao, Y Qu, EW Robinson, RD Smith, and L Pasa-Tolic. 2017. "High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics." Journal of Chromatography A 1498:99-110.  doi:10.1016/j.chroma.2017.01.008
  • Shen Y, N Tolic, PD Piehowski, AK Shukla, S Kim, R Zhao, Y Qu, EW Robinson, RD Smith, and L Pasa-Tolic. 2017. "High-Resolution Ultrahigh-PressurePhase Liquid Chromatography for To Long Column Reversed-p-Down Proteomics." Journal of Chromatography A 1498:99-110.  doi:10.1016/j.chroma.2017.01.008
  • Smith JN, KJ Tyrrell, JR Hansen, DG Thomas, TA Murphree, AK Shukla, T Luders, JM Madden, Y Li, AT Wright, and PD 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.  doi:10.1021/acs.analchem.7b03984
  • Stoddard EG, BJ Killinger, RN Nair, NC Sadler, RF Volk, SO Purvine, AK Shukla, JN Smith, and AT Wright. 2017. "Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S- Transferases." Journal of the American Chemical Society 139(45):16032-16035.  doi:10.1021/jacs.7b07378
  • Wang S, F Yang, VA Petyuk, AK Shukla, ME Monroe, MA Gritsenko, KD Rodland, RD Smith, W Qian, CX Gong, and T Liu. 2017. "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease." The Journal of Pathology 243(1):78-88.  doi:10.1002/path.4929


  • Ahmad R, CD Nicora, AK Shukla, RD Smith, W Qian, and AY Liu. 2016. "An efficient method for native protein purification in the selected range from prostate cancer tissue digests." Chinese Clinical Oncology 5(6):78.  doi:10.21037/cco.2016.12.03
  • Burnum-Johnson KE, S Nie, CP Casey, ME Monroe, DJ Orton, YM Ibrahim, MA Gritsenko, TRW Clauss, AK Shukla, RJ Moore, SO Purvine, T Shi, W Qian, T Liu, ES Baker, and RD Smith. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15(12):3694-3705.  doi:10.1074/mcp.M116.061143
  • Hatakeyama H, SY Wu, YA Lyons, S Pradeep, W Wang, Q Huang, KA Court, T Liu, S Nie, C Rodriguez-Aguayo, F Shen, Y Huang, T Hisamatsu, T Mitamura, N Jennings, J Shim, PL Dornialk, LS Mangala, M Petrillo, VA Petyuk, AA Schepmoes, AK Shukla, M Torres-Lugo, JS Lee, KD Rodland, A Fagotti, G Lopez-Bernstein, C Li, and AK Sood. 2016. "Role of CTGF in Sensitivity to Hyperthermia in Ovarian and Uterine Cancers." Cell Reports 17(6):1621-1631.  doi:10.1016/j.celrep.2016.10.020
  • Nakayasu ES, CD Nicora, AC Sims, KE Burnum-Johnson, YM Kim, JE Kyle, MM Matzke, AK Shukla, RK Chu, AA Schepmoes, JM Jacobs, R Baric, BJM Webb-Robertson, RD Smith, and TO Metz. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1(3):e00043-16.  doi:10.1128/mSystems.00043-16
  • Shukla AK. 2016. "Dissociation of Doubly Charged Clusters of Lithium Acetate: Asymmetric Fission and Breakdown of the Liquid Drop Model." Rapid Communications in Mass Spectrometry 30(13):1576-1580.  doi:10.1002/rcm.7597


  • Shukla AK, and B Bogdanov. 2015. "Lithium Formate Ion Clusters Formation during Electrospray Ionization: Evidence of Magic Number Clusters by Mass Spectrometry and ab initio Calculations." Journal of Chemical Physics 142(6):Article No. 064304.  doi:10.1063/1.4907366
  • Touchette MH, GR Bommineni, RJ Delle Bovi, J Gadbery, CD Nicora, AK Shukla, JE Kyle, TO Metz, DW Martin, NS Sampson, WT Miller, PJ Tonge, and JC Seeliger. 2015. "Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl ß-Diol Lipids." Biochemistry 54(35):5457-5468.  doi:10.1021/acs.biochem.5b00455


  • Cox JT, SR Kronewitter, AK Shukla, RJ Moore, RD Smith, and K Tang. 2014. "High Sensitivity Combined with Extended Structural Coverage of Labile Compounds via Nanoelectrospray Ionization at Subambient Pressures." Analytical Chemistry 86(19):9504-9511.  doi:10.1021/ac502767y
  • Aevermann B, BE Pickett, S Kumar, EB Klem, S Agnihothram, PS Askovich, A Bankhead, M Bolles, V Carter, JH Chang, TRW Clauss, P Dash, AH Diercks, AJ Eisfeld, AL Ellis, S Fan, MT Ferris, L Gralinski, R Green, MA Gritsenko, M Hatta, RA Heegel, JM Jacobs, S Jeng, L Josset, SM Kaiser, S Kelly, GL Law, C Li, J Li, C Long, ML Luna, MM Matzke, JE McDermott, V Menachery, TO Metz, HD Mitchell, ME Monroe, G Navarro, G Neumann, RL Podyminogin, SO Purvine, C Rosenberger, CJ Sanders, AA Schepmoes, AK Shukla, A Sims, P Sova, VC Tam, N Tchitchek, PG Thomas, SC Tilton, AL Totura, J Wang, BJM Webb-Robertson, J Wen, JM Weiss, F Yang, B Yount, Q Zhang, SK Mcweeney, RD Smith, KM Waters, Y Kawaoka, R Baric, A Aderem, MG Katze, and RH Scheuermann. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1:Article No. 140033.  doi:10.1038/sdata.2014.33
  • Kronewitter SR, I Marginean, JT Cox, R Zhao, CD Hagler, AK Shukla, TS Carlson, JN Adkins, DG Camp, II, RJ Moore, KD Rodland, and RD Smith. 2014. "Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and Electrospray ionization-mass spectrometry." Analytical Chemistry 86(17):8700-10.  doi:10.1021/ac501839b
  • Menachery V, AJ Eisfeld, A Schafer, L Josset, AC Sims, S Proll, S Fan, C Li, G Neumann, SC Tilton, JH Chang, L Gralinski, C Long, R Green, CM Williams, JM Weiss, MM Matzke, BJM Webb-Robertson, AA Schepmoes, AK Shukla, TO Metz, RD Smith, KM Waters, MG Katze, Y Kawaoka, and R Baric. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5(3):Article No. e01174-14.  doi:10.1128/mBio.01174-14
  • Nakayasu ES, S Wu, MA Sydor, AK Shukla, KK Weitz, RJ Moore, KK Hixson, JS Kim, VA Petyuk, ME Monroe, L Pasa-Tolic, W Qian, RD Smith, JN Adkins, and C Ansong. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014:Article No. 730725.  doi:10.1155/2014/730725
  • Vijayakumar M, N Govind, ED Walter, SD Burton, AK Shukla, A Devaraj, J Xiao, J Liu, CM Wang, AM Karim, and S Thevuthasan. 2014. "Molecular Structure and Stability of Dissolved Lithium Polysulfide Species." Physical Chemistry Chemical Physics. PCCP 16(22):10923-10932.  doi:10.1039/c4cp00889H
  • Webb-Robertson BJM, MM Matzke, S Datta, SH Payne, J Kang, LM Bramer, CD Nicora, AK Shukla, TO Metz, KD Rodland, RD Smith, MF Tardiff, JE McDermott, JG Pounds, and KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12):3639-3646.  doi:10.1074/mcp.M113.030932
  • Wu C, T Shi, JN Brown, J He, Y Gao, TL Fillmore, AK Shukla, RJ Moore, DG Camp, II, KD Rodland, W Qian, T Liu, and RD Smith. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13(10):4479-87.  doi:10.1021/pr500500d


  • Shukla AK. 2013. "Ion Collision, Theory." In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, ed. J Reedijk, et al.  Elsevier, Waltham, MA. 
  • Ansong C, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, AR Ollodart, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1):123-133.  doi:10.1016/j.chembiol.2012.11.008
  • Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman. 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(4):1070-1077.  doi:10.1128/AEM.02864-12
  • Dai Z, UK Aryal, AK Shukla, W Qian, RD Smith, JK Magnuson, WS Adney, GT Beckham, R Brunecky, ME Himmel, SR Decker, X Ju, X Zhang, and SE Baker. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61:120-132.  doi:10.1016/j.fgb.2013.09.004
  • Gralinski L, A Bankhead, S Jeng, V Menachery, S Proll, S Belisle, MM Matzke, BJM Webb-Robertson, ML Luna, AK Shukla, MT Ferris, M Bolles, JH Chang, LD Aicher, KM Waters, RD Smith, TO Metz, GL Law, MG Katze, SK Mcweeney, and R Baric. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4(4):Article No. e00271-13.  doi:10.1128/mBio.00271-13
  • Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJM Webb-Robertson. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13(3-4):493-503.  doi:10.1002/pmic.201200269
  • Mitchell HD, AJ Eisfeld, A Sims, JE McDermott, MM Matzke, BJM Webb-Robertson, SC Tilton, N Tchitchek, L Josset, C Li, AL Ellis, JH Chang, RA Heegel, ML Luna, AA Schepmoes, AK Shukla, TO Metz, G Neumann, A Benecke, RD Smith, R Baric, Y Kawaoka, MG Katze, and KM Waters. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8(7):e69374.  doi:10.1371/journal.pone.0069374
  • Sims AC, SC Tilton, V Menachery, L Gralinski, A Schafer, MM Matzke, BJM Webb-Robertson, JH Chang, ML Luna, C Long, AK Shukla, A Bankhead, S Burkett, G Zornester, CK Tseng, TO Metz, R Pickles, SK Mcweeney, RD Smith, MG Katze, KM Waters, and R Baric. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87(7):3885-902.  doi:10.1128/JVI.02520-12
  • Su D, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, II, DJ Bigelow, RD Smith, RN Kulkarni, and W Qian. 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 57:68-78.  doi:10.1016/j.freeradbiomed.2012.12.010
  • Wiedner SD, C Ansong, BJM Webb-Robertson, LM Pederson, S Fortuin, BA Hofstad, AK Shukla, EA Panisko, RD Smith, and AT Wright. 2013. "Disparate Proteome Responses of Pathogenic and Non-pathogenic Aspergilli to Human Serum Measured by Activity-Based Protein Profiling (ABPP)." Molecular & Cellular Proteomics. MCP 12(7):1791-1805.  doi:10.1074/mcp.M112.026534
  • Wu S, RN Brown, SH Payne, D Meng, R Zhao, N Tolic, L Cao, AK Shukla, ME Monroe, RJ Moore, MS Lipton, and L Pasa-Tolic. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans ." International Journal of Proteomics 2013:279590.  doi:10.1155/2013/279590


  • Angel TE, JM Jacobs, RP Smith, MS Pasternack, S Elias, MA Gritsenko, AK Shukla, EC Gilmore, C McCarthy, DG Camp, II, and RD Smith. 2012. "Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease." Journal of Proteome Research 11(10):4814-4822.  doi:10.1021/pr300577p
  • Brown JN, GM Ortiz, TE Angel, JM Jacobs, MA Gritsenko, EY Chan, DE Purdy, RD Murnane, K Larsen, RE Palermo, AK Shukla, TRW Clauss, MG Katze, JM McCune, and RD Smith. 2012. "Morphine Produces Immunosuppressive Effects in Non-human Primates at the Proteomic and Cellular Levels." Molecular & Cellular Proteomics. MCP 11(9):605-618.  doi:10.1074/mcp.M111.016121
  • Wiedner SD, KE Burnum, LM Pederson, LN Anderson, S Fortuin, LM Chauvigne-Hines, AK Shukla, C Ansong, EA Panisko, RD Smith, and AT Wright. 2012. "Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum." Journal of Biological Chemistry 287(40):33447-33459.  doi:10.1074/jbc.M112.394106
  • Wiedner SD, KE Burnum, LM Pederson, LN Anderson, S Fortuin, LM Chauvigne-Hines, AK Shukla, C Ansong, EA Panisko, RD Smith, and AT Wright. 2012. "Multiplexed Activity-Based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes Upon Exposure to Human Serum." Journal of Biological Chemistry 287(40):33447-33459.  doi:10.1074/jbc.M112.394106
  • Zhou J, GP Dann, T Shi, L Wang, X Gao, D Su, CD Nicora, AK Shukla, RJ Moore, T Liu, DG Camp, II, RD Smith, and W Qian. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84(6):2862-2867.  doi:10.1021/ac203394r


  • Shukla AK, R Zhang, DJ Orton, R Zhao, TRW Clauss, RJ Moore, and RD Smith. 2011. "Formation of iron complexs from trifluoroacetic acid based liquid chromatography mobile phases as interference ions in liquid chromatography/electrospray ionization mass spectrometric analysis." Rapid Communications in Mass Spectrometry 25(10):1452-1456.  doi:10.1002/rcm.5017


  • Rezayat T, and AK Shukla. 2007. "Dissociative Scattering of Hyperthermal Energy CF3+ Ions from Modified Surfaces." Journal of Chemical Physics 126(8):Art. No. 084701.  doi:10.1063/1.2484290
  • Rezayat T, and AK Shukla. 2007. "Evidence for the Bulk Nature of Self-Assembled Monolayer Surface of Fluorinated Alkyl Thiol from Hyperthermal Energy Ion-Surface Collisions." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 264(2):400-403.  doi:10.1016/j.nimb.2007.08.083
  • Shukla AK. 2007. "Bimodal Energy Distributions in the Scattering of Ar+ Ions from Modified Surfaces at Hyperthermal Energies." Chemical Physics Letters 449(1-3):53-56.  doi:10.1016/j.cplett.2007.10.043
  • Shukla AK. 2007. "Fragmentation dynamics of CS22+ on collision with a self assembled monolayer surface." Chemical Physics Letters 448(4-6):156-158.  doi:10.1016/j.cplett.2007.09.083


  • Rezayat T, and AK Shukla. 2004. "Hyperthermal Energy Collisions of CF3+ Ions With Modified Surfaces: Surface-Induced Dissociation." Journal of Undergraduate Research Volume IV, 2004:98-103. 


  • Laskin J, JH Futrell, and AK Shukla. 2003. "Surface-Induced Dissociation of Peptide Ions: Kinetics and Dynamics." Journal of the American Society for Mass Spectrometry 14(12):1340-1347. 
  • Shukla AK, JH Futrell, and A Sen. 2003. "Dynamics of the Dissociative and Non-dissociative Scattering of Hyperthermal CS2+ from a Self-Assembled Fluoroalkyl Monolayer Surface on Gold Substrate." Journal of Chemical Physics 118(24):11217-11225.  doi:DOI:10.1063/1.1574311
  • Shukla AK, and JH Futrell. 2003. ""Surface-Induced Dissociation of Acetone Cations from Self-Assembled Monolayer Surface of Flourinated Alkyl Thiol on Au (111) Substrate at Low Collision Energies"." International Journal of Mass Spectrometry 228(2-3):563-576. 
  • Shukla AK, and JH Futrell. 2003. "A Beam Scattering Instrument for the Dynamics Studies of Surface-Induced Dissociation Processes." Review of Scientific Instruments 74(1):168-175. 
  • Shukla AK, and JH Futrell. 2003. "Dynamics of Hyperthermal Energy Ion-Surface Collisions: Dissociative and non-dissociative Scattering of Ethanol cations from a Self-Assembled Monolayer Surface of Fluorinated Alkyl Thiol on Au (111)." International Journal of Mass Spectrometry 223(1-3):783-801. 


  • Laskin J, E Denisov, AK Shukla, SE Barlow, and JH Futrell. 2002. "Surface-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer: Instrument design and evaluation." Analytical Chemistry 74:3255-3261. 


  • Shukla AK, and JH Futrell. 2000. "Tandem Mass Spectrometry: Dissociation of Ions by Collisional Activation." Journal of Mass Spectrometry 35(9):1069-1090. 

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