Publications

2008 -- 2007 -- 2006 -- 2005

2009

Distinct Nitric Oxide Sources within the Aplysia californica Nervous System, X. Ye, F. Xie, E.V. Romanova, S.S. Rubakhin, J.V. Sweedler, ACS Chem. Neurosci., 2009, in press.

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, 2009, in press. Epub available. DOI:10.1074/mcp.M900362-MCP200

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., 2009, in press. Epub available. DOI:10.1021/cn900011n

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., 2009, in press. Epub available. DOI:10.1021/ac901820v

Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection for Single Cell Metabolomics, T. Lapainis, S.S. Rubakhin, J.V. Sweedler, Anal. Chem. 81, 2009, 5858-5864. DOI:10.1021/ac900936g

Analysis of Natural D-Amino Acid-Containing Peptides in Metazoa, L. Bai,  S. Sheeley, J.V. Sweedler, Bioanal. Rev., 2009, in press. Epub available. 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

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

Chapter 13: 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, 2009, 361-390. DOI:10.1016/S0091-679X(08)00613-4  

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

2008

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

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

Characterizing Intercellular Signaling Peptides in Drug Addiction, E.V. Romanova, N.G. Hatcher, S.S. Rubakhin, J.V. Sweedler, Neuropharmacology, 2008, in press. Epub available online. DOI:10.1016/j.neuropharm.2008.07.036 

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

A 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

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

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 New Encyclopedia of Neuroscience, edited by L. Squire et al., 2008, in press.

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.

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

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

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

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. 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. Abstract

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, Electrophoresis26, 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. Abstract

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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