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Herrera A, Muroski J, Sengupta R, Nguyen HH, Agarwal S, Ogorzalek Loo RR, Mattoo S, Loo JA, and Satchell KJF. “N‐terminal autoprocessing and acetylation of multifunctionalautoprocessing repeats‐in‐toxins (MARTX) Makes Caterpillars Floppy‐like effector is stimulated by adenosine diphosphate (ADP)‐Ribosylation Factor 1 in advance of Golgi fragmentation.” Celluar Microbiol 2020; 22: e13133.

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Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolic L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, and Kelleher NL. “A five-level classification system for proteoform identifications.” Nature Methods 2019; 16: 939–940.

Liu K, Singer E, Cohn W, Micewicz ED, McBride WH, Whitelegge JP, and Loo JA. “Time-Dependent Measurement of Nrf2-Regulated Antioxidant Response to Ionizing Radiation towards Biomarker Development for Acute Radiation Injury.” Proteomics Clin Appl 2019; 13 (6), e1900035.

Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chan B, Lantz C, Jung W, Johnson K, Koller A, Wolff J, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Paša-Tolić L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, and Agar JN. “Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.” Nature Methods 2019; 16: 587–594.

Campuzano IDG, Robinson J, Hui JO, Shi S, Netirojjanakul C, Nshanian M, Lippens JL, Bagal D, Egea P, Loo JA, and Bern M. “Native and Denaturing MS Protein Deconvolution for Biopharma: mAbs and Antibody-Drug Conjugates to Polydisperse Membrane Proteins and Beyond.” Anal Chem 2019; 91: 9472-9480.

Lermyte F, Tsybin YO, O’Connor PB, and Loo JA. “Top or middle? Up or down? A standard lexicon for protein top-down and allied mass spectrometry approaches.” J Am Soc Mass Spectrom 2019; 30: 1149-1157.

James KL, Kung JW, Crable BR, Mouttaki H, Sieber JR, Nguyen HH, Yang Y, Xie Y, Erde J, Wofford NQ, Karr EA, Loo JA, Ogorzalek Loo RR, Gunsalus RP, and McInerney MJ. “Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids.” Environ Microbiol 2019; 21(5): 1833-1846.

Warmack RA, Shawa H, Liu K, Lopez K, Loo JA, Horwitz J, and Clarke SG. “The L-isoaspartate modification within protein fragments in the aging lens can promote protein aggregation.” J Biol Chem 2019; 294(32): 12203-12219.

Malik R, Meng H, Wongkongkathep P, Corrales CI, Sepanj N, Atlasi RS, Klärner F-G, Schrader T, Spencer MJ, Loo JA, Wiedau M, and Bitan G. “The molecular tweezer CLR01 inhibits aberrant superoxide dismutase 1 (SOD1) self-assembly in vitro and in the G93A-SOD1 mouse model of ALS.” J Biol Chem 2019; 294: 3501–3513.

Nshanian M, Lantz C, Wongkongkathep P, Schrader T, Klärner F-G, Blümke A, Despres C, Ehrmann M, Smet-Nocca C, Bitan G, and Loo JA. “Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator.” J. Am. Soc. Mass Spectrom. 2019; 30: 16-23.

Lakshmanan R and and Loo JA. “Top-Down Protein Identification using a Time-of-Flight Mass Spectrometer and Data Independent Acquisition.” Int. J. Mass Spectrom. 2019; 435: 136–144.

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Nshanian M, Lakshmanan R, Chen H, Ogorzalek Loo RR, and Loo JA. “Enhancing Sensitivity of Liquid Chromatography/Mass Spectrometry of Peptides and Proteins Using Supercharging Agents.” Int. J. Mass Spectrom. 2018; 427: 157-164.

Susa AC, Lippens JL, Xia Z, Loo JA, Campuzano IDG, and Williams ER. “Submicrometer Emitter ESI Tips for Native Mass Spectrometry of Membrane Proteins in Ionic and Non-ionic Detergents.” J. Am. Soc. Mass Spectrom. 2018; 29: 203-206.

Lippens JL, Nshanian M, Spahr C, Egea PF, Loo JA, and Campuzano IDG. “Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry as a Platform for Characterizing Multimeric Membrane Protein Complexes.” J. Am. Soc. Mass Spectrom. 2018; 29: 183-193.

Li H, Nguyen HH, Ogorzalek Loo RR, Campuzano IDG, and Loo JA. “An Integrated Native Mass Spectrometry and Top-Down Proteomics Method that Connects Sequence to Structure and Function of Macromolecular Complexes.” Nature Chem. 2018; 10: 139-148.

Micewicz ED, Kim K, Iwamoto KS, Ratikan JA, Cheng G, Boxx GM, Damoiseaux RD, Whitelegge JP, Ruchala P, Nguyen C, Purbey P, Loo J, Deng G, Jung ME, Sayre JW, Norris AJ, Schaue D, and McBride WH. “4-(Nitrophenylsulfonyl)piperazines mitigate radiation damage to multiple tissues.” PLoS One 2017; 12(7): e0181577.

Choi TS, Lee J, Han JY, Jung BC, Wongkongkathep P, Loo JA, Lee MJ, and Kim HI. “Supramolecular Modulation of Structural Polymorphism in Pathogenic α-Synuclein Fibrils Using Copper(II) Coordination.” Angew. Chem. Int. Ed. 2018; 57, 3099-3103.

Polasky DA, Lermyte F, Nshanian M, Sobott F, Andrews PC, Loo JA, and Ruotolo BT. “Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes.” Anal. Chem. 2018; 90: 2756−2764.

Lermyte F, Valkenborg D, Loo JA, and Sobott F. “Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure.” Mass Spectrom. Rev. 2018; 37: 750–771.

Campuzano IDG, Netirojjanakul C, Nshanian M, Lippens JL, Kilgour D, Van Orden S and Loo JA. “Native-MS Analysis of Monoclonal Antibody Conjugates by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.” Anal. Chem. 2018; 90: 745−751.

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CC, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schluter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlen M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, and Zhang B. “How many human proteoforms are there?” Nature Chem. Biol. 2018; 14: 206-214

Le Duc RD, Schwammle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, and Tsybin YO. “ProForma: A Standard Proteoform Notation.” J. Proteome Res. 2018; 17: 1321-1325.

Chang C, Amer BR, Osipiuk J, McConnell SA, Huang I-H, Hsieh V, Fu J, Nguyen HH, Muroski J, Flores E, Ogorzalek Loo RR, Loo JA, Putkey JA, Joachimiak A, Das A, Clubb RT, and Ton-That H. “In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linking.” Proc. Natl. Acad. Sci. USA 2018; 115: E5477-E5486.

McConnell SA, Amer BR, Muroski J, Fu J, Chang C, Ogorzalek Loo RR, Loo JA, Osipiuk J, Ton-That H, and Clubb RT. “Protein Labeling via a Specific Lysine-Isopeptide Bond Using the Pilin Polymerizing Sortase from Corynebacterium diphtheria.” J. Am. Chem. Soc. 2018; 140: 8420-8423.

Wongkongkathep P, Han JY, Choi TS, Yin S, Kim HI, and Loo JA. “Native Top-Down Mass Spectrometry and Ion Mobility MS for Characterizing the Cobalt and Manganese Metal Binding of α-Synuclein Protein.” J. Am. Soc. Mass Spectrom. 2018; 29: 1870-1880.

Cleary SP, Li H, Bagal D, Loo JA, Campuzano IDG, and Prell JS. “Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics.” J. Am. Soc. Mass Spectrom. 2018; 29: 2067-2080.

Lippens JL, Egea PF, Spahr C, Vaish A, Keener JE, Marty MT, Loo JA, and Campuzano IDG1. “A Rapid LC-MS Method for Accurate Molecular Weight Determination of Membrane and Hydrophobic Proteins.” Anal. Chem. 2018; 90: 13616-13623.

Simonian M, Shirasaki D, Lee VS, Bervini D, Grace M, Ogorzalek Loo RR, Loo JA, Molloy MP, and Stoodley MA. “Proteomics identification of radiation-induced changes of membrane proteins in the rat model of arteriovenous malformation in pursuit of targets for brain AVM molecular therapy.” Clin Proteomics 2018; 15: 43 (8 pp).

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Halford J, Shen S, Itamura K, Levine J, Chong AC, Czerwieniec G, Glenn TC, Hovda DA, Vespa P, Bullock R, Dietrich DW, Mondello S, Loo JA and Wanner I-B. “New Astroglial Injury Defined Biomarkers for Neurotrauma Assessment.” J. Cerebral Blood Flow Metab. 2017; 37: 3278–3299.

Zhang J, Ogorzalek Loo RR, and Loo JA. “Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry.” J. Am. Soc. Mass Spectrom. 2017; 28: 1815-1822.

Briegel A, Oikonomou CM, Chang YW, Kjaer A, Huang AN, Kim KW, Ghosal D, Nguyen HH, Kenny D, Ogorzalek Loo RR, Gunsalus RP, and Jensen GJ. “Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis” EMBO Rep. (2017), e201744070. doi:10.15252/embr.201744070

Zimmer RK, Ferrier GA, Kim SJ, Ogorzalek Loo RR, Zimmer CA, and Loo JA. “Keystone predation and molecules of keystone significance” Ecology (2017), 98: 1710–1721. doi:10.1002/ecy.1849

Takemori N, Takemori A, Wongkongkathep P, Nshanian M, Ogorzalek Loo RR, Lermyte F, and Loo JA. “Top-down/bottom-up mass spectrometry workflow using dissolvable polyacrylamide gels.” Anal. Chem. 2017; 89: 8244-8250.

Simonian M, Ogorzalek Loo RR, Rannulu N, Loo JA, Molloy MP, and Stoodley MA. “Identification of protein targets in cerebral endothelial cells for brain arteriovenous malformation (AVMs) molecular therapies” Clinical Proteomics (2017)14:17

Bradley MC, Awad AM, Allan CM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Loo JA, and Clarke CF. “ Characterization of Saccharomyces cerevisiae Coenzyme Q Biosynthetic Protein Coq11 ” The FASEB Journal (2017) 31(1) Supplement 781.9

Li, H., Sheng, Y., McHee, W., Cammarata, M., Holden, D., Loo, J.A. “Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry.” Anal. Chem. 2017, 89 (5), pp 2731–2738

Erde J, Ogorzalek Loo RR, and Loo JA. “Improving Proteome Coverage and Sample Recovery with Enhanced FASP (eFASP) for Quantitative Proteomic Experiments.” Proteomics: Methods and Protocols. 2017, pp 11–18

Vopel, T., Bravo-Rodriguez, K., Mittal, S., Vachharajani, S., Gnutt, D., Sharma, A., Steinhof, A., Fatoba, O., Ellrichmann, G., Nshanian, M., Heid, C., Loo, J.A., Klarner, F.G., Schrader, T., Bitan, G., Wanker, E.E., Ebbinghaus, S., and Sanchez-Garcia, E. J. “Inhibition of Huntingtin Exon-1 Aggregation by the Molecular Tweezer CLR01.” J. Am. Chem. Soc., 2017, 139 (16), pp 5640–5643

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Poweleit, N., Ge, P., Nguyen, H.H., Ogorzalek Loo, R.R., Gunsalus, R.P., Zhou, H.Z. “CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pili.” Nature microbiology, 2016, 2(1622)

Crable, B.R., Sieber, J.R, Mao, X., Alvarez-Cohen, L., Gunsalus, R.P., Ogorzalek Loo, R.R., Nguyen, H.H., McInerney, M.J. “Membrane Complexes of Syntrophomonas wolfei Involved in Syntrophic Butyrate Degradation and Hydrogen Formation.” Front Microbiol., 2016, 7:1795

James, K.L., Rios-Hernandez, L.A., Wofford, N.Q., Mouttaki, H., Sieber, J.R., Sheik, C.S., Nguyen, H.H., Yang, Y., Xie, Y., Erde, J., Rohlin, L., Karr, E.A., Loo, J.A., Ogorzalek Loo, R.R., Hurst, G.B., Gunsalus, R.P., Szweda, L.I., McInerney, M.J. “Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation.” 2016, 7(4): e01208-16

Campuzano, I.D. ,Li, H., Bagal, D., Lippens, J.L., Svitel, J., Kurzeja, R.J.M., Xu, H., Schnier, P.D., Loo, J.A. “Native MS Analysis of Bacteriorhodopsin and an Empty Nanodisc by Orthogonal Acceleration Time-of-Flight, Orbitrap and Ion Cyclotron Resonance.” Anal. Chem., 2016, 88 (24), pp 12427–12436

Ogorzalek Loo RR, and Loo JA. “Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes.“ J. Am. Soc. Mass Spectrom. (2016) 27: 975

Vadivel, K., Kumar, Y., Ogueli, G.I., Ponnuraj, S.M., Wongkongkathep, P., Loo, J.A., Bajaj, M.S., Bajaj, S.P. “S2'-subsite variations between human and mouse enzymes (plasmin, factor XIa, kallikrein) elucidate inhibition differences by TFPI-2 domain1-wildtype, Leu17Arg-mutant and aprotinin.” J Thromb Haemost 2016; 14: 2509–23

Lohnes K, Quebbemann NR, Liu K, Kobzeff F, Loo JA, and Ogorzalek Loo RR. “Combining High-throughput MALDI-TOF Mass Spectrometry and Isoelectric Focusing Gel Electrophoresis for Virtual 2D Gel-based Proteomics.” Methods (2016), 104: 163-169.

Levine J, Kwon E, Paez P, Yan W, Czerwieniec G, Loo JA, Sofroniew MV and Wanner I-B. “Traumatically injured astrocytes release a proteomic signature modulated by STAT3-dependent cell survival.” Glia (2016), 64: 668-694. doi:10.1002/glia.22953.

Decker CG, Wang Y, Paluck SJ, Shen L, Loo JA, Levine AJ, Miller LS, and Maynard HD. “Fibroblast Growth Factor 2 Dimer with Superagonist In Vitro Activity Improves Granulation Tissue Formation During Wound Healing Biomaterials.” Biomaterials (2016), 81:157-168.

Zimmer RK, Ferrier GA, Kim SJ, Kaddis CS, Zimmer CA, and Loo JA. “A multifunctional chemical cue drives opposing demographic processes and structures ecological communities” Ecology (2016), 97: 2232–2239. doi:10.1002/ecy.1455

Ferrier GA, Kim SJ, Kaddis CS, Loo JA, Zimmer CA, and Zimmer RK. “MULTIFUNCin: A Multifunctional Protein Cue Induces Habitat Selection by, and Predation on, Barnacles” Integr Comp Biol 2016; 56 (5): 901–913. doi: 10.1093/icb/icw076

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Cheng S, Wang J, Cai Y, Loo JA, and Chen H. “Enhancing Performance of Liquid Sample Desorption Electrospray Ionization Mass Spectrometry Using Trap and Capillary Columns.” Int J Mass Spectrometry (2015), 392(3): 73-79.

Jiang J, Chan H, Cash DD, Miracco EJ, Ogorzalek Loo RR, Cascio D, O’Brien Johnson R, Loo JA, Zhou ZH, and Feigon J. “Structure of Tetrahymena telomerase reveals new subunits, functions, and interactions.” Science 2015; 350: 529 (aab4070).

Sohn CH, Yin S, Peng I, Loo JA and Beauchamp JL. “Investigation of the Mechanism of Electron Capture and Electron Transfer Dissociation of Peptides with a Covalently Attached Free Radical Hydrogen Atom Scavenger.” Int J Mass Spectrom 2015; 390: 49–55.

Wongkongkathep P, Li H, Zhang X, Ogorzalek Loo RR, Julian RR, and Loo JA. “Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry.” Int J Mass Spectrom 2015; 390: 137–145.

Cai Y, Zheng Q, Liu Y, Helmy R, Loo JA and Chen H. “Integration of Electrochemistry with Ultra Performance Liquid Chromatography/Mass Spectrometry (UPLC/MS).” Eur J Mass Spectrom 2015; 21: 341–351.

Zhang J, Malmirchegini GR, Clubb RT, and Loo JA. “Native Top-Down Mass Spectrometry for the Structural Characterization of Human Hemoglobin.” Eur J Mass Spectrom 2015; 21: 221–231.

Chantaravisoot N, Wongkongkathep P, Loo JA, Mischel PS, and Tamanoi F. “Significance of Filamin A in mTORC2 Function in Glioblastoma.” Mol Cancer 2015; 14: 127 (14 pp).

Young APA, Jiang J, Zhang J, Dang XK, Loo JA, Zhou HZ, Egea PF. “Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly.” Proc Natl Acad Sci USA 2015; 112: E3179-3188.

Allan CM, Awad AM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Merchant SS, Loo JA, and Clarke CF. “Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae.” J Biol Chem 2015; 290: 7517-7534

Leon DR, Ytterberg AJ, Boontheung P, Kim U, Loo JA, Gunsalus RP, and Ogorzalek Loo RR. “Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.” Frontiers Microbiol 2015; 6 (March): 149 (16 pp).

Pai MY, Lomenick B, Hwang H, Schiestl R, McBride W, Loo JA, and Huang J. “Drug Affinity Responsive Target Stability (DARTS) for Small-Molecule Target Identification.” Methods Mol Biol 2015; 1263: 287-298.

Ma X, Loo JA, and Wysocki VH. “Surface induced dissociation yields substructure of Methanosarcina thermophila 20S proteasome complexes.” Int J Mass Spectrom 2015; 377: 201–204.

Zhang J and Loo JA. “Increasing fragmentation of disulfide-bonded proteins for top–down mass spectrometry by supercharging.” Int J Mass Spectrom 2015; 377: 546-556.

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Dzialo MC, Travaglini KJ, Shen S, Loo JA, and Clarke SG. “A new type of protein lysine methyltransferase trimethylates Lys-79 of elongation factor 1A.” Biochem Biophys Res Commun 2014; 455: 382–389.

Zhang X, Li H, Moore B, Wongkongkathep P, Ogorzalek Loo RR, Loo JA, and Julian RR. “Radical directed dissociation of peptides and proteins by IRMPD and SORI-CID with FTICR mass spectrometry.” Rapid Commun Mass Spectrom 2014; 28: 2729-2734. PMCID: PMC4237167

Dzialo MC, Travaglini KJ, Shen S, Roy K, Chanfreau GF, Loo JA, and Clarke SG. “Translational Roles of Elongation Factor 2 Protein Lysine Methylation.” J Biol Chem 2014; 289: 30511-30524.

Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, and Merchant SS. “Sub-cellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas.” Nature Chem Biol 2014; 10: 1034–1042.

Buehler DC, Marsden MD, Shen S, Toso DB, Wu X, Loo JA, Zhou ZH, Kickhoefer VA, Wender PA, Zack JA, and Rome LH. “Bioengineered Vaults: Self-Assembling Protein Shell-Lipophilic Core Nanoparticles for Drug Delivery.” ACS Nano 2014; 8: 7723-7732 (cover article).

Ogorzalek Loo RR, Lakshmanan R, and Loo JA. “What Protein Charging (and Supercharging) Reveal about the Mechanism of Electrospray Ionization.” J Am Soc Mass Spectrom 2014; 25: 1675-1693.

Li H, Wongkongkathep P, Van Orden SL, Ogorzalek Loo RR, and Loo JA. “Revealing Ligand Binding Sites and Quantifying Subunit Variants of Non-Covalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment.” J Am Soc Mass Spectrom 2014; 25: 2060-2068.

Simonian M, Ogorzalek Loo RR, Loo JA, Stoodley MA, and Molloy MP. “Proteomics Detection of Endothelial Cell Surface Proteins Following Irradiation as Potential Targets for Brain Arteriovenous Malformations Molecular Therapy.” MOJ Proteomics Bioinform 2014; 1: 00002 (6 pp.).

Kumar Y, Vadivel K, Schmidt AE, Ogueli GI, Ponnuraj SM, Rannulu N, Loo JA, Bajaj MS, and Bajaj SP. “Decoy Plasminogen Receptor Containing a Selective Kunitz-Inhibitory Domain.” Biochemistry 2014; 53, 505−517.

Li H, Wolff JJ, Van Orden SL, and Loo JA. “Native Top-Down Electrospray Ionization-Mass Spectrometry of 158 kDa Protein Complex by High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.” Anal Chem 2014; 86: 317−320 (cover article).

Acharya S, Safaie BM, Wongkongkathep P, Ivanova MI, Attar A, Klärner F-G, Schrader T, Loo JA, Bitan G, and Lapidus LJ. “Molecular Basis for Preventing α-Synuclein Aggregation by a Molecular Tweezer.” J Biol Chem 2014; 289: 10727-10737.

Erde J, Ogorzalek Loo RR, and Loo JA. “Enhanced FASP (eFASP) to Increase Proteome Coverage and Sample Recovery for Quantitative Proteomic Experiments.” J Proteome Res 2014; 13: 1885−1895. (Comment in BioTechniques, May 2014; 56: 211) (Listed as one of the “Ten of the most interesting papers from Journal of Proteome Research in 2015; C&EN Supplement, December 2015).

Lakshmanan R, Wolff J, Alvarado R, and Loo JA. “Top-Down Protein Identification of Proteasome Proteins with nanoLC FT-ICR MS Employing Data-Independent Fragmentation Methods.” Proteomics 2014; 14: 1271-1282.

Shen S, Ogorzalek Loo RR, Wanner I-B, and Loo JA. “Addressing the Needs of Traumatic Brain Injury with Clinical Proteomics.” Clin Proteomics 2014; 11: 11 (13 pp.).

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Liu P, Zhang J, Ferguson C, Chen H, and Loo JA. “Measuring Protein-Ligand Interactions Using Liquid Sample Desorption Electrospray Ionization Mass Spectrometry.” Anal Chem 2013; 85: 11966–11972.

Shen-Miller J, Lindner P, Xie Y, Villa S, Wooding K, Steven G. Clarke SG, Loo RRO, and Loo JA. “Thermal-stable proteins of fruit of long-living Sacred Lotus Nelumbo nucifera Gaertn var. China Antique.” Tropical Plant Biol 2013; 6: 69-84.

Chen CK, Benchaar SA, Phan M, Grintsevich EE, Ogorzalek Loo RR, Loo JA, and Reisler E. “Cofilin-Induced Changes in F Actin Detected via Cross-Linking with Benzophenone-4-maleimide.” Biochemistry 2013; 52: 5503−5509.

Loo JA, Benchaar SA, and Zhang J. “Integrating Native Mass Spectrometry and Top-Down MS for Defining Protein Interactions Important in Biology and Medicine.” Mass Spectrometry 2013; 2 (Special Issue: Proceedings of 19th International Mass Spectrometry Conference): S0013 (7 pp).

Smith LM, Kelleher NL, Linial M, Goodlett D, Langridge-Smith P, Goo AH, Safford G, Bonilla L, Kruppa G, Zubarev R, Rontree J, Chamot-Rooke J, Garavelli J, Heck A, Loo J, Penque D, Hornshaw M, Hendrickson C, Pasa-Tolic L, Borchers C, Chan D, Young N, Agar J, Masselon C, Gross M, McLafferty F, Tsybin Y, Ge Y, Sanders I, Langridge J, Whitelegge J, Marshall A. “Proteoform: a single term describing protein complexity.” Nature Methods 2013; 10: 186-187.

Malasarn D, Kropat J, Hsieh SI, Finazzi G, Casero D, Loo JA, Pellegrini M, Wollman F-A, and Merchant SS. “Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii.” J Biol Chem 2013; 288: 10672-10683.

Spirig T, Malmirchegini GR, Zhang J, Robson S, Sjodt M, Liu M, Kumar KK, Dickson CF, Gell DA, Lei B, Loo JA, and Clubb RT. “Staphylococcus aureus uses a novel multidomain receptor to break apart human hemoglobin and steal its heme.” J Biol Chem 2013; 288: 1065-1078.

Nguyen TH, Kim S-H, Decker CG, Wong DY, Loo JA, and Maynard HD. “A heparin-mimicking polymer conjugate stabilizes basic fibroblast growth factor.” Nature Chem 2013; 5: 221–227.

Allan CM, Hill S, Morvaridi S, Saiki R, Johnson JS, Liau W-S, Hirano K, Kawashima T, Ji Z, Loo JA, Shepherd JN, and Clarke CF. “A Conserved START Domain Coenzyme Q-binding Polypeptide is Required for Efficient Q Biosynthesis, Respiratory Electron Transport, and Antioxidant Function in Saccharomyces cerevisiae.” Biochim Biophys Acta – Mol Cell Biol Lipids 2013; 1831: 776-791.

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Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas C, Clarke SG, Loo JA, Pellegrini M, and Merchant SS. “Systems and trans-system level analysis identifies conserved iron-deficiency responses in the plant lineage.” Plant Cell 2012; 3921-3948.

Hsieh SI, Castruita M, Malasarn D, Urzica E, Erde J, Page MD, Yamasaki H, Casero D, Pellegrini M, Merchant SS, and Loo JA. “The Proteome of Copper, Iron, Zinc, and Manganese Micronutrient Deficiency in Chlamydomonas reinhardtii.” Mol Cell Proteomics 2013; 12: 65-86.

Liu Y, Miao Z, Lakshmanan R, Ogorzalek Loo RR, Loo JA, and Chen H. “Signal and charge enhancement for protein analysis by liquid chromatography–mass spectrometry with desorption electrospray ionization.” Int J Mass Spectrom 2012; 325-327: 161-166.

Zhu W, Phan QT, Boontheung P, Solis NV, Loo JA, and Filler SG. “EGFR and HER2 receptor kinase signaling mediate epithelial cell invasion by Candida albicans during oropharyngeal infection.” Proc Natl Acad Sci USA 2012; 109: 14194-14199.

Shirasaki DI, Greiner ER, Al-Ramahi I, Gray M, Boontheung P, Geschwind DH, Botas J, Coppola G, Horvath S, Loo JA, and Yang XW. “Network Organization of the Huntingtin Proteomic Interactome in Mammalian Brain.” Neuron, 2012; 75: 41-57.

Page MD, Allen MD, Kropat J, Urzica EI, Karpowicz SJ, Hsieh SI, Loo JA, and Merchant SA. “Fe Sparing and Fe Recycling Contribute to Increased Superoxide Dismutase Capacity in Iron-Starved Chlamydomonas reinhardtii.” Plant Cell 2012; 24: 2649-2665.

Halgand FJ, Zabrouskov V, Bassilian S, Souda P, Loo JA, Faull KF, Wong DT, and Whitelegge JP. “Defining intact protein primary structures from saliva: A step toward the human proteome project.” Anal Chem 2012; 84: 4383−4395.

Rohlin L, Leon DR, Kim U, Loo JA, Ogorzaleck Loo RR, and Gunsalus RP. “Identification of the major expressed S-layer and cell surface layer related proteins in the model methanogenic archaea, Methanosarcina barkeri Fusaro and Methanosarcina acetivroans C2A.” Archaea 2012, Article ID 873589, 10 pp.

Prabhudesai S, Sinha S, Attar A, Kotagiri A, Fitzmaurice AG, Lakshmanan R, Ivanova MI, Loo JA, Klärner F-G, Schrader T, Stahl M, Bitan G, and Bronstein JM. “A Novel ‘Molecular Tweezer’ Inhibitor of α-Synuclein Neurotoxicity in Vitro and in Vivo.” Neurotherapeutics 2012; 9: 464-476.

Sohn CH, Lee JE, Sweredoski MJ, Graham RLJ, Smith GT, Hess S, Czerwieniec G, Loo JA, Deshaies RJ, and Beauchamp JL. “Click Chemistry Facilitates Formation of Reporter Ions and Simplified Synthesis of Amine-Reactive Multiplexed Isobaric Tags for Protein Quantification.” J Am Chem Soc 2012; 134: 2672-2680.

Sohn CH, Agnew HD, Lee JE, Sweredoski MJ, Graham RLJ, Smith GT, Hess S, Czerwieniec G, Loo JA, Heath JR, Deshaies RJ, and Beauchamp JL. “Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions.” Anal Chem 2012; 84: 2662-2669.

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Schneider RE, Brown MT, Shiflett AM, Dyall SD, Hayes RD, Xie Y, Loo JA, and Johnson PJ. “The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria yet complex compared to mitosomes.” Int J Parisitology 2011; 41: 1421-1434.

Sinha S, Attar A, Maiti P, Du Z, Tan M, Pang ES, Lopes DHJ, Tseng C-H, Jones MR, Talbiersky P, Tennstädt A, Lichti-Kaiser K, Liu T, Yang F, Bakshi R, Kuo P-Y, Lomakin A, Gale GD, Benedek GB, Staudinger JL, Ehrmann M, Loo JA, Xie C-W, Klärner F-G, Schrader T, Wang C, Frautschy SA, and Bitan G. “Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins.” J Am Chem Soc 2011; 133: 16958–16969. (Chemical & Engineering News report:

Zhang L, Pang E, Ogorzalek Loo RR, Rao J, Go V-L W, Loo JA, and Lu Q-Y. “Concomitant Inhibition of HSP90, its Mitochondrial Localized Homologue TRAP1 and HSP27 by Green Tea in Pancreatic Cancer HPAF-II Cells.” Proteomics 2011; 11: 4638-4647.

Ferguson CN, Benchaar SA, Miao Z, Loo JA, and Chen H. “Direct Ionization of Large Proteins and Protein Complexes by Desorption Electrospray Ionization-Mass Spectrometry.” Anal Chem 2011; 83: 6468–6473. (Chemical & Engineering News report:

Chiu ML, Ytterberg AJ, Ogorzalek Loo RR, Loo JA, and Monbouquette HG. “Characterization of Morphine-Glucose-6-Phosphate Dehydrogenase Conjugates by Mass Spectrometry.” Bioconj Chem 2011; 22: 1595-1604.

Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Loo JA, Benning C, Pellegrini M, and Merchant SS. “Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.” Plant Cell 2011; 23: 1273-1292.

Yin S and Loo JA. “Top-Down Mass Spectrometry of Supercharged Native Protein-Ligand Complexes.” Int J Mass Spectrom 2011; 300: 118-122.

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Nelson W, Peng I, Lee G-A, Loo JA, Garrell RL, and Kim C-J. “Incubated protein reduction and digestion on an EWOD digital microfluidic chip for MALDI-MS.” Anal Chem 2010; 82: 9932-9937.

Leuchter AF, Cook IA, Hamilton SP, Narr KL, Toga A, Hunter AM, Faull K, Whitelegge J, Andrews AM, Loo J, Way B, Nelson SF, Horvath S, and Lebowitz BD. “Biomarkers to Predict Antidepressant Response.” Curr Psychiatry Rep 2010; 12: 553–562.

Hogan Jr CJ, Ogorzalek Loo RR, Loo JA, and de la Mora JF. “Ion mobility–mass spectrometry of phosphorylase B ions generated with supercharging reagents but in charge-reducing buffer.” Phys Chem Chem Phys 2010; 12: 13476-13483.

Arellano-Garcia ME, Li R, Liu X, Xie Y, Yan X, Loo JA, and Hu S. “Identification of Tetranectin as a Potential Biomarker for Metastatic Oral Cancer.” Int J Mol Sci 2010; 11: 3106-3121.

Loo JA, Yan W, Ramachandran P, and Wong DT. “Comparative Human Salivary and Plasma Proteomes.” J Dental Res 2010; 89: 1016-1023.

Ryan CM, Souda P, Halgand F, Wong DT, Loo JA, Faull KF, and Whitelegge JP. “Confident Assignment of Intact Mass Tags to Human Salivary Cystatins Using Top-Down Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry.” J Am Soc Mass Spectrom 2010; 21: 908-917.

Yin S and Loo JA. “Elucidating the Site of Protein-ATP Binding by Top-Down Mass Spectrometry.” J Am Soc Mass Spectrom 2010; 21: 899-907.

Senturia R, Faller M, Yin S, Loo JA, Cascio D, Sawaya MR, Hwang D, Clubb RT, and Guo F. “Structure of the dimerization domain of DiGeorge Critical Region 8.” Protein Sci 2010; 19: 1354-1365. (cover article)

Thevis M, Thomas A, Kohler M, Beuck S, Möller I, Schäfer M, Rodchenkov G, Yin S, Loo JA, Geyer H, and Schänzer W. “Mass Spectrometry-Based Characterization of New Drugs and Methods of Performance Manipulation in Doping Control Analysis.” Eur J Mass Spectrom 2010; 16: 301-312.

Razani B, Zarnegar B, Ytterberg AJ, Shiba T, Dempsey PW, Ware CF, Loo JA, and Cheng G. “Negative Feedback in Noncanonical NF-κB Signaling Modulates NIK Stability Through IKKα-Mediated Phosphorylation.” Science Signal 2010; 3: ra41.

Sun Q, Yin S, Loo JA, and Julian RR. “Radical Directed Dissociation for Facile Identification of Iodotyrosine Residues Using Electrospray Ionization Mass Spectrometry.” Anal Chem 2010; 82: 3826-3833.

Lakshmanan R, Loo JA, Drake T, LeBlanc JF, Ytterberg AJ, McArthur DL, Etchepare M, and Vespa PM. “Metabolic Crisis after Traumatic Brain Injury is Associated with a Novel Microdialysis Proteome.” Neurocrit Care 2010; 12: 324-336.

Grintsevich EE, Galkin VE, Orlova A, Ytterberg AJ, Mikati MM, Kudryashov DS, Loo JA, Egelman EH, and Reisler E. “Mapping of drebrin binding site on F-actin.” J Mol Biol 2010; 398: 542-554. (cover article)

Halgand F, Zabrouskov V, Bassilian S, Souda P, Wong DT, Loo JA, Faull KF, and Whitelegge JP. “Micro-heterogeneity of human saliva Peptide P-C characterized by high resolution top-down Fourier-transform mass spectrometry.” J Am Soc Mass Spectrom 2010; 21: 868-877.

Peng IX, Ogorzalek Loo RR, Margalith E, Little MW, and Loo JA. “Electrospray-assisted Laser Desorption Ionization Mass Spectrometry (ELDI-MS) with an Infrared Laser for Characterizing Peptides and Proteins.” Analyst 2010; 135: 767-772.

Chatterjee D, Ytterberg AJ, Son SU, Loo JA and Garrell RL. “Integration of protein processing steps on a droplet microfluidics platform for MALDI-MS analysis.” Anal Chem 2010; 82: 2095-2101.

Kang X, Li N, Wang M, Boontheung P, Harkema JR, Bramble LA, Nel AE, and Loo JA. “Adjuvant Effects of Ambient Particulate Matter Monitored by Proteomics of Bronchoalveolar Lavage Fluid.” Proteomics 2010; 10: 520-531.

Lomeli SH, Peng IX, Yin S, Ogorzalek Loo RR, and Loo JA. “New Reagents for Increasing ESI Multiple Charging of Proteins and Protein Complexes.” J Am Soc Mass Spectrom 2010; 21: 127-131.

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Gonzalez O, Fontanes V, Raychaudhuri S, Loo R, Loo J, Arumugaswami V, Sun R, Dasgupta A, and French SW. “The Heat Shock Protein Inhibitor Quercetin Attenuates Hepatitis C Virus Production.” Hepatology 2009: 50, 1756-1764.

Lomenick B, Hao R, Jonai N, Chin RN, Aghajan M, Warburton S, Wang J, Wu RP, Gomez F, Loo JA, Wohlschlegel JA, Vondriska TM, Pelletier J, Herschman HR, Clardy J, Clarke CF, and Huang J. “Target identification using drug affinity responsive target stability (DARTS).” Proc Natl Acad Sci USA 2009; 106: 21984-21989.

Averette-Mirrashidi KM, Pratt MR, Yang Y, Bassilian S, Whitelegge JP, Loo JA, Muir TW, and Bradley KA. “Anthrax Lethal Toxin Induced Lysosomal Membrane Permeabilization and Cytosolic Cathepsin Release is Nlrp1b/Nalp1b-Depedent.” PLoS ONE 2009; 4 (11): e7913.

Mosessian S, Avliyakulov NK, Mulholland DJ, Boontheung P, Loo JA, and Wu H. “Analysis of PTEN Complex Assembly and Identification of Heterogeneous Nuclear Ribonucleoprotein C as a Component of the PTEN-associated Complex.” J Biol Chem 2009; 284: 30159-30166.

Kim HI, Kim H, Pang ES, Beegle LW, Loo JA, Goddard WA, and Kanik I. “Structural Characterization of Unsaturated Phospholipids Using Traveling Wave Ion Mobility Spectrometry.” Anal Chem 2009; 81: 8289-8297.

Tienson HL, Dabir DV, Neal SE, Loo R, Hasson SA, Boontheung P, Kim S-K, Loo JA, and Koehler CM. “Reconstitution of the Mia40-Erv1 Oxidative Folding Pathway for the Small Tim Proteins.” Mol Biol Cell 2009; 20: 3481-3490.

Lu KV, Zhu S, Cvrljevic A, Huang TT, Sarkaria S, Ahkavan D, Dang J, Dinca EB, Plaisier SB, Oderberg I, Lee Y, Chen Z, Caldwell JS, Xie Y, Loo JA, Seligson D, Chakravari A, Lee FY, Weinmann R, Cloughesy TF, Nelson SF, Bergers G, Graeber T, Furnari FB, James CD, Cavenee WK, Johns TG, and Mischel PS. “Fyn and Src Are Effectors of Oncogenic Epidermal Growth Factor Receptor Signaling in Glioblastoma Patients.” Cancer Res 2009; 69: 6889-6898.

Maji SK, Ogorzalek Loo RR, Inayathullah M, Spring SM, Vollers SS, Condron MM, Bitan G, Loo JA, and Teplow DB. “Amino Acid Position-specific Contributions to Amyloid b-Protein Oligomerization.” J Biol Chem 2009; 284: 23580-23591.

Tao L, Kaddis CS, Ogorzalek Loo RR, Grover GN, Loo JA, Maynard HD. “Synthesis of Maleimide-End Functionalized Star Polymers and Multimeric Protein-Polymer Conjugates.” Macromolecules 2009; 42: 8028-8033.

Pesek JJ, Matyska MT, Loo JA, Fischer SM, and Sana TR. “Analysis of hydrophilic metabolites in physiological fluids by HPLC-MS using a silica hydride-based stationary phase.” J Sep Sci 2009; 32: 2200-2208.

Ly T, Yin S, Loo JA, and Julian RR. “Electron-induced dissociation of protonated peptides yields backbone fragmentation consistent with a hydrogen-deficient radical.” Rapid Commun Mass Spectrom 2009; 23: 2099-2101. (Erratum: Rapid Commun Mass Spectrom 2010; 24: 242)

Nie M, Xie Y, Loo JA, and Courey AJ. “Genetic and Proteomic Evidence for Roles of Drosophila SUMO in Cell Cycle Control, Ras Signaling, and Early Pattern Formation.” PLoS ONE 2009; 4(6): e5905. doi:10.1371/journal.pone.0005905.

Nelson WC, Peng I, Loo JA, Garrell RL, and Kim C-J. “An EWOD Digital Microfluidic Chip with Integrated Localized Temperature Control for Multiplex Proteomics Sample Processing.” Proc IEEE Int Conf MEMS, Jan 2009, pp 280-283.

Tao L, Kaddis CS, Ogorzalek Loo RR, Grover GN, Loo JA, and Maynard HD. “Synthetic Approach to Homodimeric Protein-Polymer Conjugates.” Chem Commun 2009; Apr 28;(16): 2148–2150.

Francoleon DR, Boontheung P, Yang Y, Kim U, Ytterberg AJ, Denny PA, Denny PC, Loo JA, Gunsalus RP, and Ogorzalek Loo RR. “S-layer, Surface-Accessible, and Concanavalin A Binding Proteins of Methanosarcina acetivorans and Methanosarcina mazei.” J Proteome Res 2009; 8: 1972-1982.

Sohn CH, Chung CK, Yin S, Ramachandran P, Loo JA, and Beauchamp JL. “Probing the Mechanism of Electron Capture and Electron Transfer Dissociation Using Tags with Variable Electron Affinity.” J Am Chem Soc 2009; 131: 5444-5459.

Sondej M, Denny PA, Xie Y, Ramachandran P, Si Y, Takashima J, Shi W, Wong DT, Loo JA, and Denny PC. “Glycoprofiling of the Human Salivary Proteome.” Clin Proteomics 2009; 5: 52-68.

Zhang L, Wang M, Kang X, Boontheung P, Li N, Nel AE, and Loo JA. “Oxidative Stress and Asthma: Proteome Analysis of Chitinase-like Proteins and FIZZ1 in Lung Tissue and Bronchoalveolar Lavage Fluid.” J Proteome Res 2009; 9: 1631-1638.

Lomeli SH, Yin S, Ogorzalek Loo RR, and Loo JA. “Increasing Charge While Preserving Noncovalent Protein Complexes for ESI-MS.” J Am Soc Mass Spectrom 2009; 20: 593–596.

Lu Q-Y, Yang Y, Jin YS, Zhang Z-F, Heber D, Li FP, Dubinett SM, Sondej MA, Loo JA, and Rao JY. “Effects of Green Tea Extract on Lung Cancer A549 Cells: Proteomic Identification of Proteins Associated with Cell Migration.” Proteomics 2009; 9: 757-767.

Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Rhodus NL, Sevinsky JR, States D, Stephenson JL Jr, Than S, Yates III JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA , Wong DT. “Systematic Comparison of the Human Saliva and Plasma Proteomes.” Proteomics Clin Appl 2009; 3: 116-134.

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Claypool SM, Boontheung P, McCaffery JM, Loo JA, and Koehler CM. “The cardiolipin transacylase, tafazzin, associates with two distinct respiratory components providing insight into Barth Syndrome.” Mol Biol Cell 2008; 19: 5143-5155.

Peng IX, Ogorzalek Loo RR, Shiea J, and Loo JA. “Reactive-Electrospray-Assisted Laser Desorption Ionization (Reactive-ELDI) for Characterization of Peptides and Proteins.” Anal Chem 2008; 80: 6995-7003.

Kudryashov DS, Oztug Durer ZA, Ytterberg AJ, Sawaya MR, Pashkov I, Prochazkova K, Yeates TO, Ogorzalek Loo RR, Loo JA, Fullner Satchell KJ, and Reisler E. “Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin.” Proc Natl Acad Sci USA 2008; 105: 18537-18542.

Yin S, Xie Y, and Loo JA. “Mass Spectrometry of Protein-Ligand Complexes: Enhanced Gas Phase Stability of Ribonuclease-Nucleotide Complexes.” J Am Soc Mass Spectrom 2008; 19: 1199-1208.

Ramachandran P, Boontheung P, Pang E, Yan W, Wong DT, and Loo JA. “Comparison of N-Linked Glycoproteins in Human Whole Saliva, Parotid, Submandibular, and Sublingual Glandular Secretions Identified using Hydrazide Chemistry and Mass Spectrometry.” Clin Proteomics 2008; 4: 80-104.

Claypool SM, Oktay Y, Boontheung P, Loo JA, and Koehler CM. “Cardiolipin defines the interactome of the major ADP/ATP carrier protein of the mitochondrial inner membrane.” J Cell Biol 2008; 182: 937-950.

Chen H, Boontheung P, Ogorzalek Loo RR, Xie Y, Loo JA, Rao J-Y, and Collins MD. “A proteomic approach to differential mouse strain sensitivity to cadmium-induced forelimb teratogenesis.” Birth Def Res A: Clin Mol Teratol 2008; 82: 187-199.

Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, Bassilian S, Bedi GS, Boontheung P, Cociorva D, Delahunty CM, Denny P, Dunsmore J, Faull KF, Gilligan J, Gonzalez-Begne M, Halgand F, Hall SC, Han X, Henson B, Hewel J, Hu S, Jeffrey S, Jiang J, Loo JA, Ogorzalek Loo RR, Malamud D, Melvin JE, Miroshnychenko O, Navazesh M, Niles R, Park SK, Prakobphol A, Ramachandran P, Richert M, Robinson S, Sondej M, Souda P, Sullivan MA, Than S, Wang J, Whitelegge JP, Witkowska HE, Wolinsky L, Xie Y, Xu T, Yu W, Wong DT, Yates, III JR, and Fisher SJ. “The Proteomes of Human Parotid and Submandibular/Sublingual Gland Salivas Collected as the Ductal Secretions.” J Proteome Res 2008; 7: 1994-2006.

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Hønnerup Jensen P, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon M-S, Lee H-J, Lee Y-J, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik Y-K, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TSK, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez J-C, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KWM, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada J-M, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zuerbig P, and Pandey A. “Human Proteinpedia: A portal for sharing and integration of human protein data.” Nature Biotechnol 2008; 26: 164-167.

Hu S, Arellano M, Boontheung P, Wang J, Zhou H, Jiang J, Elashoff D, Wei R, Loo JA, and Wong DT. “Salivary Proteomics for Oral Cancer Biomarker Discovery.” Clin Cancer Res 2008; 14: 6246-6252.

Grintsevich EE, Benchaar SA, Warshaviak D, Boontheung P, Halgand F, Whitelegge JP, Faull KF, Ogorzalek Loo RR, Sept D, Loo JA, and Reilser E. “Mapping the cofilin binding site on yeast G-actin by chemical cross-linking.” J Mol Biol 2008: 377; 395-409.

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Hu S, Loo JA, and Wong DT. “Human saliva proteome analysis and disease biomarker discovery.” Expert Rev Proteomics 2007; 4: 531-538.

Peng IX, Shiea J, Ogorzalek Loo RR, and Loo JA. “Electrospray-Assisted Laser Desorption Ionization (ELDI) and Tandem Mass Spectrometry of Peptides and Proteins.” Rapid Commun Mass Spectrom 2007; 21: 2541–2546.

Jung EJ, Avliyakulov NK, Boontheung P, Loo JA, and Nel AE. “Pro-oxidative DEP chemicals induce heat shock proteins and an unfolding protein response in a bronchial epithelial cell line as determined by DIGE analysis.” Proteomics 2007; 7: 3906-3918.

Whitelegge JP, Zabrouskov V, Halgand F, Souda P, Bassilian S, Yan W, Wolinsky L, Loo JA, Wong DTW, and Faull KF. “Protein-sequence polymorphisms and post-translational modifications in proteins from human saliva using top down Fourier-transform ion cyclotron resonance mass spectrometry.” Int J Mass Spectrom 2007; 268: 190-197.

Laschober C, Kaddis CS, Reischl GP, Loo JA, Allmaier G, and Szymanski WW. “Comparison of various nano-differential mobility analysers (nDMAs) applying globular proteins.” J Exp Nanosci 2007; 2: 291-301.

Ogorzalek Loo R, Yang Y, Xie Y, Dunsmore J, Mouttaki H, McInerney M, Gunsalus R, and Loo J. “Slippery when Translated: Extensive Programmed Ribosomal Frameshifting Revealed by Proteomics.” J Biomol Tech. 2007; 18: 60. PMCID: PMC2291868

Ytterberg AJ, Ogorzalek Loo RR, Boontheung P, and Loo JA. “Fractionation or Affinity Purification? Using Microcolumns (TiO2, SCX, HILIC) to Isolate Phosphopeptides.” J Biomol Tech 2007; 18: 29–30.

Januszyk K, Li P W-L, Villareal V, Branciforte D, Wu H, Xie Y, Feigon J, Loo JA, Martin SL, and Clubb RT. “Identification and Solution Structure of a Highly Conserved C-terminal Domain within ORF1p Required for Retrotransposition of Long Interspersed Nuclear Element-1.” J Biol Chem 2007; 282: 24893–24904.

Hu S, Wang J, Meijer J, Ieong S, Xie Y, Yu T, Zhou H, Henry S, Vissink A, Pijpe J, Kallenberg C, Elashoff D, Loo JA, Wong DT. “Salivary Proteomic and Genomic Biomarkers for Primary Sjögren’s Syndrome.” Arthrit Rheum 2007; 56: 3588-3600.

Hu S, Yu T, Xie Y, Yang Y, Li Y, Zhou X, Tsung S, Loo RR, Loo JA, and Wong DT. “Discovery of oral fluid biomarkers for human oral cancer by mass spectrometry.” Cancer Genomics Proteomics 2007; 4: 55-64.

Tarasev M, Kaddis CS, Yin S, Loo JA, Burgner J, and Ballou DP. “Similar enzymes, different structures: Phthalate dioxygenase is an a3a3 stacked hexamer, not an a3b3 trimer like “normal” Rieske oxygenases.” Arch Biochem Biophys 2007; 466: 31-39.

Kaddis CS, Lomeli SH, Yin S, Berhane B, Apostol MI, Kickhoefer VA, Rome LH, and Loo JA. “Sizing Large Proteins and Protein Complexes by Electrospray Ionization Mass Spectrometry and Ion Mobility.” J Am Soc Mass Spectrom 2007; 18: 1206-1216.

Hu S, Loo JA, and Wong DT. “Human saliva proteome analysis.” Ann NY Acad Sci 2007; 1098(Oral-Based Diagnostics): 323-329.

Liu B, Yang Y, Chernishof V, Ogorzalek Loo RR, Jang H, Tahk S, Yang R, Mink S, Shultz D, Bellone CJ, Loo JA, and Shuai K. “Proinflammatory stimuli induce IKKα-mediated phosphorylation of PIAS1 to restrict inflammation and immunity.” Cell 2007; 129: 903-914.

Ogorzalek Loo RR and Loo JA. “Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry of Hydrophobic Proteins in Mixtures Using Formic Acid, Perfluorooctanoic Acid, and Sorbitol,” Anal Chem 2007; 79: 1115-1125.

Thevis M, Loo JA, Ogorzalek Loo RR, and Schänzer W. “Recommended criteria for the mass spectrometric identification of target peptides and proteins (< 8 kDa) in sports drug testing.” Rapid Commun Mass Spectrom 2007; 21: 297-304.

Benchaar SA, Xie Y, Phillips M, Ogorzalek Loo RR, Galkin VE, Orlova A, Thevis M, Muhlrad A, Almo SC, Loo JA, Egelman EH, and Reisler E. “Mapping the Interaction of Cofilin with Subdomain 2 on Actin.” Biochemistry 2007; 46: 225-233.

Faller M, Matsunaga M, Yin S, Loo JA, and Guo F. “Heme is involved in microRNA processing.” Nature Struct Mol Biol 2007; 14: 23-29. (cover article) (Addendum: Nature Struct Mol Biol 2008; 15: 1125)

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Hu S, Loo JA, and Wong DT. “Human body fluid proteome analysis.” Proteomics 2006; 6: 6326–6353.

Hu S, Li Y, Wang J, Xie Y, Tjon K, Wolinsky L, Ogorzalek Loo RR, Loo JA, and Wong DT. “Human Saliva Proteome and Transcriptome.” J Dent Res 2006; 85: 1129-1133.

Skaggs BK, Gorre ME, Ryvkin A, Burgess MR, Xie Y, Han Y, Komisopoulou E, Brown LM, Loo JA, Landaw EM, Sawyers CL, Graeber TG. “Phosphorylation of the ATP-binding loop directs oncogenicity of drug-resistant BCR-ABL mutants.” Proc Natl Acad Sci USA 2006; 103: 19466-19471.

Xie Y, Zhang J, Yin S, and Loo JA. “Top-Down ESI-ECD-FT-ICR Mass Spectrometry Localizes Noncovalent Protein-Ligand Binding Sites.” J Am Chem Soc 2006; 128: 14432-14433.

Lee NV, Sao M, Annis DS, Loo JA, Wu L, Mosher DF, and Iruela-Arispe ML. “ADAMTS1 mediates the release of antiangiogenic polypeptides from TSP1 and 2.” EMBO J 2006; 25: 5270-5283.

Poderycki MJ, Kickhoefer VA, Kaddis CS, Raval-Fernandes S, Johansson E, Zink JI, Loo JA, and Rome LH. “The Vault Exterior Shell is a Dynamic Structure that Allows Incorporation of Vault-Associated Proteins into its Interior.” Biochemistry 2006; 45: 12184-12193.

Moon, H, Wheeler AR, Garrell RL, Loo JA, and Kim C-J. “Integrated Digital Microfluidic Chip for Multiplexed Proteomic Sample Preparation and Analysis by MALDI-MS.” Lab-on-a-Chip 2006; 6: 1213-1219.

Ramachandran P, Boontheung P, Xie Y, Sondej M, Wong DT, and Loo JA. “Identification of N-Linked Glycoproteins in Human Saliva by Glycoprotein Capture and Mass Spectrometry.” J Proteome Res, 2006; 5: 1493-1503.

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Moon H, Wheeler AR, Garrell RL, Loo JA, and Kim C-J. “On-chip sample preparation by electrowetting-on-dielectric digital microfluidics for matrix assisted laser desorption/ionization mass spectrometry.” Tech. Dig. - IEEE Int Conf Micro Electro Mech. Syst. (MEMS), 18th 2005; 859-862.

Divakaruni AV, Ogorzalek Loo RR, Xie Y, Loo JA, and Gober JW. “The Cell-Shape Protein MreC Interacts With Extracytoplasmic Proteins Including Peptidoglycan Assembly Complexes in Caulobacter crescentus.” Proc Natl Acad Sci USA 2005; 102: 18602-18607.

Leikina E, Delanoe-Ayari H, Melikov KC, Cho M-S, Chen A, Waring AJ, Wang W, Xie Y, Loo JA, Lehrer RI, and Chernomordik LV. “Host-Defense Carbohydrate-Binding Molecules Can Inhibit Viral Fusion and Entry by Crosslinking Membrane Glycoproteins.” Nature Immunol 2005; 6: 995-1001.

Gomes AV, Zong C, Edmondson RD, Berhane BT, Wang G-W, Le S, Young G, Zhang J, Vondriska TM, Whitelegge JP, Jones RC, Joshua IG, Thyparambil S, Pantaleon D, Qiao J, Loo J, and Ping P. “The Murine Cardiac 26S Proteasome: An Organelle Awaiting Exploration.” Ann NY Acad Sci 2005; 1047: 197–207.

Loo JA, Berhane B, Kaddis CS, Wooding KM, Xie Y, Kaufman SL, and Chernushevich IV. “Electrospray Ionization Mass Spectrometry and Ion Mobility Analysis of the 20S Proteasome Complex.” J Am Soc Mass Spectrom 2005; 16: 998-1008.

Wang M, Xiao GG, Li N, Xie Y, Loo JA, and Nel AE “Use of a Fluorescent Phosphoprotein Dye to Characterize Oxidative Stress-induced Signaling Pathway Components in Macrophage and Epithelial Cultures Exposed to Diesel Exhaust Particle Chemicals.” Electrophoresis 2005; 26: 2092-2108.

Hu S, Xie Y, Ramachandran P, Ogorzalek Loo RR, Li Y, Loo JA, and Wong DT. “Large-scale identification of proteins in human salivary proteome by liquid chromatography/mass spectrometry and two-dimensional gel electrophoresis-mass spectrometry.” Proteomics 2005; 5: 1714-1728.

Kani K, Warren CM, Kaddis CS, Loo JA, and Landgraf R. “Oligomers of ErbB3 Have Two Distinct Interfaces That Differ in Their Sensitivity to Disruption by Heregulin.” J Biol Chem 2005; 280: 8238-8247.

Ogorzalek Loo RR, Hayes R, Yang Y, Hung F, Ramachandran P, Kim N, Gunsalus R, and Loo JA. “Top-Down, Bottom-Up, and Side-to-Side Proteomics with Virtual 2-D Gels.” Int J Mass Spectrom 2005; 240: 317-325.

Wheeler AR, Moon H, Bird CA, Ogorzalek Loo RR, Kim CJ, Loo JA, and Garrell RL. “Digital Microfluidics with In-line Sample Purification for Proteomics Analyses with MALDI-MS.” Anal Chem 2005; 77: 534-540.

Xiao GG, Nel AE, and Loo JA. “Nitrotyrosine-Modified Proteins and Oxidative Stress Induced by Diesel Exhaust Particles.” Electrophoresis 2005; 26: 280-292.

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Wheeler AR, Garrell RL, Moon H, Kim C-J, and Loo JA. “Electrowetting-on-Dielectric for Analysis of Peptides and Proteins by Matrix Assisted Laser Desoption/Ionization Mass Spectrometry,” in Dig Solid State Sens Act Microsys Workshop 2004, 402-403.

Wheeler AR, Moon H, Kim C-J, Loo JA, and Garrell RL. “Integrated sample purification in EWOD-MALDI-MS.” Special Publication - Royal Society of Chemistry 2004; 297 (Micro Total Analysis Systems 2004, Volume 2): 204-206.

Hu S, Denny P, Denny P, Xie Y, Loo JA, Wolinsky LE, Li Y, McBride J, Ogorzalek Loo RR, Navazesh M, and Wong DT. “Differentially Expressed Proteins Markers in Human Submandibular and Sublingular Secretions.” Int J Oncology 2004; 25: 1423-1430.

Guo S, Ferl GZ, Deora R, Riedinger M, Yin S, Kerwin JL, Loo JA, and Witte ON. “A phosphorylation site in Bruton's tyrosine kinase selectively regulates B cell calcium signaling efficiency by altering phospholipase C-γ activation.” Proc Natl Acad Sci USA 2004; 101: 14180-14185.

Dyall SD, Yan W, Delgadillo-Correa MG, Lunceford A, Loo JA, Clarke CF, and Johnson PJ. “Complex I proteins of non-mitochondrial origin in a Trichomonas hydrogenosomal oxidoreductase complex.” Nature 2004; 431: 1103-1107.

Ogorzalek Loo RR, Lam Y, Loo JA, and Schumaker VN. “Virtual 2-D Gel Electrophoresis of High Density Lipoproteins.” Electrophoresis 2004; 25: 2384-2391.

Wheeler AR, Moon H, Kim C-J, Loo JA, Garrell RL. “Digital Microfluidics for Analysis of Peptides and Proteins by Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS).” Anal Chem 2004; 76: 4833-4838.

Zhang Z, Gildersleeve J, Yang Y-Y, Xu R, Loo JA, Uryu S, Wong C-H, Schultz PG. “A New Strategy for the Synthesis of Glycoproteins.” Science 2004; 303: 371-373. (Retraction: Science 2009; 326: 1187)

Xian M, Fatima Z, Zhang W, Fang J, Li H, Pei D, Loo J, Stevenson T, Wang GP. “Identification of α-Galactosyl Epitope Mimetics through Rapid Generation and Screening of C-Linked Glycopeptide Library.” J Combinatorial Chem 2004; 6: 126-134.

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Alfonta L, Zhang Z, Uryu S, Loo JA, and Schultz PG. “Site-Specific Incorporation of a Redox-Active Amino Acid into Proteins.” J Am Chem Soc 2003; 125: 14662-14663.

Xiao GG, Wang M, Macatangay G, Li N, Loo JA, and Nel AE. “Use of Proteomics to Demonstrate a Hierarchical Oxidative Stress Response to Diesel Exhaust Particles in a Macrophage Cell Line.” J Biol Chem 2003; 278: 50781-50790.

Thevis M, Ogorzalek Loo RR, Loo JA, and Schänzer W. “Doping Control Analysis of Bovine Hemoglobin-Based Oxygen Therapeutics in Human Plasma by LC-Electrospray Ionization-MS/MS.” Anal Chem 2003; 75: 3287-3293. (Anal Chem news:

Bethem R, Boison J, Gale J, Heller D, Lehotay S, Loo J, Musser S, Price P, and Stein S. “Establishing the Fitness for Purpose of Mass Spectrometric Methods.” J Am Soc Mass Spectrom 2003; 14: 528-541.

Nitao LK, Ogorzalek Loo RR, O’Neall-Hennessey E, Loo JA, Szent-Györgyi AG, and Reisler E. “Conformation and Dynamics of the SH1-SH2 Helix in Scallop Myosin.” Biochemistry 2003; 42: 7663-7674.

Daoud Kinzie S, Thevis M, Ngo K, Whitelegge J, Loo JA, and Abu-Omar MM. “Posttranslational hydroxylation of human phenylalanine hydroxylase is a novel example of enzyme self-repair within the second coordination sphere of catalytic iron.” J Am Chem Soc 2003; 125: 4710-4711.

Thevis M, Ogorzalek Loo RR, and Loo JA. “Mass Spectrometric Characterization of Transferrins and their Fragments Derived by Reduction of Disulfide Bonds.” J Am Soc Mass Spectrom 2003; 14: 635-647.

Thevis M, Ogorzalek Loo RR, and Loo JA. “In-Gel Derivatization of Proteins for Cysteine-Specific Cleavages and their Analysis by Mass Spectrometry.” J Proteome Res 2003; 2: 163-172.

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Ogorzalek Loo RR, Loo JA, Du P, and Holler T. “In Vivo Labeling: A Glimpse of the Dynamic Proteome and Additional Constraints for Protein Identification.” J Am Soc Mass Spectrom 2002; 13: 804-812.

Wabnitz PA and Loo JA. “Drug screening of pharmaceutical discovery compounds by micro-size exclusion chromatography/mass spectrometry.” Rapid Commun Mass Spectrom 2002; 16: 85-91.

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Ogorzalek Loo RR, Cavalcoli JD, VanBogelen RA, Mitchell C, Loo JA, Moldover B, and Andrews PC. “Virtual 2-D Gel Electrophoresis: Visualization and Analysis of the E. coli Proteome by Mass Spectrometry.” Anal Chem 2001; 73: 4063-4070.

Yoshida M, Loo JA, and Lepley RA. “Proteomics as a tool in the pharmaceutical drug design process.” Curr Pharm Des 2001; 7: 291-310.

Loo JA. “Probing Protein-Metal Ion Interactions by Electrospray Ionization Mass Spectrometry: Enolase and Nucleocapsid Protein.” Int J Mass Spectrom 2001; 204: 113-123.

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Kuchumov AR, Loo JA, and Vinogradov SN. “Subunit distribution of calcium-binding sites in Lumbricus terrestris hemoglobin.” J Protein Chem 2000; 19: 139-149.

Smaill JB, Rewcastle GW, Bridges AJ, Zhou H, Showalter HDH, Fry DW, Nelson JM, Sherwood V, Elliott WL, Vincent PW, DeJohn DE, Loo JA, Greis KD, Chan OH, Reyner EL, Lipka E, and Denny WA. “Tyrosine Kinase Inhibitors. 17. Irreversible Inhibitors of the Epidermal Growth Factor Receptor: 4-(Phenylamino)quinazoline- and 4-(Phenylamino)pyrido[3,2-d]pyrimidine-6-acrylamides Bearing Additional Solubilizing Functions.” J Med Chem 2000; 43: 1380-1397.

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before 2000

Swaroop M, Bian J, Aviram M, Duan H, Bisgaier CL, Loo JA, and Sun Y. “Expression, Purification, and Biochemical Characterization of SAG, a RING Finger Redox-Sensitive Protein.” Free Rad Biol Med 1999; 27: 193-202.

Loo JA, DeJohn DD, Du P, Stevenson TI, and Ogorzalek Loo RR. “Application of Mass Spectrometry for Target Identification and Characterization.” Med Res Reviews 1999; 19: 307-319.

Sannes-Lowery KA, Mei H-Y, and Loo JA. “Studying Aminoglycoside Antibiotic Binding to the HIV-1 TAR RNA by Electrospray Ionization Mass Spectrometry.” Int J Mass Spectrom 1999; 193: 115-122.

Loo JA, Brown J, Critchley G, Mitchell C, Andrews PC, and Ogorzalek Loo RR. “High Sensitivity Methods for Obtaining Intact Molecular Weights from Gel-Separated Proteins.” Electrophoresis 1999; 20: 743-748.

Loo JA and Muenster H. “Magnetic Sector-Ion Trap Mass Spectrometry with Electrospray Ionization for High Sensitivity Peptide Sequencing.” Rapid Commun Mass Spectrom 1999; 13: 54-60.

Duan H, Wang Y, Aival M, Swaroop M, Loo JA, Bian J, Tian Y, Mueller T, Bisgaier C, and Sun Y. “SAG, a novel zinc RING finger protein that protects cells from apoptosis induced by redox agents.” Mol Cell Biol 1999; 19: 3145-3155. PMCID: PMC84108

Mei H-Y, Cui M, Heldsinger A, Lemrow SM, Loo JA., Sannes-Lowery KA, Sharmeen L, and Czarnik AW. “Inhibitors of Protein-RNA Complexation That Target the RNA: Specific Recognition of Human Immunodeficiency Virus Type 1 TAR RNA by Small Organic Molecules.” Biochemistry 1998; 37: 14204-14212.

Stevenson TI, Loo JA, and Greis KD. “Coupling Capillary High-Performance Liquid Chromatography to Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry and N-Terminal Sequencing of Peptides via Automated Microblotting onto Membrane Substrates.” Anal Biochem 1998; 262: 99-109

Fry DW, Bridges AJ, Denny WA, Doherty A, Greis KD, Hicks JL, Hook KE, Keller PR, Leopold WR, Loo JA, McNamara DJ, Nelson JM, Sherwood V, Smaill JB, Trumpp-Kallmeyer S, and Dobrusin EM. “Specific, irreversible inactivation of the epidermal growth factor receptor and erbB2, by a new class of tyrosine kinase inhibitor.” Proc Natl Acad Sci USA 1998; 95: 12022-12027. PMCID: PMC21758

Loo JA, Holler TP, Foltin SK, McConnell P, Banotai CA, Horne NM, Mueller WT, Stevenson TI, and Mack DP. “Application of Electrospray Ionization Mass Spectrometry for Studying HIV Protein Complexes.” Proteins: Func, Struct, and Genetics. 1998; Suppl. 2: 28-37.

Newcomb R, Szoke B, Palma A, Wang G, Chen X-H, Hopkins W, Cong R, Miller J, Urge L, Tarczy-Hornoch K, Loo JA, Dooley DJ, Nadasdi L, Tsien RW, Lemos J, and Miljanich G. “Selective Peptide Antagonist of the Class E Calcium Channel from the Venom of the Tarantula Hysterocrates gigas.” Biochemistry 1998; 37: 15353-15362.

Loo JA, He JX, and Cody WL. “Higher Order Structure in the Gas Phase Reflects Solution Structure.” J Am Chem Soc 1998; 120: 4542-4543.

Green BN, Sannes-Lowery KA, Loo JA, Satterlee JD, Kuchumov AR, Walz DA, and Vinogradov SN. "Electrospray Ionization Mass Spectrometric Study of the Multiple Intracellular Monomeric and Polymeric Hemoglobins of Glycera dibranchiata." J Protein Chem 1998; 17: 85-97.

Feng MR, Loo JA, and Wright J. “Disposition of the Antipsychotic Agent CI-1007 in Rats, Monkeys, Dogs, and Human Cytochrome P450 2D6 Extensive Metabolizers. Species Comparison and Allometric Scaling.” Drug Metab Disp 1998; 26: 982-988.

Stevenson TI and Loo JA. “A Simple Off-line Sample Spotter Coupling HPLC with MALDI MS.” LC-GC 1998; 16 (January): 54-60.

Vara Prasad JVN, Loo JA, Boyer FE, Stier MA, Gogliotti RD, Turner WJ, Harvey PJ, Kramer MR, Mack DP, Scholten JD, Grachek SJ, and Domagala JM. “2-2’-Dithiobisbenzamides Derived from a-, ß- and g-Amino Acids Possessing Anti-HIV Activities: Synthesis and Structure Activity Relationship.” Bioorg Med Chem 1998; 6: 1707-1730.

Sannes-Lowery KA, Hu P, Mack DP, Mei H-Y, and Loo JA. “HIV-1 Tat Peptide Binding to TAR RNA by Electrospray Ionization Mass Spectrometry.” Anal Chem 1997; 69: 5130-5135.

Ogorzalek Loo RR, Mitchell C, Stevenson TI, Loo JA, and Andrews PC. “Diffusive Transfer to Membranes as an Effective Interface Between Gel Electrophoresis and Mass Spectrometry.” Int J Mass Spectrom Ion Proc 1997; 169-170: 81-98.

Domagala JM, Gogliotti R, Sanchez JP, Stier MA, Musa K, Song Y, Loo J, Reily M, Tummino P, Harvey P, Hupe D, Sharmeen L, Mack D, Scholten J, Saunders J, and McQuade T. “2,2’-Dithiobisbenzamides and 2-Benzisothiazolones, Two New Classes of Antiretroviral Agents: SAR and Mechanistic Considerations.” Drug Design and Discovery 1997; 15: 49-61.

Mei H-Y, Mack DP, Galan AA, Halim NS, Heldsinger A, Loo JA, Moreland DW, Sannes-Lowery KA, Sharmeen L, Truong HN, and Czarnik AW. “Discovery of Selective, Small-Molecule Inhibitors of RNA Complexes--I. The Tat Protein/TAR RNA Complexes Required for HIV-1 Transcription.” Bioorg Med Chem 1997; 5: 1173-1184.

Ogorzalek Loo RR, Mitchell C, Stevenson TI, Martin SA, Hines WM, Juhasz P, Patterson DH, Peltier JM, Loo JA, and Andrews PC. “Sensitivity and Mass Accuracy for Proteins Analyzed Directly from Polyacrylamide Gels: Implications for Proteome Mapping.” Electrophoresis 1997; 18: 382-390.

Loo JA, Hu P, McConnell P, Mueller WT, Sawyer TK, and Thanabal V. “A Study of Src SH2 Domain Protein-Phosphopeptide Binding Interactions by Electrospray Ionization Mass Spectrometry.” J Am Soc Mass Spectrom 1997; 8: 234-243.

Sannes-Lowery KA, Mack DP, Hu P, Mei H-Y, and Loo JA. “Positive Ion Electrospray Ionization Mass Spectrometry of Oligonucleotides.” J Am Soc Mass Spectrom 1997; 8: 90-95.

Grammer JC, Loo JA, Edmonds CG, Cremo CR, and Yount RG. “Chemistry and Mechanism of Vanadate-Promoted Photooxidative Cleavage of Myosin.” Biochemistry 1996; 35: 15582-15592.

Loo JA, Holler TP, Sanchez J, Gogliotti R, Maloney L, and Reily MD. “Biophysical Characterization of Zinc Ejection from HIV Nucleocapsid Protein by Anti-HIV 2,2'-Dithiobis[benzamides] and Benzisothiazolones.” J Med Chem 1996; 39: 4313-4320.

Hu P, Buckel SD, Whitton MM, and Loo JA. “Calcium Binding Properties and Sequence of Frog (Rana tegrinka) Parvalbumin as Determined by Electrospray Ionization-Mass Spectrometry,” Eur Mass Spectrom 1996; 2: 69-76.

Ogorzalek Loo RR, Stevenson TI, Mitchell C, Loo JA, and Andrews PC. “Mass Spectrometry of Proteins Directly from Polyacrylamide Gels.” Anal Chem 1996; 68: 1910-1917.

Ogorzalek Loo RR, Mitchell C, Stevenson T, Loo JA, and Andrews PC. “Interfacing Polyacrylamide Gel Electrophoresis with Mass Spectrometry.” Techniques in Protein Chemistry VII, Marshak DR, Ed.; Academic Press: San Diego, 1996, pp 305-313.

Hu P and Loo JA. “Gas-Phase Coordination Properties of Zn2+, Cu2+, Ni2+, and Co2+ with Histidine-Containing Peptides.” J Am Chem Soc 1995; 117: 11314-11319.

Loo JA and Ogorzalek Loo RR. “Applying Charge Discrimination with Electrospray Ionization-Mass Spectrometry.” J Am Soc Mass Spectrom 1995; 6: 1098-1104.

Hu P and Loo JA. “Determining Calcium-Binding Stoichiometry and Cooperativity of Parvalbumin and Calmodulin by Mass Spectrometry.” J Mass Spectrom 1995; 30: 1076-1082.

Speir JP, Senko MW, Little DP, Loo JA, and McLafferty FW. “High-Resolution Tandem Mass Spectra of 37-67 kDa Proteins.” J Mass Spectrom 1995; 30: 39-42.

Loo JA. “Observation of Large Subunit Protein Complexes by Electrospray Ionization Mass Spectrometry.” J Mass Spectrom 1995; 30: 180-183.

Buckel SD, Stevenson TI, and Loo JA. “Direct Mass Spectrometric Analyses for Protein Chemistry Studies.” J Protein Chem 1994; 13: 517.

Buckel SD and Loo JA. “Applications of Direct Mass Spectrometric Analyses for Protein Chemistry Studies.” Protein Sci 1994; 3, suppl. 1: 82.

Hu P, Ye Q.-Z., and Loo JA. “Calcium Stoichiometry Determination for Calcium Binding Proteins by Electrospray Ionization Mass Spectrometry.” Anal Chem 1994; 66: 4190-4194.

Ramalingam K, Eaton SR, Cody WL, Loo JA, and Doherty AM. “Side Reactions in the Synthesis of Phosphotyrosine Containing Peptides.” Lett Peptide Sci 1994; 1: 73-79.

Loo JA and Pesch R. “Sensitive and Selective Analysis of Proteins with Electrospray Ionization-Magnetic Sector Mass Spectrometry and Array Detection.” Anal Chem 1994; 66: 3659-3663.

Loo JA, Hu P, and Smith RD. “Interaction of Angiotensin Peptides and Zinc Metal Ions Probed by Electrospray Ionization Mass Spectrometry.” J Am Soc Mass Spectrom 1994; 5: 959-965.

Goodlett DR, Ogorzalek Loo RR, Loo JA, Wahl JH, Udseth HR, and Smith RD. “A Study of the Thermal Denaturation of Ribonuclease S by Electrospray Ionization Mass Spectrometry.” J Am Soc Mass Spectrom 1994; 5: 614-622.

Loo JA, Root-Bernstein RS, and Holsworth DD. “Use of Electrospray Ionization Mass Spectrometry to Probe Antisense-Sense Peptide Interactions.” Biol Mass Spectrom 1994; 23: 6-12.

Loo JA, Ogorzalek Loo RR, and Andrews PC. “Primary to Quaternary Protein Structure Determination with Electrospray Ionization and Magnetic Sector Mass Spectrometry.” Org Mass Spectrom 1993; 28: 1640-1649.

Edmonds CG, Loo JA, Smith RD, Fuciarelli AF, Thrall BD, Morris JE, and Springer DL. “Evaluation of Histone Sequence and Modifications by Electrospray Ionization Mass Spectrometry and Tandem Mass Spectrometry.” J Toxicol Environ Health 1993; 40: 159.

Loo JA, Giordani AB, and Muenster H. “Observation of Intact (Heme-bound) Myoglobin by Electrospray Ionization on a Double Focusing Mass Spectrometer.” Rapid Commun Mass Spectrom 1993; 7: 186-189.

Ogorzalek Loo RR, Goodlett DR, Smith RD, and Loo JA. “Observation of Noncovalent Ribonuclease S-Protein/S-Peptide Complex by Electrospray Ionization Mass Spectrometry.” J Am Chem Soc 1993; 115: 4391-4392.

Loo JA, Edmonds CG, and Smith RD. “Tandem Mass Spectrometry of Very Large Molecules: II. Dissociation of Proline-Containing Proteins.” Anal Chem 1993; 65: 425-438.

Light-Wahl KJ, Loo JA, Edmonds CG, Smith RD, Witkowska¬ HE, Shackleton CHL, and Wu CSC. “Tandem Mass Spectrometry of Intact Hemoglobin Variant Proteins with Electrospray Ionization.” Biol Mass Spectrom 1993; 22: 112-120.

Loo JA, Ogorzalek Loo RR, Goodlett DR, Smith RD, Fuciarelli AF, Springer DL, Thrall BD and Edmonds CG. “Elucidation of Covalent Modifications and Noncovalent Associations in Proteins by Electrospray Ionization Mass Spectrometry.” Techniques in Protein Chemistry IV, Angeletti¬ RH, Ed.; Academic Press: San Diego, 1993, pp 23-31.

Smith RD, Light-Wahl KJ, Winger BE, and Loo JA. “Preservation of Noncovalent Associations in Electrospray Ionization-Mass Spectrometry: Multiply Charged Polypeptide and Protein Dimers.” Org Mass Spectrom 1992; 27: 811-821.

Loo JA, Quinn JP, Ryu SI, Henry KD, Senko MW, and McLafferty FW. “High Resolution Tandem Mass Spectrometry of Large Biomolecules.” Proc Natl Acad Sci USA 1992; 89: 286-289. PMCID: PMC48221

Cremo CR, Loo JA, Edmonds CG, and Hatlelid KM. “Vanadate Catalyzes Photocleavage of Adenylate Kinase at Proline-17 in the Phosphate-Binding Loop.” Biochemistry 1992; 31: 491-497.

Loo JA, Ogorzalek Loo RR, Light KJ, Edmonds CG, and Smith RD. “Multiply Charged Negative Ions by Electrospray Ionization of Polypeptides and Proteins.” Anal Chem 1992; 64: 81-88.

Ogorzalek Loo RR, Loo JA, Udseth HR, Fulton JL, and Smith RD. “Protein Structural Effects in Gas Phase Ion-Molecule Reactions with Diethylamine.” Rapid Commun Mass Spectrom 1992; 6: 159-165.

Edmonds CG, Loo JA, Ogorzalek Loo RR, Udseth HR, Barinaga CJ, and Smith RD. “Application of Electrospray Ionization Mass Spectrometry and Tandem Mass Spectrometry in Combination with Capillary Electrophoresis for Biochemical Investigations.” Biochem Soc Trans 1991; 19: 943-947.

Loo JA, Edmonds CG, and Smith RD. “Tandem Mass Spectrometry of Very Large Molecules: Serum Albumin Sequence Information from Multiply Charged Ions Formed by Electrospray Ionization.” Anal Chem 1991; 63: 2488-2499.

Smith JB, Miesbauer LR, Leeds J, Smith DL, Loo JA, Smith RD, and Edmonds CG. “Mass Spectrometric Analysis of Lens §-Crystallins.” Int J Mass Spectrom Ion Proc 1991; 111: 229-245.

Loo JA, Ogorzalek Loo RR, Udseth HR, Edmonds CG, and Smith RD. “Solvent-Induced Conformational Changes of Polypeptides Probed by Electrospray Ionization-Mass Spectrometry.” Rapid Commun Mass Spectrom 1991; 5: 101-105.

Smith RD, Fields SM, Loo JA, Barinaga CJ, Udseth HR, and Edmonds CG. “Capillary Isotachophoresis with UV and Tandem Mass Spectrometric Detection for Peptides and Proteins.” Electrophoresis 1990; 11: 709-717.

Smith RD, Loo JA, Edmonds CG, Barinaga CJ, and Udseth HR. “Sensitivity Considerations for Large Molecule Detection by Capillary Electrophoresis-Electrospray Ionization Mass Spectrometry.” J Chromatogr 1990; 516: 157-165.

Loo JA, Edmonds CG, Udseth HR, and Smith RD. “Collisional Activation and Dissociation of Large Multiply Charged Proteins Produced by Electrospray Ionization.” Anal Chim Acta 1990; 241: 167-173.

Loo JA, Edmonds CG, and Smith RD. “Primary Sequence Information from Intact Proteins by Electrospray Ionization Tandem Mass Spectrometry.” Science 1990; 248: 201-204.

Loo JA, Edmonds CG, Smith RD, Lacey MP, and Keough T. “Comparison of Electrospray Ionization and Plasma Desorption Mass Spectra of Peptides and Proteins.” Biomed Environ Mass Spectrom 1990; 19: 286-294.

Smith RD, Loo JA, Barinaga CJ, Edmonds CG, and Udseth HR. “Collisional Activation and Collision Induced Dissociation of Multiply Charged Ions of Large Peptides and Proteins Produced by Electrospray Ionization.” J Am Soc Mass Spectrom 1990; 1: 53-65.

Loo JA, Edmonds CG, Udseth HR, and Smith RD. “Effect of Reducing Disulfide-Containing Proteins on Electrospray Ionization-Mass Spectrometry.” Anal Chem 1990; 62: 693-698.

Smith RD, Loo JA, Barinaga CJ, Edmonds CG, and Udseth HR. “Capillary Zone Electrophoresis and Isotachophoresis-Mass Spectrometry of Polypeptides and Proteins Based Upon an Electrospray Ionization Interface.” J Chromatogr 1989; 480: 211-232.

Loo JA, Jones HK, Udseth HR, and Smith RD. “Capillary Zone Electrophoresis-Mass Spectrometry with Electrospray Ionization of Peptides and Proteins.” J Microcolumn Sep 1989; 1: 223-229.

Loo JA, Udseth HR, and Smith RD. “Peptide and Protein Analysis by Electrospray Ionization-Mass Spectrometry and Capillary Electrophoresis-Mass Spectrometry.” Anal Biochem 1989; 179: 404-412.

Edmonds CG, Loo JA, Barinaga CJ, Udseth HR, and Smith RD. “Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry.” J Chromatogr 1989; 474: 21-37.

Loo JA, Udseth HR, and Smith RD. “Solvent Effects on the Charge Distribution Observed with Electrospray Ionization-Mass Spectrometry of Large Molecules.” Biomed Environ Mass Spectrom 1988; 17: 411-414.

Loo JA, Udseth HR, and Smith RD. “Collision Effects on the Charge Distribution of Ions from Large Molecules, Formed by Electrospray Ionization-Mass Spectrometry.” Rapid Commun Mass Spectrom 1988; 2: 207-210.

Udseth HR, Loo JA, and Smith RD. “Capillary Isotachophoresis/Mass Spectrometry.” Anal Chem 1989; 61: 228-232.

Smith RD, Udseth HR, Loo JA, Wright BW, and Ross GA. “Sample Introduction and Separation in Capillary Electrophoresis, and Combination with Mass Spectrometric Detection.” Talanta 1989; 36: 161-169.

McLafferty FW, Henry KD, Loo JA, Wang BH, and Williams ER. “Tandem Fourier-Transform Mass Spectrometry of Large Molecules.” Adv Mass Spectrom 1989; 11: 254-255.

McLafferty FW, Williams ER, Wang BH, Loo JA, Loh SY, and Henry KD. “Tandem Fourier-Transform Mass Spectrometry.” Anal Proc (London) 1988; 25: 358-359.

Loo JA, Williams ER, Furlong JJP, Wang BH, McLafferty FW, Chait BT, and Field FH. “Cf-252 Plasma Desorption Fourier Transform Mass Spectrometry of Involatile Compounds.” Int J Mass Spectrom Ion Proc 1987; 78: 305-313.

Loo JA, Wang BH, Wang FC-Y, McLafferty FW, and Klymko P. “Radiation Degradation of Poly(butene-1 sulfone). Mechanistic Data from Fourier-Transform Mass Spectrometry.” Macromolecules 1987; 20: 698-700.

Loo JA, Williams ER, Amster IJ, Furlong JJP, Wang BH, McLafferty FW, Chait BT, and Field FH. “Californium-252 Plasma Desorption with Fourier Transform Mass Spectrometry.” Anal Chem 1987; 59: 1880-1882.

Amster IJ, Loo JA, Furlong JJP, and McLafferty FW. “Cesium Ion Desorption Ionization with Fourier Transform Mass Spectrometry.” Anal Chem 1987; 59: 313-317.

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