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All Shaffer Lab publications can be viewed on myNCBI.

C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.
Gao XD, Tu LC, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ.
Nat Methods. 2018 May 7.  

Egg turning behavior and incubation temperature in Forster's terns in relation to mercury contamination.
ylor GT, Ackerman JT, Shaffer SA.
PLoS One. 2018 Feb 15;13(2):e0191390. 

Population-level plasticity in foraging behavior of western gulls (Larus occidentalis).
Shaffer SA, Cockerham S, Warzybok P, Bradley RW, Jahncke J, Clatterbuck CA, Lucia M, Jelincic JA, Cassell AL, Kelsey EC, Adams J.
Mov Ecol. 2017 Dec 19;5:27.

Extracellular Vesicles from Mice with Alcoholic Liver Disease Carry a Distinct Protein Cargo and Induce Macrophage Activation via Hsp90 
B. Saha, F. Momen-Heravi, I. Furi, K. Kodys, D. Catalano, A. Gangopadhyay, R. Haraszti, A. Satishchandran, A. Iracheta-Vellve, A. Adejumo, S. A. Shaffer, and G. Szabo.
Hepatology. 2018 May;67(5):1986-2000.

Cyclic GMP-AMP Synthase Is the Cytosolic Sensor of Plasmodium falciparum Genomic DNA and Activates Type I IFN in Malaria 
C. Gallego-Marin, J. E. Schrum, W. A. Andrade, S. A. Shaffer, L. F. Giraldo, A. M. Lasso, E. A. Kurt-Jones, K. A. Fitzgerald, and D. T. Golenbock.
Journal of Immunology, 200, 768-774.

RNA Sequencing and Proteomics Approaches Reveal Novel Deficits in the Cortex of Mecp2-deficient Mice, a Model for Rett Syndrome
N. L. Pacheco, M. R. Heaven, L. M. Holt, D. K. Crossman, K. J. Boggio, S. A. Shaffer, D. L. Flint, and M. L. Olsen.
Molecular Autism, 2017, 8:56.

Menthol Enhances Nicotine-induced Locomotor Sensitization and in vivo Functional Connectivity in Adolescence
M. F. Thompson, G. L. Poirier, M. I. Dávila-García, W. Huang, K. Tam, M. Robidoux, M. L. Dubuke, S. A. Shaffer, L. Colon-Perez, M. Febo, J. R. DiFranza, and J. A. King.
Journal of Psychopharmacology, 2017, 32, 332-343.

Nitric Oxide Prevents a Pathogen-permissive Granulocytic Inflammation During Tuberculosis
B. Mishra, R. Lovewell, A. Olive, G. Zhang, W. Wang, E. Eugenin, C. Smith, J. Phuah, J. Long, M. Dubuke, S. Palace, J. Goguen, R. Baker, S. Nambi, R. Mishra, M. Booty, C. Baer, S. A. Shaffer, V. Dartois, B. McCormick, X. Chen, and C. Sassetti.
Nature Microbiology, 2017, 2, 17072.

Innate Immune Signaling in Drosophila is Regulated by TGFβ-activated Kinase (Tak1)-triggered Ubiquitin Editing.
L. Chen, N. Paquette, S. Mamoor, F. Rus, A. Nandy, J. Leszyk, S. A. Shaffer, and N. Silverman.
Journal of Biological Chemistry, 2017, 292, 8738-8749.

Novel Allele-specific Quantification Methods Reveal No Effects of Adult Onset CAG Repeats on HTT mRNA and Protein Levels
A. Shin, B. Shin, J. W. Shin, K. H. Kim, R. S. Atwal, J. M. Hope, T. Gillis, J. D. Leszyk, S. A. Shaffer, R. Lee, S. Kwak, M. E. MacDonald, J. F. Gusella, I. S. Seong, J. M. Lee.
Human Molecular Genetics, 2017, 26, 1258-1267.

High-resolution Proteomic and Lipidomic Analysis of Exosomes and Microvesicles from Different Cell Sources
R. A. Haraszti, M. C. Didiot, E. Sapp, J. Leszyk, S. A. Shaffer, H. E. Rockwell, F. Gao, N. R. Narain, M. DiFiglia, M. A. Kiebish, N. Aronin, and A. Khvorova.
Journal of Extracellular Vesicles, 2016, 5, 32570.

A Novel Transgenic Mouse Model of Lysosomal Storage Disorder
S. Ortiz-Miranda, R. Ji, A. Jurczyk, K. E. Aryee, S. Mo, T. Fletcher, S. A. Shaffer, D. L. Greiner, R. Bortell, R. Gregg, A. Cheng, L. J. Hennings, and A. R. Rittenhouse.
American Journal of Physiology-Gastrointestinal and Liver Physiology, 2016, 311, G903-G919.

Type I Interferon Induction by Neisseria gonorrhoeae: Dual Requirement of Cyclic GMP-AMP Synthase and Toll-like Receptor 4.
W. A. Andrade, S. Agarwal, S. Mo, S. A. Shaffer, J. P. Dillard, T. Schmidt, V. Hornung, K. A. Fitzgerald, E. A. Kurt-Jones, and D. T. Golenbock.
Cell Reports, 2016, 15, 2438-2448.

Peripartum Neuroactive Steroid and γ-aminobutyric Acid Profiles in Women At-risk for Postpartum Depression
K. M. Deligiannidis, A. R. Kroll-Desrosiers, S. Mo, H. P. Nguyen, A. Svenson, N. Jaitly, J. E. Hall, B. A. Barton, A. J. Rothschild, and S. A. Shaffer.
Psychoneuroendocrinology, 2016, 70, 98-107.

Spatially Distinct and Metabolically Active Membrane Domain in Mycobacteria
J. M. Hayashi, C. Y. Luo, J. A. Mayfield, T. Hsu, T. Fukuda, A. L. Walfield, S. R. Giffen, J. D. Leszyk, C. E. Baer, O. T. Bennion, A. Madduri, S. A. Shaffer, B. B. Aldridge, C. M. Sassetti, S. J. Sandler, T. Kinoshita, D. B. Moody, and Y. S. Morita.
Proceedings of the National Academy of Sciences, 2016, 113, 5400-5405

The Dendritic Cell MHC II Peptidome Derives from a Variety of Processing Pathways and Includes Peptides with a Broad Spectrum of HLA-DM Sensitivity.
C. C. Clement, A. Becerra, L. Yin, V. Zolla, L. Huang, S. Merlin, A. Follenzi, S. A. Shaffer, L. J. Stern, and L. Santambrogio.
Journal of Biological Chemistry, 2016, 291, 5576-5595.

The Exocyst Subunit Sec6 Interacts with Assembled Exocytic SNARE Complexes
M. L. Dubuke, S. Maniatis, S. A. Shaffer and M. Munson.
Journal of Biological Chemistry, 2015, 290, 28245-28256.

Macrophage Secretome from Women with HIV-associated Neurocognitive Disorders
K. Colon, J. Perez-Laspiur, R. Quiles, Y. Rodriguez, V. Wojna, S. A. Shaffer, J. Leszyk, R. L. Skolasky, and L. M. Meléndez.
Proteomics Clinical Applications, 2015, 10, 136-143.

Interacting Partners of Macrophage-secreted Cathepsin B Contribute to HIV-induced Neuronal Apoptosis.
Y. M. Cantres-Rosario, N. Hernandez, K. Negron, J. Perez-Laspiur, J. Leszyk, S. A. Shaffer, and L. M. Meléndez.
AIDS, 2015, 29, 2081-2092.

Mass Spectrometry Analysis of Wild-Type and Knock-in Q140/Q140 Huntington's Disease Mouse Brains Reveals Changes in Glycerophospholipids Including Alterations in Phosphatidic Acid and Lyso-Phosphatidic Acid
P. Vodicka, S. Mo, A. Tousley, K. M. Green, E. Sapp, M. Iuliano, G. Sadri-Vakili, S. A. Shaffer, N. Aronin, M. DiFiglia, and K. B. Kegel-Gleason.
Journal of Huntington's Disease, 2015, 4, 187-201.

Opposing Calcium-dependent Signalling Pathways Control Skeletal Muscle Differentiation by Regulating a Chromatin Remodelling Enzyme
B. T. Nasipak, T. Padilla-Benavides, K. M. Green, J. D. Leszyk, W. Mao, S. Konda, S. Sif, S. A. Shaffer, Y. Ohkawa, and A. N. Imbalzano.
Nature Communications, 2015, 6, 7441.

The Oxidative Stress Network of Mycobacterium tuberculosis Reveals Coordination between Radical Detoxification Systems
S. Nambi, J. E. Long, B. B. Mishra, R. Baker, K. C. Murphy, A. J. Olive, H. P. Nguyen, S. A. Shaffer, and C. M. Sassetti.
Cell Host & Microbe, 2015, 17, 829-837.

Systemic AAV9 Gene Transfer in Adult GM1 Gangliosidosis Mice Reduces Lysosomal Storage in CNS and Extends Lifespan
C. M. Weismann, J. Ferreira, A. M. Keeler, Q. Su, L. Qui, S. A. Shaffer, Z. Xu, G. Gao, and M. Sena-Esteves.
Human Molecular Genetics, 2015, 24, 4353-4364.

Subnuclear Domain Proteins in Cancer Cells Support Transcription Factor RUNX2 Functions in DNA Damage Response
S. Yang, A. J. Quaresma, J. A. Nickerson, K. M. Green, S. A. Shaffer, A. N. Imbalzano, L. A. Martin-Buley, J. B. Lian, J. L. Stein, A. J. van Wijnen, and G. S. Stein.
Journal of Cell Science, 2015, 128, 728-740.

A Loss of FUS/TLS Function Leads to Impaired Cellular Proliferation
C. L. Ward, K. J. Boggio, B. N. Johnson, J. B. Boyd, S. Douthwright, S. A. Shaffer, J. E. Landers, M. A. Glicksman, and D. A. Bosco.
Cell Death and Disease, 2014, 5, e1572.

Comparison of Data Acquisition Strategies on Quadrupole Ion Trap Instrumentation for Shotgun Proteomics
J. D. Canterbury, G. E. Merrihew, M. J. MacCoss, D. R. Goodlett, and S. A. Shaffer.
Journal of the American Society of Mass Spectrometry, 2014, 25, 2048-2059.

Identification of a Misfolded Region in Superoxide Dismutase 1 that is Exposed in Amyotrophic Lateral Sclerosis.
M. S. Rotunno, J. R. Auclair, S. Maniatis, S. A. Shaffer, J. Agar, and D. A. Bosco.
Journal of Biological Chemistry, 2014, 289, 28527-28538.

Phosphorylation Within the Cysteine-rich Region of Dystrophin Enhances its Association with β-dystroglycan and Identifies a Potential Novel Therapeutic Target for Skeletal Muscle Wasting
K. Swiderski, S. A. Shaffer, B. Gallis, G. L. Odom, A. L. Arnett, J. S. Edgar, D. M. Baum, A. Chee, T. Naim, P. Gregorevic, K. T. Murphy, J. Moody, D. R. Goodlett, G. S. Lynch, and J. S. Chamberlain.
Human Molecular Genetics, 2014, 23, 6697-6711.

Serum-induced Differentiation of Human Meibomian Gland Epithelial Cells
D. A. Sullivan, Y. Liu, W. R. Kam, J. Ding, K. M. Green, S. A. Shaffer, M. P. Hatton, and S. Liu.
Investigative Ophthalmology & Visual Science, 2014, 55, 3866-3877.

Inhibition of Heat Shock Protein 90 Alleviates Steatosis and Macrophage Activation in Murine Alcoholic Liver Injury
A. Ambade, D. Catalano, A. Lim, A. Kopoyan, S. A. Shaffer, and P. Mandrekar.
Journal of Hepatology, 2014, 61, 903-911.

Striatal Synaptosomes from Hdh140Q/140Q Knock-in Mice have Altered Protein Levels, Novel Sites of Methionine Oxidation, and Excess Glutamate Release after Stimulation
A. Valencia, E. Sapp, J. S. Kimm, H. McClory, K. A. Ansong, G. Yohrling, S. Kwak, K. B. Kegel, K. M. Green, S. A. Shaffer, N. Aronin, and M. DiFiglia.
Journal of Huntington's Disease, 2013, 2, 459-475.

Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers
K. A. Jones, P. D. Kim, B. B. Patel, S. G. Kelsen, A. Braverman, D. J. Swinton, P. R. Gafken, L. A. Jones, W. S. Lane, J. M. Neveu, H. C. Leung, S. A. Shaffer, J. D. Leszyk, B. A. Stanley, T. E. Fox, A. Stanley, M. J. Hall, H. Hampel, C. D. South, A. de la Chapelle, R. W. Burt, D. A. Jones, L. Kopelovich, and A. T. Yeung.
Journal of Proteome Research, 2013, 12, 4351-4365.

GABAergic Neuroactive Steroids and Resting-state Functional Connectivity in Postpartum Depression: A Preliminary Study
K. M. Deligiannidis, E. M. Sikoglu, S. A. Shaffer, B. Frederick, A. E. Svenson, A. Kopoyan, C. A. Kosma, A. J. Rothschild, and C. M. Moore.
Journal of Psychiatric Research, 2013, 47, 816-828.

Interlaboratory Studies and Initiatives Developing Standards for Proteomics
A. R. Ivanov, C. Colangelo, C. P. Dufresne, D. B. Friedman, K. S. Lilley, K. Mechtler, B. S. Phinney, K. L. Rose, P. A. Rudnick, B. C. Searle, S. A. Shaffer, and S. T. Weintraub.
Proteomics, 2013, 13, 904-909.

Cross-Linking Mass Spectrometry and Mutagenesis Confirm the Functional Importance of Surface Interactions between CYP3A4 and Holo/Apo Cytochrome b(5)
C. Zhao, Q. Gao, A. G. Roberts, S. A. Shaffer, C. E. Doneanu, S. Xue, D. R. Goodlett, S. D. Nelson, and W. M. Atkins.
Biochemistry, 2012, 51, 9488-9500.

The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus
G. Singh, A. Kucukural, C. Cenik, J. D. Leszyk, S. A. Shaffer, Z. Weng, and M. J. Moore.
Cell, 2012, 151, 750-764.

Transcription Factor Foxp3 and its Protein Partners Form a Complex Regulatory Network
D. Rudra, P. Deroos, A. Chaudhry, R. E. Niec, A. Arvey, R. M. Samstein, C. Leslie, S. A. Shaffer, D. R. Goodlett, and A. Y. Rudensky.
Nature Immunology, 2012, 13, 1010-1019.

Serine/threonine Acetylation of TGFβ-activated Kinase (TAK1) by Yersinia pestis YopJ Inhibits Innate Immune Signaling
N. Paquette, J. Conlon, C. Sweet, F. Rus, L. Wilson, A. Pereira, C. V. Rosadini, N. Goutagny, A. N. Weber, W. S. Lane, S. A. Shaffer, S. Maniatis, K. A. Fitzgerald, L. Stuart, and N. Silverman.
Proceedings of the National Academy of Sciences, 2012, 109, 12710-12715.

FANCJ/BACH1 Acetylation at Lysine 1249 Regulates the DNA Damage Response
J. Xie, M. Peng, S. Guillemette, S. Quan, S. Maniatis, Y. Wu, A. Venkatesh, S. A. Shaffer, R. M. Brosh Jr., and S. B. Cantor.
PLoS Genetics, 2012, 8, e1002786.

LPS Remodeling is an Evolved Survival Strategy for Bacteria
Y. Li, D. A. Powell, S. A. Shaffer, D. A. Rasko, M. R. Pelletier, J. D. Leszyk, A. J. Scott, A. Masoudi, D. R. Goodlett, X. Wang, C. R. Raetz, and R. K. Ernst.
Proceedings of the National Academy of Sciences, 2012, 109, 8716-8721.

Long-term Correction of Very Long-chain Acyl-CoA Dehydrogenase Deficiency in Mice Using AAV9 Gene Therapy
A. M. Keeler, T. Conlon, G. Walter, H. Zeng, S. A. Shaffer, F. Dungtao, K. Erger, T. Cossette, Q. Tang, C. Mueller, and T. R. Flotte.
Molecular Therapy, 2012, 20, 1131-1138.

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms
E. J. Foss, D. Radulovic, S. A. Shaffer, D. R. Goodlett, L. Kruglyak, and A. Bedalov.
PLoS Biology, 2011, 9, e1001144.

Substrate Specificity and Ligand Interactions of CYP26A1, the Human Liver Retinoic Acid Hydroxylase
J. E. Thatcher, B. Buttrick, S. A. Shaffer, J. A. Shimshoni, D. R. Goodlett, W. L. Nelson, and N. Isoherranen.
Molecular Pharmacology, 2011, 80, 228-239.

Automated Lipid A Structure Assignment From Hierarchical Tandem Mass Spectrometry Data
Y. S. Ting, S. A. Shaffer, J. W. Jones, W. V. Ng, R. K. Ernst, and D. R. Goodlett.
Journal of the American Society of Mass Spectrometry, 2011, 22, 856-866.

Faster, Quantitative, and Accurate Precursor Acquisition Independent From Ion Count
A. Panchaud, S. Jung, S. A. Shaffer, J. D. Aitchison, and D. R. Goodlett.
Analytical Chemistry, 2011, 83, 2250-2257.

New Structural Proteins of Halobacterium salinarum Gas Vesicle Revealed by Comparative Proteomics Analysis
L. J. Chu, M. C. Chen, J. Setter, Y.S. Tsai, H. Yang, X. Fang, Y. S. Ting, S. A. Shaffer, G. K. Taylor, P. D. von Haller, D. R. Goodlett, and W. V. Ng.
Journal of Proteome Research, 2011, 10, 1170-1178.

Mitochondrial Dysfunction in NnaD Mutant Flies and Purkinje Cell Degeneration Mice Reveals a Role for Nna Proteins in Neuronal Bioenergetics
L. Chakrabarti, R. Zahra, S. M. Jackson, P. Kazemi-Esfarjani, B. L. Sopher, A. G. Mason, T. Toneff, S. Ryu, S. Shaffer, J. W. Kansy, J. Eng, G. Merrihew, M. J. MacCoss, A. Murphy, D. R. Goodlett, V. Hook, C. L. Bennett, L. J. Pallanck, and A. R. La Spada.
Neuron, 2010, 66, 835-847.

Surface Acoustic Wave Nebulization of Peptides As a Microfluidic Interface for Mass Spectrometry
S. R. Heron, R. Wilson, S. A. Shaffer, D. R. Goodlett, and J. M. Cooper.
Analytical Chemistry, 2010, 82, 3985-3989.

xComb: a Cross-linked Peptide Database Approach to Protein-protein Interaction Analysis
A. Panchaud, P. Singh, S. A. Shaffer, and D. R. Goodlett.
Journal of Proteome Research, 2010, 9, 2508-2515.

Of Mice and Men: Comparative Proteomics of Bronchoalveolar Fluid
S. A. Gharib, E. Nguyen, W. A. Altemeier, S. A. Shaffer, C. E. Doneanu, D. R. Goodlett , and L. M. Schnapp.
European Respiratory Journal, 2010, 35, 1388-1395.

Identification, Cloning, Expression, and Purification of Francisella lpp3: An Immunogenic Lipoprotein
M. C. Parra, S. A. Shaffer, A. M. Hajjar, B. M. Gallis, A. Hager, D. R. Goodlett, T. Guina, S. Miller, and C. M. Collins.
Microbiological Research, 2010, 165, 531-545.

Precursor Ion Independent Algorithm for Top-Down Shotgun Proteomics
Y. S. Tsai, A. Scherl, J. L. Shaw, C. L. Mackay, S. A. Shaffer, P. R. Langridge-Smith, and D. R. Goodlett.
Journal of the American Society of Mass Spectrometry, 2009, 20, 2154-2166.

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean
A. Panchaud, A. Scherl, S. A. Shaffer, P. D. von Haller, H. D. Kulasekara, S. I. Miller and D. R. Goodlett.
Analytical Chemistry, 2009, 81, 6481-6488.

Deciphering Diatom Biochemical Pathways via Whole-cell Proteomics
B. L. Nunn, J. R. Aker, S. A. Shaffer, Y. Tsai, R. F. Strzepek, P. W. Boyd, T. L. Freeman, M. Brittnacher, L. Malmström, and D. R. Goodlett.
Aquatic Microbial Ecology, 2009, 55, 241-253.

Proteomics on Fixed Tissue Specimens – A Review
B. A. Reimel, S. Pan, D. H. May, S. A. Shaffer, D. R. Goodlett, M. W. McIntosh, L. M. Yerian, M. P. Bronner, R. Chen and T. A. Brentnall.
Current Proteomics, 2009, 6, 63-69.

Tandem Mass Spectrometry Investigation of ADP-ribosylated Kemptide
S. M. Hengel, S. A. Shaffer, B. L. Nunn, and D. R. Goodlett.
Journal of the American Society of Mass Spectrometry, 2009, 20, 477-483.

Shotgun Proteomics Implicates Extracellular Matrix Proteins and Protease Systems in Neuronal Development Induced by Astrocyte Cholinergic Stimulation
N. H. Moore, L. G. Costa, S. A. Shaffer, D. R. Goodlett, and M. Guizzetti.
Journal of Neurochemistry, 2009, 108, 891-908.

Identification of Secreted Glycoproteins of Human Prostate and Bladder Stromal Cells by Comparative Quantitative Proteomics
Y. A. Goo, A. Y. Liu, S. Ryu, S. A. Shaffer, L. Malmström, L. Page, L. T. Nguyen, C. E. Doneanu, and D. R. Goodlett.
The Prostate, 2009, 69, 49-61.

Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy
P. Singh, S. A. Shaffer, A. Scherl, C. Holman, R. A. Pfuetzner, T. J. Larson Freeman, S. I. Miller, P. Hernandez, R. D. Appel, and D. R. Goodlett.
Analytical Chemistry, 2008, 80, 8799-8806.

Minimize the Detection of False Positives by the Software Program DetectShift for 18O-labeled Cross-linked Peptide Analysis
Q. Gao, S. Xue, S. A. Shaffer, C. E. Doneanu, D. R. Goodlett, and S. D. Nelson.
European Journal of Mass Spectrometry, 2008, 14, 275-280.

Determination of Pyrophosphorylated Forms of Lipid A in Gram-negative Bacteria using a Multivaried Mass Spectrometric Approach
J. W. Jones, S. A. Shaffer, R. K. Ernst, D. R. Goodlett, and F. Tureček.
Proceedings of the National Academy of Sciences, 2008, 105, 12742-12747.

Increasing Information From Shotgun Proteomic Data by Accounting for Misassigned Precursor Ion Masses
A. Scherl, Y. S. Tsai, S. A. Shaffer, and D. R. Goodlett.
Proteomics, 2008, 8, 2791-2797.

On the Benefits of Acquiring Peptide Fragment Ions at High Measured Mass Accuracy
A. Scherl, S. A. Shaffer, G. K. Taylor, P. Hernandez, R. D. Appel, P.-A. Binz, and D. R. Goodlett.
Journal of the American Society of Mass Spectrometry, 2008, 19, 891-901.

Determination and Comparison of the Francisella tularensis subsp. novicida U112 Proteome to Other Bacterial Proteomes
L. Rohmer, T. Guina, J. Chen, B. Gallis, G. K. Taylor, S. A. Shaffer, S. I. Miller, M. J. Brittnacher, and D. R. Goodlett.
Journal of Proteome Research, 2008, 7, 2016-2024.

A Francisella Mutant in Lipid A Carbohydrate Modification Elicits Protective Immunity
D. Kanistanon, A. M. Hajjar, M. R. Pelletier, L. A. Gallagher, T. Kalhorn, S. A. Shaffer, D. R. Goodlett, L. Rohmer, M. J. Brittnacher, S. J. Skerrett, and R. K. Ernst.
PLoS Pathogens, 2008, 4, e24.

Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method
S. Ryu, B. Gallis, Y. A. Goo, S. A. Shaffer, D. Radulovic, and D. R. Goodlett.
Cancer Informatics, 2008, 4, 243-255.

Genome-Specific Gas-Phase Fractionation Strategy for Improved Shotgun Proteomic Profiling of Proteotypic Peptides
A. Scherl, S. A. Shaffer, G. K. Taylor, H. D. Kulasekara, S. I. Miller, and D. R. Goodlett.
Analytical Chemistry, 2008, 80, 1182-1191.

Genetic Basis of Proteome Variation in Yeast
E. J. Foss, D. Radulovic, S. A. Shaffer, D. M. Ruderfer, A. Bedalov, D. R. Goodlett, and L. Kruglyak.
Nature Genetics, 2007, 39, 1369-1375.

Assessing Bias in Experiment Design for Large-scale Mass Spectrometry-based Quantitative Proteomics
A. Prakash, B. Piening, J. Whiteaker, H. Zhang, S. A. Shaffer, D. Martin, L. Hohmann, K. Cooke, J. Olson, S. Hansen, M. R. Flory, H. Lee, J. Watts, D. R. Goodlett, R. Aebersold, A. Paulovich, and B. Schwikowski.
Molecular & Cellular Proteomics, 2007, 6, 1741-1748.

Comparison of Francisella tularensis Genomes Reveals Evolutionary Events Associated with the Emergence of Human Pathogenic Strains
L. Rohmer, C. Fong, S. Abmayr, M. Wasnick, T. J. L. Freeman, M. Radey, T. Guina, K. Svensson, H. S. Hayden, M. Jacobs, L. A. Gallagher, C. Manoil, R. K. Ernst, B. Drees, D. Buckley, E. Haugen, D. Bovee, Y. Zhou, J. Chang, R. Levy, R. Lim, W. Gillett, D. Guenthener, A. Kang, S. A. Shaffer, G. Taylor, J. Chen, B. Gallis, D. A. D'Argenio, M. Forsman, M. V. Olson, D. R. Goodlett, R. Kaul, S. I. Miller, and M. J. Brittnacher.
Genome Biology, 2007, 8, R102.

Structural Heterogeneity and Environmentally Regulated Remodeling of Francisella tularensis subspecies novicida Lipid A Characterized by Tandem Mass Spectrometry
S. A. Shaffer, T. F. Kalhorn, M. D. Harvey, D. R. Goodlett, and R. K. Ernst.
Journal of the American Society of Mass Spectrometry, 2007, 18, 1080-1092.

Systematic Investigation of Lycopene Effects in LNCaP Cells by Use of Novel Large-scale Proteomic Analysis Software
Y. A. Goo, Z. Li, N. Pajkovic, S. Shaffer, G. Taylor, J. Chen, D. Campbell, L. Arnstein, D. R. Goodlett, and R. B. van Breemen.
Proteomics Clinical Applications, 2007, 1, 513-523.

In Vitro and In Vivo Metabolism of Paclitaxel Poliglumex: Identification of Metabolites and Active Proteases
S. A. Shaffer, C. B. Lee, J. Kennedy, M. S. Lai, P. de Vries, K. Buhler, and J. W. Singer.
Cancer Chemotherapy and Pharmacology, 2007, 59 (537-548).

Characterization of Hepatic Glutathione S-transferases in Coho Salmon (Oncorhynchus kisutch)
M. Trute, B. Gallis, C. Doneanu, S. Shaffer, D. Goodlett, and E. Gallagher.
Aquatic Toxicolgy, 2006, 81, 126-136.

Lack of In Vitro and In Vivo Recognition of Francisella Subspecies LPS by Toll-like Receptors
A. M. Hajjar, M. D. Harvey, S. A. Shaffer, D. R. Goodlett, A. Sjostedt, H. Edebro, M. Forsman, M. Bystrom, M. Pelletier, C. B. Wilson, S. I. Miller, S. J. Skerrett, and R. K. Ernst.
Infection and Immunity, 2006, 74, 6730-6738.

Identification of the Interactions between Cytochrome P450 2E1 and Cytochrome b5 by Mass Spectrometry and Site-directed Mutagenesis
Q. Gao, C. E. Doneanu, S. A. Shaffer, E. T. Adman, D. R. Goodlett, and S. D. Nelson.
Journal of Biological Chemistry, 2006, 281, 20404-20417.

Comparison of a Salmonella typhimurium Proteome Defined by Shotgun Proteomics Directly on an LTQ-FT and by Proteome Pre-fractionation on an LCQ-DUO
B. L. Nunn, S. A. Shaffer, A. Scherl, B. Gallis, M. Wu, S. I. Miller, and D. R. Goodlett.
Briefings in Functional Genomics and Proteomics, 2006, 5, 154-168.

Pro-CrossLink. Software Tool for Protein Cross-Linking and Mass Spectrometry
Q. Gao, S. Xue, C. E. Doneanu, S. A. Shaffer, D. R. Goodlett, and S. D. Nelson.
Analytical Chemistry, 2006, 78, 2145-2149.

Paclitaxel Poliglumex (XYOTAX; CT-2103): an Intracellularly Targeted Taxane
J. W. Singer, S. Shaffer, B. Baker, A. Bernareggi, S. Stromatt, D. Nienstedt, and M. Besman.
Anticancer Drugs, 2005, 3, 243-54.

Poly-(L)-Glutamic Acid-Paclitaxel (CT-2103)[XYOTAXTM], a Biodegradable Polymeric Drug Conjugate: Characterization, Preclinical Pharmacology, and Preliminary Clinical Data
J. Singer, B. Baker, P. de Vries , A. Kumar, S. Shaffer, E. Vawter, M. Bolton, and P. Garzone.
Advances in Experimental Medicine and Biology, 2003, 519, 81-99.

Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry
S. A. Shaffer, A. Tomachev, D. C. Prior, G. A. Anderson, H. R. Udseth and R. D. Smith.
Analytical Chemistry, 1999, 71, 2957-2964.

An Ion Funnel Interface for Improved Ion Focusing and Sensitivity Using Electrospray Ionization Mass Spectrometry
S. A. Shaffer, D. C. Prior, G. A. Anderson, H. R. Udseth and R. D. Smith.
Analytical Chemistry, 1998, 70, 4111-4119.

A Novel Ion Funnel for Ion Focusing at Elevated Pressure Using Electrospray Ionization Mass Spectrometry
S. A. Shaffer, K. Tang, G. A. Anderson, D. C. Prior, H. R. Udseth and R. D. Smith.
Rapid Communications in Mass Spectrometry, 1997, 11, 1813-1817.

Neutralization-Reionization of Alkenylammonium Cations. An Experimental and Ab Initio Study of Intramolecular N-H...C=C Interactions in Cations and Hypervalent Radicals
S. A. Shaffer, J. K. Wolken, and F. Tureček.
Journal of the American Society for Mass Spectrometry, 1997, 8, 1111-1123.

Protonation of Isomeric Methoxyhexenes. Effects of Double Bond...H+...OCH¬3 Interaction
S. A. Shaffer, M. Sadilek, F. Tureček, and C. E. C. A. Hop.
International Journal of Mass Spectrometry and Ion Processes, 1997, 160, 137-155.

Hypervalent Ammonium Radicals. Effects of Alkyl Groups and Aromatic Substituents
S. A. Shaffer, M. Sadilek, and F. Tureček.
Journal of Organic Chemistry, 1996, 61, 5234-5245.

Hydrogen Bonding in Transient Bifunctional Hypervalent Radicals by Neutralization-Reionization Mass Spectrometry
S. A. Shaffer and F. Tureček.
Journal of the American Society for Mass Spectrometry, 1995, 6, 1004-1018.

Franck-Condon Dominated Chemistry. Dissociations of Silicon-Centered Radicals Prepared by Femtosecond Reduction of Their Cations in the Gas Phase
V. Q. Nguyen, S. A. Shaffer, F. Tureček, and C. E. C. A. Hop.
Journal of Physical Chemistry, 1995, 99, 15454-15464.

Hydrogentrimethylammonium: A Marginally Stable Hypervalent Radical
S. A. Shaffer and F. Tureček.
Journal of the American Chemical Society, 1994, 116, 8647-8653.

The Methylthiomethyl Radical. A Variable-Time Neutralization-Reionization and Ab Initio Study
D. W. Kuhns, S. A. Shaffer, T. B. Tran, and F. Tureček.
Journal of Physical Chemistry, 1994, 98, 4845-4853.

The (Dimethylamino)methyl Radical. A Neutralization-Reionization and Ab Initio Study
S. A. Shaffer, R. L. Cerny, and F. Tureček.
Journal of the American Chemical Society, 1993, 115, 12117-12124.

A Novel Tandem Quadrupole Acceleration-Deceleration Mass Spectrometer for Neutralization-Reionization Studies
F. Tureček, M. Gu, and S. A. Shaffer.
Journal of the American Society for Mass Spectrometry, 1992, 3, 493-501.