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2017

MALDI MS Guided Liquid Microjunction Extraction for Capillary Electrophoresis–Electrospray Ionization MS Analysis of Single Pancreatic Islet Cells, T.J. Comi, M.A. Makurath, M.C. Philip, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 2017, Epub available. DOI:10.1021/acs.analchem.7b01782

microMS: A Python Platform for Image-guided Mass Spectrometry Profiling, T.J. Comi, E.K. Neumann, T.D. Do, J.V. Sweedler, J. Am. Soc. Mass Spectrom., 2017, Epub available. DOI:10.1007/s13361-017-1704-1

Quantitative Reflection Imaging for Morphology and Dynamics of Live Aplysia Californica Pedal Ganglion Neurons Cultured on Nanostructured Plasmonic Crystals, S. Kang, A. Badea, S.S. Rubakhin, J.V. Sweedler, J. Rogers, R. Nuzzo, Langmuir, 2017. Epub available: DOI:10.1021/acs.langmuir.6b04454

Dopamine-Modified TiO2 Monolith-Assisted LDI MS Imaging: Development and Application to Simultaneous Localization of Small Metabolites and Large Lipids in Mouse Brain Tissue with High Detection Selectivity and Sensitivity, Q. Wu, J.L. Chu, S.S. Rubakhin, M.U. Gillette, J.V. Sweedler, Chem. Sci. 8, 2017, 3926–3938. DOI:10.1039/C7SC00937B

Single Cell Profiling using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation, T.D. Do, T.J. Comi, S.J.B. Dunham, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 89, 2017, 3078–3086. DOI:10.1021/acs.analchem.6b04819

Categorizing Cells Based on their Chemical Profiles: Progress in Single Cell Mass Spectrometry, T.J. Comi, T.D. Do, S.S. Rubakhin, J.V. Sweedler, J. Am. Chem. Soc. 139, 2017, 3920–3929. DOI:10.1021/jacs.6b12822

2016

A D-Amino Acid-Containing Neuropeptide Discovery Funnel, I. Livnat, H-C Tai, E.T. Jansson, L. Bai, E.V. Romanova, T. Chen, K. Yu, S. Chen, Y. Zhang, Z. Wang, D. Liu, K.R. Weiss, J. Jing, J.V. Sweedler, Anal. Chem. 88, 2016, 11868–11876. DOI:10.1021/acs.analchem.6b03658

Single Cell Peptide Heterogeneity of Rat Islets of Langerhans, E.T. Jansson, T.J. Comi, S.S. Rubakhin, J.V Sweedler, ACS Chem. Biol. 11, 2016, 2588–2595. DOI:10.1021/acschembio.6b00602

Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors, K. Caetano-Anolles, J.S. Rhodes, T. Garland, Jr., S.D. Perez, A.G. Hernandez, B.R. Southey, S.L. Rodriguez-Zas, PLoS One 11, 2016, e0167095. DOI:10.1371/journal.pone.0167095

Identification of Prohormones and Pituitary Neuropeptides in the African cichlid, Astatotilapia burtoni, C. Hu, B.R. Southey, E.V. Romanova, K.P. Maruska, J.V. Sweedler, R.D. Fernald, BMC Genomics 17, 2016, 660. DOI:10.1186/s12864-016-2914-9

On-tissue Derivatization Via Electrospray Deposition for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Endogenous Fatty Acids in Rat Brain Tissues, Q. Wu, T.J. Comi, B. Li, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 88, 2016, 5988–5995. DOI:10.1021/acs.analchem.6b01021

Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages, D. Gonzalez-Pena, S.E. Nixon, B.R. Southey, M.A. Lawson, R.H. McCusker, A.G. Hernandez, R. Dantzer, K.W. Kelley, S.L. Rodriguez-Zas, PLoS One 11, 2016, e0157727. DOI:10.1371/journal.pone.0157727

A Neuron-in-Capillary Platform for Facile Collection and Mass Spectrometric Characterization of a Secreted Neuropeptide, C.Y. Lee, Y. Fan, S.S. Rubakhin, S. Yoon, J.V. Sweedler, Sci. Rep. 6, 2016, 26940. DOI:10.1038/srep26940

Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge, D. Gonzalez-Pena, S.E. Nixon, J.C. O'Connor, B.R. Southey, M.A. Lawson, R.H. McCusker, T. Borras, D. Machuca, A.G. Hernandez, R. Dantzer, K.W. Kelley, S.L. Rodriguez-Zas, PLoS One 11, 2016, e0150858. DOI:10.1371/journal.pone.0150858

Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea, T-H. Ong, E.V. Romanova, R.H. Roberts-Galbraith, N. Yang, T.A. Zimmerman, J.J. Collins III, J.E. Lee, N.L. Kelleher, P.A. Newmark, J.V. Sweedler, J. Biol. Chem. 291, 2016, 8109–8120. DOI:10.1074/jbc.M115.709196

Quantitation and Identification of Thousands of Human Proteoforms Below 30 Kda, K.R. Durbin, L. Fornelli, R.T. Fellers, P.F. Doubleday, M. Narita, N.L. Kelleher, J. Proteome Res. 4, 2016, 976–982. DOI:10.1021/acs.jproteome.5b00997

Targeted Analysis of Recombinant NF kappa B (RelA/p65) by Denaturing and Native Top Down Mass Spectrometry, J.P. Savaryn, O.S. Skinner, L. Fornelli, R.T. Fellers, P.D. Compton, S.S. Terhune, M.M. Abecassis, N.L. Kelleher, J. Proteomics 134, 2016, 76–84. DOI:10.1016/j.jprot.2015.04.025

2015

Characterization of Genomic Variants Associated with Scout and Recruit Behavioral Castes in Honey Bees Using Whole-Genome Sequencing, B.R. Southey, P. Zhu, M.K. Carr-Markell, Z.S. Liang, A. Zayed, R. Li, G.E. Robinson, S.L. Rodriguez-Zas, PloS One 11, 2016, e0146430. DOI: 10.1371/journal.pone.0146430

Peptidomics and Secretomics of the Mammalian Peripheral Sensory-Motor System, E.G. Tillmaand, N. Yang, C.A.C. Kindt, E.V. Romanova, S.S. Rubakhin, J.V. Sweedler, J. Am. Soc. Mass Spectrom. 26, 2015, 2051–2061. DOI:10.​1007/​s13361-015-1256-1

Differential Peptidomics Assessment of Strain and Age Differences in Mice in Response to Acute Cocaine Administration, E.V. Romanova, S.S. Rubakhin, J.R. Ossyra, J.A. Zombeck, M.R. Nosek, J.V. Sweedler, J.S. Rhodes, J. Neurochem. 135, 2015, 1038-1048. DOI:10.1111/jnc.13265

Peptidomics for the Discovery and Characterization of Neuropeptides and Hormones, E.V. Romanova and J.V. Sweedler, Trends Pharmacol. Sci. 36, 2015, 579–586. DOI:10.1016/j.tips.2015.05.009

Classification of Large Cellular Populations and Discovery of Rare Cells Using Single Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, T.H. Ong, D.J. Kissick, E.T. Jansson, T.J. Comi, E.V. Romanova, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 87, 2015, 7036–7042. DOI:10.1021/acs.analchem.5b01557

Rapid Mitogenic Regulation of the Mtorc1 Inhibitor, Deptor, by Phosphatidic Acid, M.S. Yoon, C.L. Rosenberger, C. Wu, N. Truong, J.V. Sweedler, J. Chen, Mol. Cell 58, 2015, 549–556. DOI:10.1016/j.molcel.2015.03.028

Nanopipet-Based Liquid-Liquid Interface Probes for the Electrochemical Detection of Acetylcholine, Tryptamine, and Serotonin Via Ionic Transfer, M.L. Colombo, J.V. Sweedler, M. Shen, Anal. Chem. 87, 2015, 5095–5100. DOI:10.1021/ac504151e

Mass Spectrometry Imaging and GC-MS Profiling of the Mammalian Peripheral Sensory-Motor Circuit, S.S. Rubakhin, A. Ulanov, J.V. Sweedler, J. Am. Soc. Mass Spectrom. 26, 2015, 958–966. DOI:10.1007/s13361-015-1128-8

Mass Spectrometry-based Characterization of Endogenous Peptides and Metabolites in Small Volume Samples, T-H. Ong, E.G. Tillmaand, M. Makurath, S.S. Rubakhin, J.V. Sweedler, Biochim. Biophys. Acta 1854, 2015, 732–740. DOI:10.1016/j.bbapap.2015.01.008

2014

Identification of Best Indicators of Peptide-Spectrum Match Using a Permutation Resampling Approach, M.N. Akhtar, B.R. Southey, P.E. Andren, J.V. Sweedler, S.L. Rodriguez-Zas, J. Bioinform. Comput. Biol. 12, 2014, 1440001. DOI:10.1142/S0219720014400010

Accurate Assignment of Significance to Neuropeptide Identifications Using Monte Carlo K-Permuted Decoy Databases, M.N. Akhtar, B.R. Southey, P.E. Andrén, J.V. Sweedler, S.L. Rodriguez-Zas, PLoS ONE 9, 2014, e111112. DOI:10.1371/journal.pone.0111112

Analysis of Endogenous Nucleotides by Single Cell Capillary Electrophoresis-Mass Spectrometry, J-X. Liu, J.T. Aerts, S.S. Rubakhin, X-X. Zhang, J.V. Sweedler, Analyst 139, 2014, 5835–5842. DOI:10.1039/C4AN01133C

Ultraviolet Photodissociation for Characterization of Whole Proteins on a Chromatographic Time Scale, J.R. Cannon, M.B. Cammarata, S.A. Robotham, V.C. Cotham, J.B. Shaw, R.T. Fellers, B.P. Early, P.M. Thomas, N.L. Kelleher, J.S. Brodbelt, Anal. Chem. 86, 2014, 2185-2192. DOI:10.1021/ac403859a

Applying Label-Free Quantitation to Top Down Proteomics, I. Ntai, K. Kim, R.T. Fellers, O.S. Skinner, A.D. Smith, B.P. Early, J.P. Savaryn, R.D. LeDuc, P.M. Thomas, N.L. Kelleher, Anal. Chem. 86, 2014, 4961-4968. DOI:10.1021/pr401277r

Fragmentation of Integral Membrane Proteins in the Gas Phase, O.S. Skinner, A.D. Catherman, B.P. Early, P.M. Thomas, P.D. Compton, N.L. Kelleher, Anal. Chem. 86, 2014, 4627-4634. DOI:10.1021/ac500864w

Top-Down Proteomics with Mass Spectrometry Imaging: A Pilot Study Towards Discovery of Biomarkers for Neurodevelopmental Disorders, H. Ye, R. Mandal, A. Catherman, P.M. Thomas, N.L. Kelleher, C. Ikonomidou, L. Li, PLoS One 9, 2014, e92831. DOI:10.1371/journal.pone.0092831

Optimizing Capillary Electrophoresis for Top-Down Proteomics of 30-80 kDa Proteins, Y. Li, P.D. Compton, J.C. Tran, I. Ntai, N.L. Kelleher, Proteomics 14, 2014, 1158-1164. DOI:10.1002/pmic.201300381

The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics, R.D. LeDuc, R.T. Fellers, B.P. Early, J.B. Greer, P.M. Thomas, N.L. Kelleher, J. Proteome Res. 13, 2014, 3231-3240. DOI: 10.1021/pr401277r

The Ctenophore Genome and the Evolutionary Origins of Neural Systems, L.L. Moroz, K.M. Kocot, M.R. Citarella, S. Dosung, T.P. Norekian, I.S. Povolotskaya, A.P. Grigorenko, C. Dailey, E. Berezikov, K.M. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T.P. Moroz, Y. Bobkova, F. Yu, V.V. Kapitonov, J. Jurka, Y.V. Bobkov, J.J. Swore, D.O. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.E. Mills, J.P. Rast, R. Derelle, V.V. Solovyev, F.A. Kondrashov, B.J. Swalla, J.V. Sweedler, E.I. Rogaev, K.M. Halanych, A.B. Kohn, Nature 510, 2014,109–114. DOI:10.1038/nature13400

Fibrinogen-α Chain-derived Peptide is Upregulated in Hippocampus of Rats Exposed to Acute Morphine Injection and Spontaneous Alternation Testing,A.E. Maki, K.A. Morris, K. Catherman, X. Chen, N.G. Hatcher, P.E. Gold, J.V. Sweedler, Pharma. Res. Perspect. 2, 2014, e00037. DOI:10.1002/prp2.37

d-Alanine in the Islets of Langerhans of Rat Pancreas, N. Ota, S.S. Rubakhin, J.V. Sweedler, Biochem. Biophys Res. Commun. 447, 2014, 328–333. DOI:10.1016/j.bbrc.2014.03.153

Patch Clamp Electrophysiology and Capillary Electrophoresis–Mass Spectrometry Metabolomics for Single Cell Characterization, J.T. Aerts, K.R. Louis, S.R. Crandall, G. Govindaiah, C.L. Cox, J.V. Sweedler, Anal. Chem. 86, 2014, 3203–3208. DOI:10.1021/ac500168d

Comparing Label-free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus, B.R. Southey, J.E. Lee, L. Zamdborg, N. Atkins, Jr., J.W. Mitchell, M. Li, M.U. Gillette, N.L. Kelleher, J.V. Sweedler, Anal. Chem., 86, 2014, 443–452. DOI:10.1021/ac4023378

Small-Volume Analysis of Cell-Cell Signaling Molecules in the Brain, E.V. Romanova, J.T. Aerts, C.A. Croushore, J.V. Sweedler, Neuropsychopharmacology 39, 2014, 50–64. DOI:10.1038/npp.2013.145

 TOP

2013

Characterization of GdFFD, a D-Amino Acid-Containing Neuropeptide, that Functions as an Extrinsic Modulator of the Aplysia Feeding Circuit, L. Bai, I. Livnat, E.V. Romanova, V. Alexeeva, P.M. Yau, F.S. Vilim, K.R. Weiss, J.Jing, J.V. Sweedler, J. Biol. Chem. 288, 2013, 32837–32851. DOI:10.1074/jbc.M113.486670

Bivariate Genome-wide Association Analysis of the Growth and Intake Components of Feed Efficiency, N.V. Serão, D. González-Peña, J.E. Beever, G.A. Bollero, B.R. Southey, D.B. Faulkner, S.L. Rodriguez-Zas, PLoS One 8, 2013, e78530. DOI:10.1371/journal.pone.0078530

Single Nucleotide Polymorphisms and Haplotypes Associated with Feed Efficiency in Beef Cattle, N.V. Serao, D. Gonzalez-Pena, J.E. Beever, D.B. Faulkner, B.R. Southey, S.L. Rodriguez-Zas, BMC Genet. 14, 2013, 94. DOI:10.1186/1471-2156-14-94

Stimulation and Release from Neurons via a Dual Capillary Collection Device Interfaced to Mass Spectrometry, Y. Fan, C.Y Lee, S.S. Rubakhin, J.V. Sweedler, Analyst 138, 6337–6346. DOI:10.1039/C3AN01010D

Signals from the Brainstem Sleep/Wake Centers Regulate Behavioral Timing via the CIrcadian Clock, S.M. Abbott, J.M. Arnold, Q. Chang, H. Miao, N. Ota, C. Cecala, P.E. Gold, J.V. Sweedler, M.U. Gillette, PLoS One 8, 2013, e70481. DOI:10.1371/journal.pone.0070481

Quantitation of Endogenous Peptides by Mass Spectrometry Based Methods, E.V. Romanova, S.E. Dowd, J.V. Sweedler, Curr. Opin. Chem. Biol. 17, 2013, 801–808. DOI:10.1016/j.cbpa.2013.05.030

Laminar Stream of Detergents for Subcellular Neurite Damage in a Microfluidic Device: A Simple Tool for the Study of Neuroregeneration, C.Y. Lee, E.V. Romanova, J.V. Sweedler, J. Neural Eng. 10, 2013, 036020. DOI:10.1088/1741-2560/10/3/036020 [Featured on the journal cover.]

Qualitative and Quantitative Metabolomic Investigation of Single Neurons by Capillary Electrophoresis Electrospray Ionization Mass Spectrometry, P. Nemes, S.S. Rubakhin, J.T. Aerts, J.V. Sweedler, Nat. Protoc. 8, 2013, 783–799. DOI:10.1038/nprot.2013.035

Microfluidic Systems for Studying Neurotransmitters and Neurotransmission, C.A. Croushore and J.V. Sweedler, Lab Chip 13, 2013, 1666–1676. DOI:10.1039/C3LC41334A

Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments, Z. Fazal, B.R. Southey, J.V. Sweedler, S.L. Rodriguez-Zas, J. Proteomics Bioinform. 6, 2013, 023–029. DOI:10.4172/jpb.1000256

Combining Small-Volume Metabolomic and Transcriptomic Approaches for Assessing Brain Chemistry, A.M. Knolhoff, K.M. Nautiyal, P.Nemes, S. Kalachikov, I. Morozova, R. Silver, J.V. Sweedler, Anal. Chem. 85, 2013, 3136–3143. DOI:10.1021/ac3032959

Correlated Imaging - A Grand Challenge in Chemical Analysis, R. Masyuko, E.J. Lanni, J.V. Sweedler, P.W. Bohn, Analyst 138, 2013, 1924–1939. DOI:10.1039/C3AN36416J

Storage and Uptake of D-Serine into Astrocytic Synaptic-like Vesicles Specify Gliotransmission, M. Martineau, T. Shi, J. Puyal, A.M. Knolhoff, J. Dulong, B. Gasnier, J. Klingauf, J.V. Sweedler, R. Jahn, J.-P. Mothet, J. Neuroscience. 33, 2013, 3413–3423. DOI:10.1523/JNEUROSCI.3497-12.2013

Automated Method for Analysis of Tryptophan and Tyrosine Metabolites Using Capillary Electrophoresis with Native Fluorescence Detection, C.A. Dailey, N. Garnier, S.S. Rubakhin, J.V. Sweedler, Anal. Bioanal. Chem. 405, 2013, 2451–2459. DOI:10.1007/s00216-012-6685-0

Quantitative Peptidomics for Discovery of Circadian-related Peptides from the Rat Suprachiasmatic Nucleus, J. E. Lee, L. Zamdborg, B. Southey, N. Atkins, Jr., J.W. Mitchell, M. Li, M.U. Gillette, N.L. Kelleher, J.V. Sweedler, J. Proteome Res. 12, 2013, 585–593. DOI:10.1021/pr300605p

Progress Toward Single Cell Metabolomics, S.S. Rubakhin, E.J. Lanni, J.V. Sweedler, Curr. Opin. Biotechnol. 24, 2013, 95–104. DOI:10.1016/j.copbio.2012.10.021

Top Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions, A.D Catherman, M. Li, J.C. Tran, K.R. Durbin, P.D. Compton, B.P. Early, P.M. Thomas, N.L. Kelleher, Anal. Chem. 85, 2013, 1880–1888. DOI:10.1021/ac3031527

TOP

2012

Evaluation of Database Search Programs for Accurate Detection of Neuropeptides in Tandem Mass Spectrometry Experiment, M.N. Akhtar, B.R.Southey, P.E.Andrén, J.V. Sweedler, S.L. Rodriguez-Zas, J. Proteome Res. 11, 2012, 6044–6055. DOI:10.1021/pr3007123

Analyses of Pig Genomes Provide Insight into Porcine Demography and Evolution,M.A. Groenen et al., Nature 491, 2012, 393–398. DOI:10.1038/nature11622 [Featured on the journal cover.]

Urotensin II in Invertebrates: From Structure to Function in Aplysia californica, E.V. Romanova, K. Sasaki, V. Alexeeva, F.S. Vilim, J. Jing, T.A. Richmond, K.R. Weiss, J.V. Sweedler, PlosOne 7, 2012, e48764. Free Article

Microfluidic Device for the Selective Chemical Stimulation of Neurons and Characterization of Peptide Release with Mass Spectrometry, C.A. Croushore, S.Supharoek, C.Y. Lee, J. Jakmunee, J. V. Sweedler, Anal. Chem. 84, 2012, 9446–9452. DOI:10.1021/ac302283u

Relative Quantitation of Neuropeptides Over a Thousand-fold Concentration Range, X. Hou, F. Xie, J.V. Sweedler, J. Amer. Soc. Mass Spectrom. 23, 2012, 2083–2093. DOI: 10.1007/s13361-012-0481-0

Single-cell Metabolomics: Changes in the Metabolome of Freshly Isolated and Cultured Neurons, P. Nemes, A.M. Knolhoff, S.S. Rubakhin, J.V. Sweedler, ACS Chem. Neurosci. 3, 2012, 782–792. DOI:10.1021/cn300100u [Featured on the journal cover.]

Secondary Ion Mass Spectrometry Imaging of Molecular Distributions in Cultured Neurons and their Processes: Comparative Analysis of Sample Preparation, K.R. Tucker, Z. Li, S. S. Rubakhin, J.V. Sweedler, J. Amer. Soc. Mass Spectrom. 23, 2012, 1931–1938. DOI:10.1007/s13361-012-0472-1

Comparative Peptidomics Analysis of Neural Adaptations in Rats Repeatedly Exposed to Amphetamine, E.V. Romanova, J.E. Lee, N.L. Kelleher, J.V. Sweedler, J.M. Gulley, J. Neurochem. 123, 2012, 276–287. DOI:10.1111/j.1471-4159.2012.07912.x

Circadian Rhythm of Redox State Regulates Excitability in Suprachiasmatic Nucleus Neurons, T.A. Wang, Y.V. Yu , G. Govindaiah, X.Ye, L. Artinian, T.P. Coleman, J.V. Sweedler, C.L. Cox, M.U. Gillette, Science 337, 2012, 839–842. DOI:10.1126/science.1222826

Evaluation of the Compact High-Field Orbitrap for Top-Down Proteomics of Human Cells, D.R. Ahlf, P.D. Compton, J.C.Tran, B.P. Early, P.M. Thomas, N.L. Kelleher, J. Proteome Res 11, 2012, 4308–14. DOI:10.1021/pr3004216

Microarray Analysis of Natural Socially Regulated Plasticity in Circadian Rhythms of Honey Bees, S.L. Rodriguez-Zas, B.R. Southey, Y. Shemesh, E.B. Rubin, M. Cohen, G.E. Robinson,G. Bloch, J. Biol. Rhythms 27, 2012, 12–24. DOI:10.1177/0748730411431404

D-aspartate Acts as a Signaling Molecule in Nervous and Neuroendocrine Systems, N. Ota,T. Shi, J.V. Sweedler, Amino Acids 43, 2012, 1873–1886. DOI:10.1007/s00726-012-1364-1

Targeted Single Cell Microchemical Analysis: MS-based Peptidomics of Individual Paraformaldehyde-fixed Immunolabeled Neurons, S. Neupert, S.S. Rubakhin, J.V. Sweedler, Chem. Biol. 19, 2012, 1010–1019. DOI:10.1016/j.chembiol.2012.05.023

First Survey and Functional Annotation of Prohormone and Convertase Genes in the Pig, K.I. Porter, B.R. Southey, J.V. Sweedler, S. L. Rodriguez-Zas, BMC Genomics 15, 2012, 582. DOI:10.1186/1471-2164-13-582

Peptidomic Analyses of Mouse Astrocytic Cell Lines and Rat Primary Cultured Astrocytes, P. Yin, A.M. Knolhoff, H.J. Rosenberg, L.J. Millet, M.U. Gillette, J.V. Sweedler, J. Proteome Res. 75, 2012, 5036–5051. DOI:10.1021/pr201066t

A Protease for Middle Down Proteomics, C. Wu, J.C. Tran, L.Zamdborg, K.R. Durbin, M. Li, D.R. Ahlf, B.P. Early, P.M. Thomas, J.V. Sweedler, N.L. Kelleher, Nat. Methods 9, 2012, 822–824. DOI:10.1038/nmeth.2074

Mass Spectrometry Imaging and Profiling of Single Cells, E. J. Lanni, S.S. Rubakhin, J.V. Sweedler, J. Proteomics 75, 2012, 5036–5051. DOI:10.1016/j.jprot.2012.03.017

Therapeutic Peptide Production in Drosophila, D. Park, X. Hou, J. V. Sweedler, P. H. Taghert, Peptides 36, 2012, 251–256. DOI:10.1016/j.peptides.2012.05.003

Serotonin of Mast Cell Origin Contributes to Hippocampal Function, K.M. Nautiyal, C.A. Dailey, J.A. Jahn, E. Rodriguez, N.H. Son, J.V Sweedler, R. Silver, Eur. J. Neuroscience 36, 2012, 2347–2359. DOI:10.1111/j.1460-9568.2012.08138.x

Label-Free Quantitation of Peptide Release from Neurons in a Microfluidic Device with Mass Spectrometry Imaging, M. Zhong, C.Y. Lee, C. Croushore, J.V. Sweedler, Lab Chip 12, 2012, 2037–2045. DOI:10.1039/C2LC21085A

The Hypothalamo-Neurohypophyseal System: from Genome to Physiology, D. Murphy, A. Konopacka, C. Hindmarch, J. F.R. Paton, J.V. Sweedler, M.U. Gillette, Y. Ueta, V. Grinevich, M. Lozic, N. Japundzic-Zigon, J. Neuroendocrinol. 24, 2012, 539–553. DOI:10.1111/j.1365-2826.2011.02241.x

Sampling Techniques for Single Cell Electrophoresis, C. Cecala and J.V. Sweedler, Analyst 137, 2012, 2922–2929. DOI:10.1039/C2AN16211C

An Enhanced Protein Crosslink Identification Strategy using CID-Cleavable Chemical Crosslinkers and LC/MS(n) Analysis, F. Liu, C. Wu, J.V. Sweedler, M.B. Goshe, Proteomics 12, 2012, 401–405. DOI:10.1002/pmic.201100352

TOP

2011

Probing the Production of Amidated Peptides Following Genetic and Dietary Copper Manipulations, P. Yin, D. Bousquet-Moore, S.P. Annangudi, B.R. Southey, R.E. Mains, B.A. Eipper, J.V. Sweedler, PLOS ONE 6(12): e28679, 2011. DOI:10.1371/journal.pone.0028679

Collection of Peptides Released from Single Neurons with Particle-Embedded Monolithic Capillaries followed by Detection with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry, Y. Fan, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 83, 2011, 9557–9563. DOI:10.1021/ac202338e

Stretched Tissue Mounting for MALDI Mass Spectrometry Imaging, K.R. Tucker, E.J. Lanni, L.A. Serebryannyy, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 83, 2011, 9181–9185. DOI:10.1021/ac201857k

Neuropeptidomics: Mass Spectrometry-based Qualitative and Quantitative Analysis, P. Yin, X. Hou, E.V. Romanova, J.V. Sweedler, Methods Mol. Biol. 789, 2011, 223–236. DOI: 10.1007/978-1-61779-310-3_14

Mice Deficient in Endothelin-Converting Enzyme-2 (ECE-s) Exhibit Altered Morphine Responses and Peptide Levels in the Spinal Cord,L. Miller, X. Hou, R.M. Rodriguiz, K. Gagnidze, J.V. Sweedler, W.C. Wetsel, L.A. Devi, J. Neurochem. 119, 2011, 1074–1085. DOI:10.1111/j.1471-4159.2011.07513.x

Chronic Morphine Alters the Presynaptic Protein Profile: Identification of Novel Molecular Targets using Proteomics and Network Analysis, N.S. Abul-Husn, S.P. Annangudi, A. Ma’ayan, D.L. Ramos-Ortolaza, J.V. Sweedler, L.A. Devi, PLOS ONE 6, 2011, e25535s. DOI:10.1371/journal.pone.0025535

Molecular Organization of Drosophila Neuroendocrine Cells by DIMMED,
D. Park, T. Hadžić, P. Yin, J. Rusch, K. Abruzzi, M. Rosbash, J.B. Skeath, S. Panda, J.V Sweedler, P.Taghert, Curr. Biol. 21, 2011, 1515–1524. DOI:10.1016/j.cub.2011.08.015 

Small Molecule Analysis and Imaging of Fatty Acids in the Zebra Finch Song System Using Time-of-Flight-Secondary Ion Mass Spectrometry,
K.R. Amaya, J.V. Sweedler, and D. F. Clayton, J. Neurochem. 118, 2011, 499–511. DOI:10.1111/j.1471-4159.2011.07274.x

Direct Cellular Peptidomics of Hypothalamic Neurons, J.W. Mitchell, N. Atkins, Jr., J.V. Sweedler, M.U. Gillette, Front. Neuroendocrinol. 32, 2011, 377–386. DOI:10.1016/j.yfrne.2011.02.005

The Notch Effector Gene Hes1 Regulates Migration of Hypothalamic Neurons, Neuropeptide Content and Axon Targeting to the Pituitary, P.K. Aujla, A. Bora, P. Monahan, J.V. Sweedler, L.T. Raetzman, Dev. Biol. 353, 2011, 61–71. DOI:10.1016/j.ydbio.2011.02.018

MALDI Mass Spectrometric Imaging of Neuronal Cell Cultures, T.A. Zimmerman, S.S. Rubakhin, J.V. Sweedler, J. Amer. Soc. Mass Spectrom. 5, 2011, 828–836. DOI:10.1007/s13361-011-0111-2

Profiling Metabolites and Peptides in Single Cells, S.S. Rubakhin, E.V. Romanova, P. Nemes, J.V. Sweedler, Nat. Methods 8, 2011, S20–S29. DOI:10.1038/nmeth.1549

The Modified-Bead Stretched Sample Method: Development and Application to MALDI-MS Imaging of Protein Localization in the Spinal Cord, K.R. Tucker, L.A. Serebryannyy, T.A. Zimmerman, S.S. Rubakhin, J.V. Sweedler, Chem. Sci. 2, 2011, 785–795. DOI: 10.1039/C0SC00563K

Diversity of Conotoxin Types from Conus californicus Reflects a Diversity of Prey Types and a Novel Evolutionary History, C.A. Elliger, T.A. Richmond, Z.N. Lebaric, N.T. Pierce, J.V. Sweedler, W. F. Gilly, Toxicon 57, 2011, 311–322. DOI:10.1016/j.toxicon.2010.12.008

A Diverse Family of Novel Peptide Toxins from an Unusual Cone Snail, Conus californicus, W.F. Gilly, T.A. Richmond, T.F. Duda, Jr., C. Elliger, Z. Lebaric, J. Schulz, J.P. Bingham, J.V. Sweedler, J. Exp. Biol. 214, 2011, 147–161. DOI: 10.1242/jeb.046086

Microarray Analysis of Natural Socially Regulated Plasticity in Circadian Rhythms of Honey Bees,  S.L.  Rodriguez-Zas,  B.R.  Southey,  Y.  Shemesh,  E.B.  Rubin,  M.  Cohen,  G.E. Robinson, G. Bloch, J. Biol. Rhythms 27, 2012, 12–24. DOI:10.1177/0748730411431404

Analysis of Intact Protein Isoforms by Mass Spectrometry, J.D. Tipton, J.C. Tran, A.D. Catherman, D.R. Ahlf, K.R. Durbin, N.L. Kelleher, J. Biol. Chem. 286, 2011, 25451–25458.DOI:10.1074/jbc.R111.239442

On the Scalability and Requirements of Whole Protein Mass Spectrometry, P.D. Compton, L. Zamdborg, P.M. Thomas, N.L. Kelleher, Anal Chem. 83, 2011, 6868–6874. DOI:10.1021/ac2010795

Mapping Intact Protein Isoforms in Discovery Mode Using Top-Down Proteomics, J.C. Tran, L. Zamdborg, D.R. Ahlf, J.E. Lee, A.D. Catherman, K.R. Durbin, J.D. Tipton, A. Vellaichamy, J.F. Kellie, M. Li, C. Wu, S.M. Sweet, B.P. Early, N. Siuti, R.D. LeDuc, P.D. Compton, P.M. Thomas, N.L. Kelleher, Nature 480, 2011, 254–258. DOI:10.1038/nature10575

Voluntary Wheel Running Reverses Age-Induced Changes in Hippocampal Gene Expression, R.A. Kohman, S.L. Rodriguez-Zas, B.R. Southey, K.W. Kelley, R. Dantzer, J.S. Rhodes, PLoS One 6, 2011, e22654. DOI:10.1371/journal.pone.0022654

Cell Cycle and Aging, Morphogenesis, and Response to Stimuli Genes are Individualized Biomarkers of Glioblastoma Progression and Survival, N.V. Serão, K.R. Delfino, B.R. Southey, J.E. Beever, S.L. Rodriguez-Zas, BMC Med. Genomics 4, 2011, 49. DOI:10.1186/1755-8794-4-49

Transferase Activity Function and System Development Process are Critical in Cattle Embryo Development, H.A. Adams, B.R. Southey, R.E. Everts, S.L. Marjani, C.X. Tian, H.A. Lewin, S.L. Rodriguez-Zas, Funct. Integr. Genomics 11, 2011,139–150. DOI:10.1007/s10142-010-0189-9

Therapy-, Gender- and Race-Specific MicroRNA Markers,Target Genes and Networks Related To Glioblastoma Recurrence and Survival, K.R. Delfino, N.V. Serão, B.R. Southey, S.L. Rodriguez-Zas, Cancer Genomics Proteomics 8, 2011, 173–83. 

Transferase Activity Function and System Development Process are Critical in Cattle Embryo Development, H.A. Adams, B.R. Southey, R.E. Everts, S.L. Marjani, C.X. Tian, H.A. Lewin, S.L. Rodriguez-Zas, Funct. Integr. Genomics 1, 2011, 139–150. DOI:10.1007/s10142-010-0189-9

Discovery of Gene Network Variability Across Samples Representing Multiple Classes, Y. Ko, C. Zhai, S.L. Rodriguez-Zas, Int. J. Bioinform. Res. Appl. 6, 2010, 402–417.

TOP

2010

Feedforward Compensation Mediated by the Central and Peripheral Actions of a Single Neuropeptide Discovered Using Representational Difference Analysis, J. Jing, J.V. Sweedler, E.C. Cropper, V. Alexeeva, J.-H. Park, E.V. Romanova, F. Xie, N.C. Dembrow, B.C. Ludwar, Kl.R. Weiss, F.S. Vilim, J. Neurosci. 30, 2010, 16545–16558. DOI:10.1523/JNEUROSCI.4264-10.2010 [Featured on the journal cover.]

Synthesis, Accumulation, and Release of D-Aspartate in the Aplysia californica Central Nervous System, C. Scanlan, T. Shi, N.G. Hatcher, S.S. Rubakhin, J.V. Sweedler, J. Neurochem. 115, 2010,1234–1244. DOI:10.1111/j.1471-4159.2010.07020.x

Genome-Wide Analyses Reveal a Role for Peptide Hormones in Planarian Germline Development, J.J. Collins, III, X. Hou, E.V. Romanova, B.G. Lambrus, C.M. Miller, A. Saberi, J.V. Sweedler, P.A. Newmark, PLOS Biol. 8, 2010, e10000509. Epub available. DOI:10.1371/journal.pbio.1000509

Circadian Integration of Glutamatergic Signals by Little SAAS in Novel Suprachiasmatic Circuits, N. Atkins, Jr., J.W. Mitchell, E.V. Romanova, D.J. Morgan, T.P. Cominski, J.L. Ecker, J.E. Pintar, J.V. Sweedler, M.U. Gillette, PLOS One 5, 2010, e12612. DOI:10.1371/journal.pone.0012612

Mass Spectrometry Screening Reveals Peptides Modulated Differentially in the Medial Prefrontal Cortex of Rats with Disparate Initial Sensitivity to Cocaine, E.V. Romanova, J.E. Lee, N.L. Kelleher, J.V. Sweedler, J.M. Gulley, AAPS J. 12, 2010, 443–454. DOI:10.1208/s12248-010-9204-2

Intact Mass Detection, Interpretation, and Visualization to Automate Top-Down Proteomics on a Large Scale. K.R. Durbin, J.C. Tran, L. Zamdborg, S.M. Sweet, A.D. Catherman, J.E. Lee, M. Li, J.K. Kellie, N.L. Kelleher, Proteomics 10, 2010, 3589–3597. DOI:10.1002/pmic.201000177

Serotonin and its Metabolism in Basal Deuterostomes: Insights from Strongylocentrotus purpuratus and Xenoturbella bocki, L.N. Squires, S.S. Rubakhin, A. Amare, K.N. Talbot, H. Nakano, L.L. Moroz, J.V. Sweedler, J. Exp. Biol. 213, 2010, 2647–2654. DOI:10.1242/jeb.042374

The Zebra Finch Neuropeptidome: Prediction, Detection and Expression, F. Xie, S.E. London, B.R. Southey, S.P. Annangudi, A. Amare, S.L. Rodriguez-Zas, D.F. Clayton, J.V. Sweedler, BMC Biology 8, 2010, 28. DOI:0.1186/1741-7007-8-28.

The Genome of a Songbird, W.C. Warren et al., Nature 464, 2010, 757–762. DOI:10.1038/nature08819

A Mass Spectrometry Primer for Mass Spectrometry Imaging, S.S. Rubakhin, J.V. Sweedler, Methods Mol. Biol. 656, 2010, 21–49. DOI:10.1007/978-1-60761-746-4_2

Mass Spectrometry Imaging using the Stretched Sample Approach, T.A. Zimmerman, S.S. Rubakhin, J.V. Sweedler, Methods Mol. Biol. 656, 2010, 465–479. DOI:10.1007/978-1-60761-746-4_27

Composite Modulatory Feedforward Loop Contributes to the Establishment of a Network State, J-S Wu, F.S. Vilim, N. G. Hatcher, M.R. Due, J.V. Sweedler, K.R. Weiss, J. Jing, J. Neurophysiol. 103, 2010, 2174–2184. DOI:10.1152/jn.01054.2009

Single Cell Mass Spectrometry, A.M. Knolhoff, S.S. Rubakhin, J.V. Sweedler, in Chemical Cytometry – Ultrasensitive Analysis of Single Cells, John Wiley & Sons, Inc., 2010, 197–218.

Quantitative Neuroproteomics of the Synapse, D.L. Ramos-Ortolaza, I. Bushlin, N. Abul-Husn, S.P. Annangudi, J.V. Sweedler, L.A. Devi, Methods Mol. Biol. 615, 2010, 227–246. DOI:10.1007/978-1-60761-535-4_18

Neuropeptide Release is Impaired in a Mouse Model of Fragile-X Mental Retardation Syndrome, S.P. Annangudi,  A.E. Luszpak, S.H..Kim, S. Ren,  N.G. Hatcher,  I.J. Weiler,  K.T. Thornley, B.M. Kile, R.M. Wightman, W.T. Greenough, J.V. Sweedler, ACS Chem. Neurosci. 1, 2010, 306–314. DOI:10.1021/cn900036x

A Hybrid, De Novo Based, Genome-Wide Database Search Approach Applied to the Sea Urchin Neuropeptidome. G. Menschaert, T.T. Vandekerckhove, G. Baggerman, B. Landuyt, J.V. Sweedler, L. Schoofs, W. Luyten, W. Van Criekinge, J. Proteome Res. 9, 2010, 990–996. DOI:10.1021/pr900885k

Direct Cellular Peptidomics of Supraoptic Magnocellular and Hippocampal Neurons in Low-Density Co-Cultures, L.J Millet, A. Bora, J.V. Sweedler, M.U. Gillette, ACS Chem. Neurosci. 1, 2010, 36–48. DOI:10.1021/cn9000022

Production of Nitric Oxide within the Aplysia californica Nervous System, X. Ye, F. Xie, E.V. Romanova, S.S. Rubakhin, J.V. Sweedler, ACS Chem. Neurosci. 1, 2010, 182–193. DOI:10.1021/cn900016z

Endogenous Peptide Discovery of the Rat Circadian Clock: A Focused Study of the Suprachiasmatic Nucleus by Ultra-High Performance Tandem Mass Spectrometry, J.E. Lee, N.A. Atkins, Jr., N.G. Hatcher, L. Zamdborg, M.U. Gillette, J.V. Sweedler, N.L. Kelleher, Mol. Cell Proteomics 9, 2010, 285–297. DOI:10.1074/mcp.M900362-MCP200

Genome-wide Census and Expression Profiling of Chicken Neuropeptide and Prohormone Convertase Genes, K.R. Delfino, B.R. Southey, J.V. Sweedler, S.L. Rodriguez-Zas, Neuropeptides 44, 2010, 31–44. DOI:10.1016/j.npep.2009.11.002

Distinct Mechanisms Produce Functionally Complementary Actions of Neuropeptides that are Structurally Related but Derived from Different Precursors, F. Vilim, K. Sasaki, J. Rybak, V. Alexeeva, E. Cropper, J. Jing, I. Orekhova, V. Brezina, D. Price, E.V. Romanova, S.S. Rubakhin, N.G. Hatcher, J.V. Sweedler, K. Weiss, J. Neurosci. 30, 2010, 131–147. DOI:10.1523/​JNEUROSCI.3282-09.2010

Evaluating the Performance of New Approaches to Spot Quantification and Differential Expression in 2-Dimensional Gel Electrophoresis Studies, J.S. Morris, B.N. Clark, W. Wei, H.B. Gutstein, J. Proteome Res. 9, 2010, 595–604. DOI:10.1021/pr9005603

Discovery of Gene Network Variability Across Samples Representing Multiple Classes, Y. Ko, C. Zhai, S.L. Rodriguez-Zas, Int. J. Bioinform. Res. Appl. 6, 2010, 402-17. DOI:10.1504/IJBRA.2010.036002

Statistical Contributions to Proteomic Research, J.S. Morris, K.A. Baggerly, H.B. Gutstein, K.R. Coombes, Methods Mol. Biol 641, 2010, 143–66. DOI:10.1007/978-1-60761-711-2_9

Transcriptional Orchestration of the Regulated Secretory Pathway in Neurons by the bHLH Protein DIMM. Y. Hamanaka, D. Park, P. Yin, S.P. Annangudi, T.N. Edwards, J.V.Sweedler, I.A. Meinertzhagen, P.H. Taghert, Curr. Biol. 20, 2010, 1–10. DOI:10.1016/j.cub.2009.11.065

TOP

2009

MALDI Mass Spectrometric Imaging using the Stretched Sample Method to Reveal Neuropeptide Distributions in Aplysia Nervous Tissue, T.A. Zimmerman, S.S. Rubakhin, E.V. Romanova, K.R. Tucker, Jonathan V. Sweedler, Anal. Chem. 81, 2009, 9402–9409. DOI:10.1021/ac901820v

Characterizing Intercellular Signaling Peptides in Drug Addiction, E.V. Romanova, N.G. Hatcher, S.S. Rubakhin, J.V. Sweedler, Neuropharmacology 56, 2009, 196–204.DOI:10.1016/j.neuropharm.2008.07.036 

Analysis of Natural D-Amino Acid-Containing Peptides in Metazoa, L. Bai,  S. Sheeley, J.V. Sweedler, Bioanal. Rev. 1, 2009, 7–24. DOI:10.1007/s12566-009-0001-2

Discrete Molecular States in the Brain Accompany Changing Responses to a Vocal Signal, S. Dong, K.L. Replogle, L. Hasadsri, B.S. Imai, P.M. Yau, S.L Rodriguez-Zas, B.R. Southey, J.V. Sweedler, D.F. Clayton, Proc. Natl. Acad. Sci. U.S.A. 106, 2009, 11364–11369. DOI:10.1073/pnas.0812998106

Collecting Peptide Release from the Brain using Porous Polymer Monolith-Based Solid Phase Extraction Capillaries, J.M. Iannacone, S. Ren, N.G. Hatcher, J.V. Sweedler, Anal. Chem. 81, 2009, 5433–5438. DOI:10.1021/ac9005843

Characterization of the Prohormone Complement in Cattle using Genomic Libraries and Cleavage Prediction Approaches, B.R. Southey, S.L. Rodriguez-Zas, J.V Sweedler, BMC Genomics 10, 2009, 228. Open Access, BioMed Central

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution, Bovine Genome Sequencing and Analysis Consortium, Science 324, 2009, 522–528. DOI:10.1126/science.1169588 [Featured on the journal cover.]

Quantitative Peptidomics Reveal Brain Peptide Signatures of Behavior, A. Brockmann, S.P. Annangudi, T.A. Richmond, S.A. Ament, F. Xie, B.R. Southey, S.R. Rodriguez-Zas, G.E. Robinson, J.V. Sweedler, Proc. Natl. Acad. Sci. U.S.A. 106, 2009, 2383–2388. DOI:10.1073/pnas.0813021106

A Robust Two-Dimensional Separation for Top-Down Tandem Mass Spectrometry of the Low-Mass Proteome, J.-E. Lee, J.F. Kellie, J.C. Tran, J.D. Tipton, A.D. Catherman, H.M. Thomas, D R. Ahlf, K.R. Durbin, A. Vellaichamy, I. Ntai, A.G. Marshall, N.L. Kelleher, J. Am. Soc. Mass Spectrom. 20, 2009, 2183-91. DOI:10.1016/j.jasms.2009.08.001

A Python Analytical Pipeline to Identify Prohormone Precursors and Predict Prohormone Cleavage Sites, B. Southey, J.V. Sweedler, S.L. Rodriguez-Zas, Front. Neuroinformatics 2, 2009, Article 7. DOI:10.3389/neuro.11.007.2008

Inference of Gene Pathways using Mixture Bayesian Networks, Y. Ko, C. Zhai, S.L. Rodriguez-Zas, BMC Syst. Biol. 3, 2009, 54. DOI:10.1186/1752-0509-3-54

Textural Guidance Cues for Controlling Process Outgrowth of Mammalian Neurons, J.N. Hanson, M.J. Motola, M.L. Heien, J.W. Mitchell, M.U. Gillette, J.V. Sweedler, R.G. Nuzzo, Lab Chip 9, 2008, 122–131. DOI:10.1039/B803595D

TOP

2008

 Neuropeptidomics of the Rat Supraoptic Nucleus, A. Bora, S.P. Annangudi, L.J. Millet, S.S. Rubakhin, A.J. Forbes, N.L. Kelleher, M.U. Gillette, J.V. Sweedler, J. Proteome Res. 7, 2008, 4992–5003. DOI:10.1021/pr800394e

Quantitative Measurements of Cell-Cell Signaling Peptides with Single Cell MALDI MS, S.S. Rubakhin and J.V. Sweedler, Anal. Chem. 80, 2008, 7128–7136. DOI:10.1021/ac8010389

Imaging of Cells and Tissues with Mass Spectrometry: Adding Chemical Information to Imaging, T.A. Zimmerman, E.B. Monroe, K.R. Tucker, S.S. Rubakhin, J.V. Sweedler, Methods Cell Biol. 89, 2008, 361–390. DOI:10.1016/S0091-679X(08)00613-4  

Adapting the Stretched Sample Method from Tissue Profiling to Imaging, T.A. Zimmerman, E.B. Monroe, J.V. Sweedler, Proteomics 8, 2008, 3809–3815. DOI:10.1002/pmic.200800331

Mass Spectrometry-Based Discovery of Circadian Peptides, N.G. Hatcher, N. Atkins, Jr., S.P. Annangudi, A.J. Forbes, N.L. Kelleher, M.U. Gillette, J.V. Sweedler, Proc. Natl. Acad. Sci., U.S.A. 105, 2008, 12527–12532. DOI:10.1073/pnas.0804340105

SIMS and MALDI MS Imaging of the Spinal Cord. E.B. Monroe, S.P. Annangudi, N.G. Hatcher, H.B. Gutstein, S.S. Rubakhin, J.V. Sweedler, Proteomics 8, 2008, 3746–3754. DOI:10.1002/pmic.200800127

Proteotyping: Population Proteomics of Human Leukocytes using Top Down Mass Spectrometry. M.J. Roth, B.A. Parks, J.T. Ferguson, M.T. Boyne II, N.L. Kelleher, Anal. Chem. 80, 2008, 2857–2866. DOI:10.1021/ac800141g

Peptides in our Brain: Mass Spectrometric-Based Measurement Approaches and Challenges. L. Li and J.V. Sweedler, Annu. Rev. Anal. Chem. 1, 2008, 451–483. DOI:10.1146/annurev.anchem.1.031207.113053

Detecting D-Amino Acid-Containing Neuropeptides using Selective Enzymatic Digestion. M.A. Ewing, J. Wang, S.A. Sheeley, J.V. Sweedler, Anal. Chem. 80, 2008, 2874–2880. DOI:10.1021/ac7025173

One Step Sampling, Extraction and Storage Protocol for Neuropeptidomics using Dihydroxybenzoic Acid. E. Romanova, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 80, 2008, 3379–3386. DOI:10.1021/ac7026047

Insulin Signaling is Involved in the Regulation of Worker Division of Labor in Honey Bee Colonies. S.A Ament, M. Corona, H.S. Pollock, G.E. Robinson. Proc. Natl. Acad. Sci. U.S.A. 105, 2008, 4226–4231. DOI:10.1073/pnas.0800630105

Meta-Analysis of Genome-wide Expression Patterns Associated with Behavioral Maturation in Honey Bees, H.A. Adams, B. R. Southey, G.E. Robinson, S.L. Rodriguez-Zas, BMC Genomics 9, 2008, 503. DOI:10.1186/1471-2164-9-503

The Myth of Automated, High-throughput Two-dimensional Gel Analysis, B.N. Clark, N. Brittan, H.B. Gutstein, Proteomics 8, 2008, 1197–1203. DOI: 10.1002/pmic.200700709

Pinnacle: A Fast, Automatic and Accurate Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data. J.S. Morris, B.N. Clark, H.B. Gutstein, Bioinformatics 24, 2008, 529–536. DOI:10.1093/bioinformatics/btm590

Detection of Nitric Oxide in Single Cells. X. Ye, S.S Rubakhin, J.V. Sweedler, Analyst 133, 2008, 423–433 (review). DOI:10.1039/b716174c [Featured on the journal cover.]

Prediction of Neuropeptide Cleavage Sites in Insects. B.R. Southey, A.B. Hummon, T.A. Richmond, J.V. Sweedler, S.L. Rodriguez-Zas, Bioinformatics 24 , 2008, 815–825. DOI:10.1093/bioinformatics/btn044

Comparative Analysis of Neuropeptide Cleavage Sites in Human, Mouse, Rat, and Cattle. A.N. Tegge, B.R. Southey, J.V. Sweedler, S.L. Rodriguez-Zas, Mamm. Genome 19, 2008,106–120. DOI:10.1007/s00335-007-9090-9

Advancing the Understanding of the Embryo Transcriptome Co-Regulation Using Meta-, Functional, and Gene Network Analysis Tools: Focus on Mammalian Embryogenomics, S.L. Rodriguez-Zas, Y. Ko, H.A. Adams, B.R. Southey, Reproduction 135, 2008, 213–224. DOI:10.1530/REP-07-0391

Microproteomics: Analysis of Protein Diversity in Small Samples. H.B. Gutstein, J.S. Morris, S.B.A. Palani, J.V. Sweedler, Mass Spectrom. Rev. 27, 2008, 316–330. DOI:10.1002/mas.20161

Biological Interpretations of Transcriptomic Profiles in Mammalian Oocytes and Embryos: Focus on Mammalian Embryogenomics.S.L. Rodriguez-Zas, K. Schellander, and H.A. Lewin, Reproduction 135, 2008, 129–139. DOI:10.1530/REP-07-0426

Simultaneous Nitric Oxide and Dehydroascorbic Acid Imaging by Combining Diaminofluoresceins and Diaminorhodamines. X. Ye, S.S. Rubakhin, J.V. Sweedler, J. Neuro. Methods 15, 2008, 373–382. DOI:10.1016/j.jneumeth.2007.10.026 

5-HT and 5-HT-SO4, but not Tryptophan or 5-HIAA Levels in Single Feeding Neurons Track Animal Hunger State. N.G. Hatcher, X. Zhang, J.N. Stuart, L.L. Moroz, J.V. Sweedler, R. Gillette, J. Neurochem. 104, 2008, 1358–1363. DOI:10.1111/j.1471-4159.2007.05084.x

Aplysia Bag Cells Function as a Distributed Neurosecretory Network. N.G. Hatcher and J.V. Sweedler, J. Neurophysiol. 99, 2008, 333–343. DOI:10.1152/jn.00968.2007

Contributions of Capillary Electrophoresis to Neuroscience. T. Lapainis, J.V. Sweedler, J. Chromatogr. A 1184, 2008, 144–158. DOI:10.1016/j.chroma.2007.10.098

Mass Spectrometry of Proteins. E.V. Romanova, S.P. Annangudi, J.V. Sweedler, in The Encyclopedia of Neuroscience, edited by L. Squire et al., Elsevier Science, 2008, available online via Science Direct.

Light-Based Detection Methods for Capillary Electrophoresis. C. Scanlan, T. Lapainis and J.V. Sweedler, in CRC Handbook for Capillary Electrophoresis, 3rd Edition, edited by J.P. Landers, CRC Press, 2008, 305–334.

TOP

2007

Transparent Triethylamine Containing MALDI Matrices. S.S. Rubakhin, J.V. Sweedler, Israel J. Chem. 47, 2007, 185–193. DOI:10.1560/IJC.47.2.185

Mass Spectrometric Imaging of the Nervous System. S.S. Rubakhin, N.G. Hatcher, E.B. Monroe, M.L. Heien, J.V. Sweedler, Curr. Pharma. Design 13, 2007, 3325–3334. Abstract, DOI:10.2174/138161207782360708

Single Cell Measurements with Mass Spectrometry. E.B. Monroe, J.C. Jurchen, S.S. Rubakhin, J.V. Sweedler, in New Frontiers in Ultrasensitive Bioanalysis: Advanced Analytical Chemistry Applications in Nanobiotechnology, Single Molecule Detection, and Single Cell Analysis, Wiley Chemical Analysis Series, Edited by Xiaohong N. Xu, 2007, p. 269–293.

Using ProSight PTM v2.0 and Related Tools for Targeted Protein Identification and Characterization with High Mass Accuracy Tandem MS Data. R.D. LeDuc, N.L. Kelleher, Curr. Protoc. Bioinform. 19, 2007, 13.6.1–13.6.28. DOI:10.1002/0471250953.bi1306s19

Imaging MS in Proteomics. E.B. Monroe and J.V. Sweedler, in Encyclopedia of Separation Science, First On-line Update, Level III: Practical Applications, “Omics”: Proteomics, Edited by Ian D. Wilson, Elsevier Science, 2007. DOI:10.1016/B978-012226770-3/10714-9 

Serotonin Catabolism in the Central and Enteric Nervous Systems of Rats upon Induction of Serotonin Syndrome. L.N. Squires, K.N. Talbot, S.S. Rubakhin, J.V. Sweedler, J. Neurochem. 103, 2007, 174–180. DOI:10.1111/j.1471-4159.2007.04739.x

Enhanced Prediction of Cleavage in Bovine Precursor Sequences.A.N. Tegge, B.R. Southey, J.V. Sweedler, S.L. Rodriguez-Zas, Lecture Notes in Computer Science, Bioinformatics Research and Applications, Vol. 4463, pp. 350-360, 2007, Springer. DOI:10.1007/978-3-540-72031-7_32

ProSight PTM 2.0: Improved Protein Identification and Characterization for Top Down Mass Spectrometry. L. Zamdborg, R.D. LeDuc, K.J. Glowacz, Y.B. Kim, V. Viswanathan, I.T. Spaulding, B.P. Early, E.J. Bluhm, S. Babai, N.L. Kelleher, Nucleic Acids Res. 35 (web server issue), W701-706. DOI 10.1093/nar/gkm371

Top-down Proteomics on a Chromatographic Time Scale using Linear Ion Trap Fourier Transform Hybrid Mass Spectrometers. B.A. Parks, L. Jiang, P.M. Thomas, C.D. Wenger, M.J. Roth, M.T. Boyne II, P.V. Burke, K.E. Kwast, N.L. Kelleher, Anal. Chem. 79, 2007, 7984–7991. DOI:10.1021/ac070553t

Characterizing Individual Mammalian Cells using Mass Spectrometry. S.S. Rubakhin and J.V. Sweedler, Nat. Protoc. 8, 2007, 1987–1997. DOI:10.1038/nprot.2007.277

Microfluidic Devices for Culturing Primary Mammalian Neurons at Low Densities. L.J. Millet, M.E. Stewart, J.V. Sweedler, R.G. Nuzzo, M.U. Gillette, Lab Chip 7, 2007, 987–984. DOI:10.1039/b705266a [Featured on the journal cover.]

Neuropeptide Precursors in Tribolium castaneum. A. Amare and J.V. Sweedler, Peptides 28, 2007, 1282-1290. DOI:10.1016/j.peptides.2007.04.014 

Direct Immobilization of Fab' in Nanocapillaries for Manipulating Mass Limited Samples. B.Y. Kim, C.B. Swearingen, J.A. Ho, E.V. Romanova, P.W. Bohn, J.V. Sweedler, J. Am. Chem. Soc. 129, 2007, 7620-7626. DOI:10.1021/ja070041w

From Hunger to Satiety: Reconfiguration of a Feeding Network by Aplysia Neuropeptide Y. J. Jing, F.S. Vilim, C.C. Horn, V. Alexeeva, N.G. Hatcher, K. Sasaki, I. Yashina, Y. Zhurov, I. Kupfermann, J.V. Sweedler, K.R. Weiss, J. Neurosci. 27, 2007, 3490–3502. DOI:10.1523/JNEUROSCI.0334-07.2007

An Autonomic Control Network in Aplysia Driven by Central Command During Locomotion Includes Neurons that Express Splice-Variants of R15-Neuropeptides, E.V. Romanova, U.T. Koch, N. McKay, A.T. Green, K.R. Weiss, J.V. Sweedler, J. Koester, J. Neurophysiol. 97, 181–191, 2007. DOI:10.1152/jn.00581.2006

Laser Capture Sampling and Analytical Issues in Proteomics, H.B. Gutstein, J.S. Morris, Expert Rev Proteomics 4, 2007, 627–37. DOI:10.1586/14789450.4.5.627

Lipid Imaging in the Zebra Finch Brain with Secondary Ion Mass Spectrometry, K.R. Amaya, E.B. Monroe, J.V. Sweedler, D.F. Clayton, Int. J. Mass Spectrom. 260, 2007, 121–127. DOI:10.1016/j.ijms.2006.09.032

Measuring Salty Samples without Adducts with MALDI MS. E.B. Monroe, B.A. Koszczuk, J.L. Losh, J.V. Sweedler, Int. J. Mass Spectrom. 260, 2007, 237–242. DOI:10.1016/j.ijms.2006.08.019

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2006

From the Genome to the Proteome: Uncovering Peptides in the Apis Brain. A.B. Hummon, T.A. Richmond, P. Verleyen, G. Baggerman, J. Huybrechts, M A. Ewing, E. Vierstraete, S.L. Rodriguez-Zas, L. Schoofs, G.E. Robinson, J.V. Sweedler, Science 314, 2006, 647–649. DOI:10.1126/science.1124128

Insights into Social Insects from the Genome of the Honey Bee Apis mellifera, The Honey Bee Genome Sequencing Consortium, Nature 443, 2006, 931–949. DOI:10.1038/nature05260 [Featured on the journal cover.]

Profiling Signaling Peptides in Single Mammalian Cells using Mass Spectrometry. S.S. Rubakhin, J.D. Churchill, W.T. Greenough, J.V. Sweedler, Anal. Chem. 78, 2006, 7267–7272. DOI:10.1021/ac0607010

Massively Parallel Sample Preparation for the MALDI MS Analyses of Tissue. E.B. Monroe, J.C. Jurchen, B.A. Koszczuk, J.L. Losh, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 78, 2006, 6826–6832. DOI:10.1021/ac060652r

Identification and Characterization of Homologues of Vertebrate β-Thymosin in the Marine Mollusk Aplysia californica. E.V. Romanova, M.J. Roth, S.S. Rubakhin, J.A. Jakubowski, W.P. Kelley, M.D. Kirk, N.L. Kelleher, J.V. Sweedler, J. Mass Spectrom. 41, 2006, 1030–1040. DOI:10.1002/jms.1060

NeuroPred: A Tool to Predict Cleavage Sites in Neuropeptide Precursors and Provide the Masses of the Resulting Peptides. B. R. Southey, A. Amare, T.A. Zimmerman, S.L. Rodriguez-Zas, J.V. Sweedler, 2006, Nucleic Acids Res. 34, 2006, W267-272. Web server article

Bridging Neuropeptidomics and Genomics with Bioinformatics: Prediction of Mammalian Neuropeptide Prohormone Processing. A. Amare, A.B. Hummon, B.R. Southey, T.A. Zimmerman, S.L. Rodriguez-Zas, J.V. Sweedler, J. Proteome Res. 5, 2006, 1162–1167. DOI:10.1021/pr0504541

5-HT Catabolism and the Formation and Fate of 5-Hydroxyindole Thiazolidine Carboxylic Acid. L.N. Squires, J.A. Jakubowski, J.N. Stuart, S.S. Rubakhin, N.G. Hatcher, W.-S. Kim, K. Chen, J.C. Shih, I. Seif, J.V. Sweedler, J. Biol. Chem. 281, 2006, 13463–13471. DOI:10.1074/jbc.M602210200

Prediction of Neuropeptide Prohormone Cleavages with Application to Rfamides. B.R. Southey, S L. Rodriguez-Zas, J.V. Sweedler, Peptides 27, 2006, 1087–1098. DOI:10.1016/j.peptides.2005.07.026

The First γ-Carboxyglutamate-Containing Neuropeptide. J.A. Jakubowski, N.G. Hatcher, F. Xie, J.V. Sweedler, Neurochem. Intl. 49, 2006, 223–229. DOI:10.1016/j.neuint.2006.01.007

D-Aspartate as a Putative Cell-Cell Signaling Molecule in the Aplysia californica Central Nervous System. H. Miao, S.S. Rubakhin, C.R. Scanlan, L. Wang, J.V. Sweedler, J. Neurochem. 97, 2006, 595–606. DOI:10.1111/j.1471-4159.2006.03791.x

Discovering New Invertebrate Neuropeptides Using Mass Spectrometry. A.B. Hummon, A. Amare, J.V. Sweedler, Mass Spectrom. Rev. 25, 2006, 77–98. DOI:10.1002/mas.20055

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2005

A Multilayer Poly(dimethylsiloxane) Electrospray Ionization Emitter for Sample Injection and Online Mass Spectrometric Detection. J.M. Iannacone, J.A. Jakubowski, P.W. Bohn, J.V. Sweedler, Electrophoresis 26, 2005, 4684–4690. DOI:10.1002/elps.200500498

Identification of a New Neuropeptide Precursor Reveals a Novel Source of Extrinsic Modulation in the Feeding System of Aplysia. A. Proekt, F.S. Vilim, V. Alexeeva, V. Brezina, A. Friedman, J. Jing, L. Li, Y. Zhurov, J.V. Sweedler, K.R. Weiss, J. Neurosci. 25, 2005, 9637–9648. DOI:10.1523/JNEUROSCI.2932-05.2005

Profiling Ph Gradients Across Nanocapillary Array Membranes Connecting Microfluidic Channels. K. Fa, J.J. Tulock, J.V. Sweedler, P.W. Bohn, J. Am. Chem. Soc. 127, 2005, 13928–13933. DOI:10.1021/ja052708p

Vitamin E Imaging and Localization in the Neuronal Membrane. E.B. Monroe, J.C. Jurchen, J. Lee, S.S. Rubakhin, J.V. Sweedler, J. Am. Chem. Soc. 127, 2005, 12152–12153. DOI:10.1021/ja051223y

MALDI-MS Imaging of Features Smaller than the Size of the Laser Beam. J.C. Jurchen, S.S. Rubakhin, J.V. Sweedler, J. Am. Soc. Mass. Spectrom. 16, 2005, 1654–1659. DOI:10.1016/j.jasms.2005.06.006

Measuring D-Amino Acid-Containing Neuropeptides with Capillary Electrophoresis. S.A. Sheeley, H. Miao, M.A. Ewing, S.S. Rubakhin, J.V. Sweedler, Analyst 130, 2005, 1198-1203. DOI:10.1039/b504717j

Imaging Mass Spectrometry: Fundamentals and Applications to Drug Discovery. S.S. Rubakhin, J.C. Jurchen, E.B. Monroe, J.V. Sweedler, Drug Discov. Today 10, 2005, 823–837. DOI:10.1016/S1359-6446(05)03458-6

Online Microdialysis-Dynamic Nanoelectrospray Ionization-Mass Spectrometry for Monitoring Neuropeptide Secretion. J.A. Jakubowski, N.G. Hatcher, J.V. Sweedler, J. Mass Spectrom. 40, 2005, 924–931. DOI:10.1002/jms.869

The Detection of Nitrated Tyrosine in Neuropeptides: A MALDI Matrix-Dependent Response. S.A. Sheeley, S.S. Rubakhin, J.V. Sweedler, Anal. Bioanal. Chem. 382, 2005, 22–27. DOI:10.1007/s00216-005-3145-0

New and Automated MSn Approaches for Top-Down Identification of Modified Proteins. V. Zabrouskov, M.W. Senko, Y. Du, R.D. Leduc, N.L. Kelleher, J. Am. Soc. Mass. Spectrom. 16, 2005, 2027–2038. DOI:10.1016/j.jasms.2005.08.004

Precise and Parallel Characterization of Coding Polymorphisms, Alternative Splicing, and Modifications in Human Proteins by Mass Spectrometry. M.J. Roth, A.J. Forbes, M.T. Boyne 2nd, Y.B. Kim, D.E. Robinson, N.L. Kelleher, Mol. Cell Proteomics 4, 2005, 1002–1008. DOI:10.1074/mcp.M500064-MCP20

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