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    Scott A Shaffer PhD

    TitleResearch Professor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentBiochemistry and Molecular Pharmacology
    AddressUniversity of Massachusetts Medical School
    222 Maple Avenue
    Shrewsbury MA 01545
    Phone508-856-8917
      Other Positions
      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBiochemistry and Molecular Pharmacology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

        Overview 
        Narrative
        Director, UMMS Proteomics and Mass Spectrometry Facility

        Dr.  Scott Shaffer



        Bibliographic 
        selected publications
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        1. Sullivan DA, Liu Y, Kam WR, Ding J, Green KM, Shaffer SA, Hatton MP, Liu S. Serum-induced differentiation of human meibomian gland epithelial cells. Invest Ophthalmol Vis Sci. 2014; 55(6):3866-77.
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        2. Ambade A, Catalano D, Lim A, Kopoyan A, Shaffer SA, Mandrekar P. Pharmacological Inhibition of Heat Shock Protein 90 Alleviates Steatosis and Macrophage Activation in Murine Acute and Chronic Alcoholic Liver Injury. J Hepatol. 2014 May 22.
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        3. Valencia A, Sapp E, Kimm JS, McClory H, Ansong KA, Yohrling G, Kwak S, Kegel KB, Green KM, Shaffer SA, Aronin N, Difiglia M. Striatal Synaptosomes from Hdh(140Q/140Q) Knock-in Mice have Altered Protein Levels, Novel Sites of Methionine Oxidation, and Excess Glutamate Release after Stimulation. J Huntingtons Dis. 2013 Oct 1; 2(4):459-475.
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        4. Jones KA, Kim PD, Patel BB, Kelsen SG, Braverman A, Swinton DJ, Gafken PR, Jones LA, Lane WS, Neveu JM, Leung HC, Shaffer SA, Leszyk JD, Stanley BA, Fox TE, Stanley A, Hall MJ, Hampel H, South CD, de la Chapelle A, Burt RW, Jones DA, Kopelovich L, Yeung AT. Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers. J Proteome Res. 2013 Oct 4; 12(10):4351-65.
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        5. Deligiannidis KM, Sikoglu EM, Shaffer SA, Frederick B, Svenson AE, Kopoyan A, Kosma CA, Rothschild AJ, Moore CM. GABAergic neuroactive steroids and resting-state functional connectivity in postpartum depression: a preliminary study. J Psychiatr Res. 2013 Jun; 47(6):816-28.
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        6. Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST. Interlaboratory studies and initiatives developing standards for proteomics. Proteomics. 2013 Mar; 13(6):904-9.
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        7. Zhao C, Gao Q, Roberts AG, Shaffer SA, Doneanu CE, Xue S, Goodlett DR, Nelson SD, Atkins WM. Cross-linking mass spectrometry and mutagenesis confirm the functional importance of surface interactions between CYP3A4 and holo/apo cytochrome b(5). Biochemistry. 2012 Nov 27; 51(47):9488-500.
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        8. Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell. 2012 Nov 9; 151(4):750-64.
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        9. Rudra D, deRoos P, Chaudhry A, Niec RE, Arvey A, Samstein RM, Leslie C, Shaffer SA, Goodlett DR, Rudensky AY. Transcription factor Foxp3 and its protein partners form a complex regulatory network. Nat Immunol. 2012 Oct; 13(10):1010-9.
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        10. Paquette N, Conlon J, Sweet C, Rus F, Wilson L, Pereira A, Rosadini CV, Goutagny N, Weber AN, Lane WS, Shaffer SA, Maniatis S, Fitzgerald KA, Stuart L, Silverman N. Serine/threonine acetylation of TGFß-activated kinase (TAK1) by Yersinia pestis YopJ inhibits innate immune signaling. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12710-5.
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        11. Xie J, Peng M, Guillemette S, Quan S, Maniatis S, Wu Y, Venkatesh A, Shaffer SA, Brosh RM, Cantor SB. FANCJ/BACH1 acetylation at lysine 1249 regulates the DNA damage response. PLoS Genet. 2012 Jul; 8(7):e1002786.
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        12. Li Y, Powell DA, Shaffer SA, Rasko DA, Pelletier MR, Leszyk JD, Scott AJ, Masoudi A, Goodlett DR, Wang X, Raetz CR, Ernst RK. LPS remodeling is an evolved survival strategy for bacteria. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8716-21.
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        13. Keeler AM, Conlon T, Walter G, Zeng H, Shaffer SA, Dungtao F, Erger K, Cossette T, Tang Q, Mueller C, Flotte TR. Long-term correction of very long-chain acyl-coA dehydrogenase deficiency in mice using AAV9 gene therapy. Mol Ther. 2012 Jun; 20(6):1131-8.
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        14. Foss EJ, Radulovic D, Shaffer SA, Goodlett DR, Kruglyak L, Bedalov A. Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol. 2011 Sep; 9(9):e1001144.
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        15. Thatcher JE, Buttrick B, Shaffer SA, Shimshoni JA, Goodlett DR, Nelson WL, Isoherranen N. Substrate specificity and ligand interactions of CYP26A1, the human liver retinoic acid hydroxylase. Mol Pharmacol. 2011 Aug; 80(2):228-39.
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        16. Ting YS, Shaffer SA, Jones JW, Ng WV, Ernst RK, Goodlett DR. Automated lipid A structure assignment from hierarchical tandem mass spectrometry data. J Am Soc Mass Spectrom. 2011 May; 22(5):856-66.
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        17. Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR. Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem. 2011 Mar 15; 83(6):2250-7.
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        18. Chu LJ, Chen MC, Setter J, Tsai YS, Yang H, Fang X, Ting YS, Shaffer SA, Taylor GK, von Haller PD, Goodlett DR, Ng WV. New structural proteins of Halobacterium salinarum gas vesicle revealed by comparative proteomics analysis. J Proteome Res. 2011 Mar 4; 10(3):1170-8.
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        19. Chakrabarti L, Zahra R, Jackson SM, Kazemi-Esfarjani P, Sopher BL, Mason AG, Toneff T, Ryu S, Shaffer S, Kansy JW, Eng J, Merrihew G, MacCoss MJ, Murphy A, Goodlett DR, Hook V, Bennett CL, Pallanck LJ, La Spada AR. Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics. Neuron. 2010 Jun 24; 66(6):835-47.
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        20. Heron SR, Wilson R, Shaffer SA, Goodlett DR, Cooper JM. Surface acoustic wave nebulization of peptides as a microfluidic interface for mass spectrometry. Anal Chem. 2010 May 15; 82(10):3985-9.
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        21. Panchaud A, Singh P, Shaffer SA, Goodlett DR. xComb: a cross-linked peptide database approach to protein-protein interaction analysis. J Proteome Res. 2010 May 7; 9(5):2508-15.
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        22. Gharib SA, Nguyen E, Altemeier WA, Shaffer SA, Doneanu CE, Goodlett DR, Schnapp LM. Of mice and men: comparative proteomics of bronchoalveolar fluid. Eur Respir J. 2010 Jun; 35(6):1388-95.
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        23. Parra MC, Shaffer SA, Hajjar AM, Gallis BM, Hager A, Goodlett DR, Guina T, Miller S, Collins CM. Identification, cloning, expression, and purification of Francisella lpp3: an immunogenic lipoprotein. Microbiol Res. 2010 Sep 20; 165(7):531-45.
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        24. Tsai YS, Scherl A, Shaw JL, MacKay CL, Shaffer SA, Langridge-Smith PR, Goodlett DR. Precursor ion independent algorithm for top-down shotgun proteomics. J Am Soc Mass Spectrom. 2009 Nov; 20(11):2154-66.
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        25. Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem. 2009 Aug 1; 81(15):6481-8.
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        26. Nunn BL, Aker JR, Shaffer SA, Tsai S, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmström L, Goodlett DR. Deciphering diatom biochemical pathways via whole-cell proteomics. Aquat Microb Ecol. 2009 Jun 3; 55(3):241-253.
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        27. Reimel BA, Pan S, May DH, Shaffer SA, Goodlett DR, McIntosh MW, Yerian LM, Bronner MP, Chen R, Brentnall TA. Proteomics on Fixed Tissue Specimens - A Review. Curr Proteomics. 2009 Apr 1; 6(1):63-69.
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        28. Goo YA, Liu AY, Ryu S, Shaffer SA, Malmström L, Page L, Nguyen LT, Doneanu CE, Goodlett DR. Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. Prostate. 2009 Jan 1; 69(1):49-61.
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        29. Moore NH, Costa LG, Shaffer SA, Goodlett DR, Guizzetti M. Shotgun proteomics implicates extracellular matrix proteins and protease systems in neuronal development induced by astrocyte cholinergic stimulation. J Neurochem. 2009 Feb; 108(4):891-908.
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        30. Hengel SM, Shaffer SA, Nunn BL, Goodlett DR. Tandem mass spectrometry investigation of ADP-ribosylated kemptide. J Am Soc Mass Spectrom. 2009 Mar; 20(3):477-83.
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        31. Singh P, Shaffer SA, Scherl A, Holman C, Pfuetzner RA, Larson Freeman TJ, Miller SI, Hernandez P, Appel RD, Goodlett DR. Characterization of protein cross-links via mass spectrometry and an open-modification search strategy. Anal Chem. 2008 Nov 15; 80(22):8799-806.
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        32. Jones JW, Shaffer SA, Ernst RK, Goodlett DR, Turecek F. Determination of pyrophosphorylated forms of lipid A in Gram-negative bacteria using a multivaried mass spectrometric approach. Proc Natl Acad Sci U S A. 2008 Sep 2; 105(35):12742-7.
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        33. Scherl A, Tsai YS, Shaffer SA, Goodlett DR. Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses. Proteomics. 2008 Jul; 8(14):2791-7.
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        34. Ryu S, Gallis B, Goo YA, Shaffer SA, Radulovic D, Goodlett DR. Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer Inform. 2008; 6:243-55.
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        35. Rohmer L, Guina T, Chen J, Gallis B, Taylor GK, Shaffer SA, Miller SI, Brittnacher MJ, Goodlett DR. Determination and comparison of the Francisella tularensis subsp.novicida U112 proteome to other bacterial proteomes. J Proteome Res. 2008 May; 7(5):2016-24.
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        36. Scherl A, Shaffer SA, Taylor GK, Hernandez P, Appel RD, Binz PA, Goodlett DR. On the benefits of acquiring peptide fragment ions at high measured mass accuracy. J Am Soc Mass Spectrom. 2008 Jun; 19(6):891-901.
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        37. Kanistanon D, Hajjar AM, Pelletier MR, Gallagher LA, Kalhorn T, Shaffer SA, Goodlett DR, Rohmer L, Brittnacher MJ, Skerrett SJ, Ernst RK. A Francisella mutant in lipid A carbohydrate modification elicits protective immunity. PLoS Pathog. 2008 Feb 8; 4(2):e24.
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        38. Scherl A, Shaffer SA, Taylor GK, Kulasekara HD, Miller SI, Goodlett DR. Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. Anal Chem. 2008 Feb 15; 80(4):1182-91.
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        39. Gao Q, Xue S, Shaffer SA, Doneanu CE, Goodlett DR, Nelson SD. Minimize the detection of false positives by the software program DetectShift for 18O-labeled cross-linked peptide analysis. Eur J Mass Spectrom (Chichester, Eng). 2008; 14(5):275-80.
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        40. Foss EJ, Radulovic D, Shaffer SA, Ruderfer DM, Bedalov A, Goodlett DR, Kruglyak L. Genetic basis of proteome variation in yeast. Nat Genet. 2007 Nov; 39(11):1369-75.
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        41. Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S, Flory MR, Lee H, Watts J, Goodlett DR, Aebersold R, Paulovich A, Schwikowski B. Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics. 2007 Oct; 6(10):1741-8.
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        42. Goo YA, Li Z, Pajkovic N, Shaffer S, Taylor G, Chen J, Campbell D, Arnstein L, Goodlett DR, van Breemen RB. Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software. Proteomics Clin Appl. 2007 May 1; 1(5):513-523.
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        43. Shaffer SA, Harvey MD, Goodlett DR, Ernst RK. Structural heterogeneity and environmentally regulated remodeling of Francisella tularensis subspecies novicida lipid A characterized by tandem mass spectrometry. J Am Soc Mass Spectrom. 2007 Jun; 18(6):1080-92.
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        44. Rohmer L, Fong C, Abmayr S, Wasnick M, Larson Freeman TJ, Radey M, Guina T, Svensson K, Hayden HS, Jacobs M, Gallagher LA, Manoil C, Ernst RK, Drees B, Buckley D, Haugen E, Bovee D, Zhou Y, Chang J, Levy R, Lim R, Gillett W, Guenthener D, Kang A, Shaffer SA, Taylor G, Chen J, Gallis B, D'Argenio DA, Forsman M, Olson MV, Goodlett DR, Kaul R, Miller SI, Brittnacher MJ. Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biol. 2007; 8(6):R102.
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        45. Trute M, Gallis B, Doneanu C, Shaffer S, Goodlett D, Gallagher E. Characterization of hepatic glutathione S-transferases in coho salmon (Oncorhynchus kisutch). Aquat Toxicol. 2007 Feb 28; 81(2):126-36.
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        46. Hajjar AM, Harvey MD, Shaffer SA, Goodlett DR, Sjöstedt A, Edebro H, Forsman M, Byström M, Pelletier M, Wilson CB, Miller SI, Skerrett SJ, Ernst RK. Lack of in vitro and in vivo recognition of Francisella tularensis subspecies lipopolysaccharide by Toll-like receptors. Infect Immun. 2006 Dec; 74(12):6730-8.
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        47. Shaffer SA, Baker-Lee C, Kennedy J, Lai MS, de Vries P, Buhler K, Singer JW. In vitro and in vivo metabolism of paclitaxel poliglumex: identification of metabolites and active proteases. Cancer Chemother Pharmacol. 2007 Mar; 59(4):537-48.
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        48. Nunn BL, Shaffer SA, Scherl A, Gallis B, Wu M, Miller SI, Goodlett DR. Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO. Brief Funct Genomic Proteomic. 2006 Jun; 5(2):154-68.
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        49. Gao Q, Doneanu CE, Shaffer SA, Adman ET, Goodlett DR, Nelson SD. Identification of the interactions between cytochrome P450 2E1 and cytochrome b5 by mass spectrometry and site-directed mutagenesis. J Biol Chem. 2006 Jul 21; 281(29):20404-17.
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        50. Gao Q, Xue S, Doneanu CE, Shaffer SA, Goodlett DR, Nelson SD. Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry. Anal Chem. 2006 Apr 1; 78(7):2145-9.
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        51. Singer JW, Shaffer S, Baker B, Bernareggi A, Stromatt S, Nienstedt D, Besman M. Paclitaxel poliglumex (XYOTAX; CT-2103): an intracellularly targeted taxane. Anticancer Drugs. 2005 Mar; 16(3):243-54.
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        52. Singer JW, Baker B, De Vries P, Kumar A, Shaffer S, Vawter E, Bolton M, Garzone P. Poly-(L)-glutamic acid-paclitaxel (CT-2103) [XYOTAX], a biodegradable polymeric drug conjugate: characterization, preclinical pharmacology, and preliminary clinical data. Adv Exp Med Biol. 2003; 519:81-99.
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        53. Shaffer SA, Tolmachev A, Prior DC, Anderson GA, Udseth HR, Smith RD. Characterization of an improved electrodynamic ion funnel interface for electrospray ionization mass spectrometry. Anal Chem. 1999 Aug 1; 71(15):2957-64.
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        54. Shaffer SA, Prior DC, Anderson GA, Udseth HR, Smith RD. An ion funnel interface for improved ion focusing and sensitivity using electrospray ionization mass spectrometry. Anal Chem. 1998 Oct 1; 70(19):4111-9.
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        55. Shaffer SA, Tang K, Anderson GA, Prior DC, Udseth HR, Smith RD. A Novel Ion Funnel for Ion Focusing at Elevated Pressure Using Electrospray Ionization Mass Spectrometry. Rapid. Commun. Mass Spectrom. 1997; 11(16):1813-17.
        56. Shaffer SA, Wolken JK, Turecek F. Neutralization-Reionization of Alkenylammonium Cations. An Experimental and Ab Initio Study of Intramolecular N-H…C=C Interactions in Cations and Hypervalent Radicals. J Am Soc Mass Spectrom. 1997; 8(11):1111-23.
        57. Shaffer SA, Sadilek M, Turecek F, Hop CECA. Protonation of Isomeric Methoxyhexenes. Effects of Double Bond…H+…OCH3 Interaction. Int J Mass Spectrom. 1996; 160(1-3):137-55.
        58. Shaffer SA, Sadilek M, Turecek F. Hypervalent Ammonium Radicals. Effects of Alkyl Groups and Aromatic Substituents. J Org Chem. 1996; 61(16):5234-45.
        59. Shaffer SA, Turecek F. Hydrogen Bonding in Transient Bifunctional Hypervalent Radicals by Neutralization-Reionization Mass Spectrometry. J Am Soc Mass Spectrom. 1995; 6(11):1004-18.
        60. Nguyen VQ, Shaffer SA, Turecek F, Hop CECA. Franck-Condon Dominated Chemistry. Dissociations of Silicon-Centered Radicals Prepared by Femtosecond Reduction of Their Cations in the Gas Phase. J Phys Chem. 1995; 99(42):15454-64.
        61. Shaffer SA, Turecek F. Hydrogentrimethylammonium: A Marginally Stable Hypervalent Radical. J Am Chem Soc. 1994; 116(19):8647-53.
        62. Kuhns DW, Shaffer SA, Tran TB, Turecek F. The Methylthiomethyl Radical. A Variable-Time Neutralization-Reionization and Ab Initio Study. J Phys Chem. 1994; 98(18):4845-53.
        63. Shaffer SA, Cerny RL, Turecek F. The (Dimethylamino)methyl Radical. A Neutralization-Reionization and Ab Initio Study. J Am Chem Soc. 1993; 115(25):12117-24.
        64. Turecek F, Gu M, Shaffer SA. Novel tandem quadrupole-acceleration-deceleration mass spectrometer for neutralization-reionization studies. J Am Soc Mass Spectrom. 1992 Jul; 3(5):493-501.
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