Anil Shukla

Anil Shukla
Staff Member Title: 
Chief Scientist
Phone: 
(509) 371-6239
Contact Email: 
Anil.Shukla@pnnl.gov
Overview: 

[ Ion Dissociation by Collisional Activation : We have constructed a sector/quadrupole tandem hybrid mass spectrometer to study the energetics and dissociation dynamics of low energy ions from collision with a surface. Primary ion beam energy can be varied from a few eV to several hundred eV and energy/ intensity distributions of scattered ions (primary and fragments) can be measured by rotating the detector assembly (energy analyzer, quadrupole mass filter and electron multiplier) with respect to the collosion center. The role played by various parameters in enhancing dissociation efficiency will be explored before extending dynamics studies to small peptides. Surface-Induced Dissociation in the FT-ICR MS: A high-sensitivity FT-ICR mass spectrometer has been constructed using a 6-Tesla superconducting magnet to perform SID studies on singly and multiply charged peptides formed by electrospray ionization. Collisional activation with a surface has significant advantages over collision with a neutral gas because of increased efficiency of energy transfer and lower pressure in the ICR cell enabling to perform experiments at higher resolution and reduced acquisition times for MS/MS experiments.]

Details: 

Research Associate III, University of Delaware, 1986 - 1992 Associate Scientist, University of Delaware, 1992 - 1999

Education: 

Ph. D. Southampton University, U.K., 1982 M. Sc. Kanpur University (Christ Church College, Kanpur), India, 1971 B. Sc. Agra University (Swami Shukdevanand College, Shahjahanpur), India, 1969

Awards & Honors: 

Southampton University Research Scholarship, 1978 - 1981 National Scholarship, 1969 - 1971 Merit Scholarship, Agra University, 1967 - 1969

Research Interests: 

[Tandem Mass Spectrometry (MS/MS): Kinematics and Dynamics of collision-induced dissociation and surface-induced dissociation processes in singly and multiply charged ions of energies from eV to keV. Ion-Molecule Reactions at Low collision Energies: Charge transfer and inelastic scattering. Gaseous Clusters and Supersonic Molecular Beams: Cluster formation by supersonic expansion and electrospray ionization. Instrumentation: Instrumental development related to tandem mass spectrometry studies, supersonic molecular beams.]

Publications

2016

  • ES Nakayasu, 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, TO Metz. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1(3)e00043-16. 10.1128/mSystems.00043-16

2015

  • AK Shukla, 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. 10.1063/1.4907366
  • MH Touchette, GR Bommineni, RJ Delle Bovi, J Gadbery, CD Nicora, AK Shukla, JE Kyle, TO Metz, DW Martin, NS Sampson, WT Miller, PJ Tonge, JC Seeliger. 2015. "Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids." Biochemistry 54(35)5457-5468. 10.1021/acs.biochem.5b00455

2014

  • M Vijayakumar, N Govind, ED Walter, SD Burton, AK Shukla, A Devaraj, J Xiao, J Liu, CM Wang, AM Karim, S Thevuthasan. 2014. "Molecular Structure and Stability of Dissolved Lithium Polysulfide Species." Physical Chemistry Chemical Physics. PCCP 16(22)10923-10932. 10.1039/c4cp00889H
  • C Wu, T Shi, JN Brown, J He, Y Gao, TL Fillmore, AK Shukla, RJ Moore, DG Camp, KD Rodland, W Qian, T Liu, RD Smith. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13(10)4479-87. 10.1021/pr500500d
  • ES Nakayasu, 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, C Ansong. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014Article No. 730725. 10.1155/2014/730725
  • JT Cox, SR Kronewitter, AK Shukla, RJ Moore, RD Smith, 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. 10.1021/ac502767y
  • SR Kronewitter, I Marginean, JT Cox, R Zhao, CD Hagler, AK Shukla, TS Carlson, JN Adkins, DG Camp, RJ Moore, KD Rodland, 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. 10.1021/ac501839b
  • B Aevermann, 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, RH Scheuermann. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1Article No. 140033. 10.1038/sdata.2014.33
  • V Menachery, 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, 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. 10.1128/mBio.01174-14
  • BJM Webb-Robertson, 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, KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12)3639-3646. 10.1074/mcp.M113.030932

2013

  • Z Dai, UK Aryal, AK Shukla, W Qian, RD Smith, JK Magnuson, WS Adney, GT Beckham, R Brunecky, ME Himmel, SR Decker, X Ju, X Zhang, 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 61120-132. 10.1016/j.fgb.2013.09.004
  • UK Aryal, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, 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. 10.1128/AEM.02864-12
  • S Wu, RN Brown, SH Payne, D Meng, R Zhao, N Tolic, L Cao, AK Shukla, ME Monroe, RJ Moore, MS Lipton, L Pasa-Tolic. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans ." International Journal of Proteomics 2013279590. 10.1155/2013/279590
  • C Ansong, 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, AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1)123-133. 10.1016/j.chembiol.2012.11.008
  • AC Sims, 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, 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. 10.1128/JVI.02520-12
  • L Gralinski, 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, R Baric. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury.." mBio 4(4)Article No. e00271-13. 10.1128/mBio.00271-13
  • MM Matzke, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, 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. 10.1002/pmic.201200269
  • D Su, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, DJ Bigelow, RD Smith, RN Kulkarni, 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 5768-78. 10.1016/j.freeradbiomed.2012.12.010
  • SD Wiedner, C Ansong, BJM Webb-Robertson, LM Pederson, S Fortuin, BA Hofstad, AK Shukla, EA Panisko, RD Smith, 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. 10.1074/mcp.M112.026534
  • HD Mitchell, 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, 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. 10.1371/journal.pone.0069374

2012

  • J Zhou, GP Dann, T Shi, L Wang, X Gao, D Su, CD Nicora, AK Shukla, RJ Moore, T Liu, DG Camp, RD Smith, W Qian. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84(6)2862-2867. 10.1021/ac203394r
  • TE Angel, JM Jacobs, RP Smith, MS Pasternack, S Elias, MA Gritsenko, AK Shukla, EC Gilmore, C McCarthy, DG Camp, RD Smith. 2012. "Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease." Journal of Proteome Research 11(10)4814-4822. 10.1021/pr300577p
  • JN Brown, 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, 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. 10.1074/mcp.M111.016121
  • SD Wiedner, KE Burnum, LM Pederson, LN Anderson, S Fortuin, LM Chauvigne-Hines, AK Shukla, C Ansong, EA Panisko, RD Smith, 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. 10.1074/jbc.M112.394106

2011

  • AK Shukla, R Zhang, DJ Orton, R Zhao, TRW Clauss, RJ Moore, 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. 10.1002/rcm.5017

2007

  • T Rezayat, AK Shukla. 2007. "Dissociative Scattering of Hyperthermal Energy CF3+ Ions from Modified Surfaces." Journal of Chemical Physics 126(8)Art. No. 084701. 10.1063/1.2484290
  • T Rezayat, 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. 10.1016/j.nimb.2007.08.083

2004

  • T Rezayat, AK Shukla. 2004. "Hyperthermal Energy Collisions of CF3+ Ions With Modified Surfaces: Surface-Induced Dissociation." Journal of Undergraduate Research Volume IV, 200498-103.

2003

  • AK Shukla, JH Futrell, 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:10.1063/1.1574311
  • AK Shukla, JH Futrell. 2003. "A Beam Scattering Instrument for the Dynamics Studies of Surface-Induced Dissociation Processes." Review of Scientific Instruments 74(1)168-175.
  • AK Shukla, 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.
  • AK Shukla, 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.

2002

  • J Laskin, E Denisov, AK Shukla, SE Barlow, JH Futrell. 2002. "Surface-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer: Instrument design and evaluation." Analytical Chemistry 743255-3261.

2000

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