Loo, Joseph A.

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Structural and Computational Biology
Systems Biology and Biological Regulation
Proteomics and Bioinformatics

Contact Information

Boyer Hall 402
(310) 794-7023
Boyer Hall 416; Molecular Sciences Building 1424
(310) 794-7308

Short Biography

Professor Loo received his B.S. in Chemistry from Clarkson University, Potsdam, NY in 1982 and his Ph.D. in Analytical Chemistry in 1988 from Cornell University in Ithaca, NY. In 1988-1990, he was a postdoctoral fellow at Pacific Northwest National Laboratory (PNNL), Richland, WA, prior to joining PNNL as a staff scientist. In 1992-2001, he was employed at Parke-Davis Pharmaceutical Research/Warner-Lambert Company (later became Pfizer Global Research and Development) in Ann Arbor, MI as Group Leader of Biological Mass Spectrometry. He joined the faculty at UCLA in 2001.


Dr. Joseph A. Loo is a Professor in the Department of Biological Chemistry, David Geffen School of Medicine, and in the Department of Chemistry & Biochemistry at the University of California, Los Angeles (UCLA), and he is the Faculty Director of the UCLA Mass Spectrometry and Proteomics Technology Center. He is also a member of UCLA/DOE Laboratory for Genomics and Proteomics, the UCLA Molecular Biology Institute, and the UCLA Jonsson Comprehensive Cancer Center.

He is an expert in the mass spectrometry characterization of proteins and their post-translational modifications, and is the author of over 180 scientific publications. In 2000-2002, he served on the Board of Directors for the American Society for Mass Spectrometry. He has been on the Editorial Boards of the journals Bioconjugate Chemistry, Analytical Chemistry, Journal of the American Society for Mass Spectrometry (JASMS), and Chemical & Engineering News and currently he serves on the Editorial Advisory Board for Rapid Communications in Mass Spectrometry and as an Associate Editor for JASMS.

His research interests include the development of bioanalytical methods for the structural characterization of proteins and their application for proteomics and disease biomarkers. He was one of the first researchers to apply electrospray ionization mass spectrometry (ESI-MS) to directly measure noncovalently-bound macromolecular assemblies and their interactions with other binding partners and ligands. The method can be applied to measure drug binding to their targeted proteins to even larger complexes in excess of 1 MDa.

Currently, his laboratory is developing technologies to profile proteins in human salivary fluids for their application for human disease biomarker discovery. He co-authored a study with a consortium composed of groups from UCLA, UCSF, and Scripps that details the first catalog and preliminary analysis of ductal salivary proteins.

In 2008, he received one of the first grants made under the new "Exceptional, Unconventional Research Enabling Knowledge Acceleration (EUREKA)" NIH program. The goal of this program is to "help investigators test novel, often unconventional hypotheses or tackle major methodological or technical challenges". The Loo award is to study the "Impact of Non-Canonical Decoding on the Proteome".

Before he joined UCLA in 2001, he was Group Leader of the Biological Mass Spectrometry and Proteomics Teams at Warner-Lambert/Parke-Davis Pharmaceutical (currently Pfizer Global Research). He worked at Parke-Davis/Pfizer for nearly 10 years before moving to UCLA.

Research Interest

Structural characterization of proteins and post-translational modifications, and proteomics-based research

The Loo research group focuses on the development of bioanalytical mass spectrometry (MS) methods for the structural characterization of peptides and proteins and the application of MS for proteomics and disease biomarkers. Research projects include: development of novel modes of electrospray ionization and matrix-assisted laser desorption ionization for applicability to structural biology and proteomics; mass spectrometry and ion mobility analysis of noncovalently-bound macromolecular complexes and their interactions with other binding partners and ligands; gas phase protein structures and the relationship to their solution phase counterparts; development of separation and MS-sequencing tools for large-scale proteome profiling; top-down protein mass spectrometry; elucidation of protein complexes, interactions, and post-translational modifications found in complex, biological systems; discovering protein markers of human diseases; MS-based characterization of protein aggregation and its role in neurodegenerative diseases.



Honors & Awards

  • Clarkson U. American Chemical Society Analytical Chemistry Division Award
  • Clarkson U. Chemical Rubber Company Achievement Award
  • Clarkson U. George L. Jones, Jr. Memorial Award
  • Clarkson U. Merck Chemistry Award
  • Cornell Chemistry Teaching Assistant Award
  • Clarkson U. Stephen Brunauer Senior Thesis Award
  • Bridges to the Professorate NIGMS Program Compact for Faculty Diversity Faculty Mentor of the Year Award
  • Australian and New Zealand Society for Mass Spectrometry (ANZSMS) Visiting Lecturer
  • Allan Maccoll Organic Mass Spectrometry Journal Award




Shirasaki DI, Greiner ER, Al-Ramahi I, Gray M, Boontheung P, Geschwind DH, Botas J, Coppola G, Horvath S, Loo JA, Yang XW. "Network Organization of the Huntingtin Proteomic Interactome in Mammalian Brain." Neuron 2012; 75 (1), 41-57.

Liu Y, Miao Z, Lakshmanan R, Ogorzalek Loo RR, Loo JA, Chen H. "Signal and Charge Enhancement for Protein Analysis by Liquid Chromatography-Mass Spectrometry with Desorption Electrospray Ionization." Intl Jour Mass Spec 2012; In Press.

Page MD, Allen MD, Kropat J, Urzica EI, Karpowicz SJ, Hsieh SI, Loo JA, Merchant SS. "Fe Sparing and Fe Recycling Contribute to Increased Superoxide Dismutase Capacity in Iron-Starved Chlamydomonas reinhardtii." The Plant Cell 2012.

Rohlin L, Leon DR, Kim U, Loo JA, Ogorzalek Loo RR, 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 acetivorans C2A." Archaea 2012.

Halgand F, 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 (10), 4383-4395.

Prabhudesai S, Sinha S, Attar A, Kotagiri A, Fitzmaurice AG, Lakshmanan R, Ivanova MI, Loo JA, Klärner F-G, Schrader T, et al. "A Novel "Molecular Tweezer" Inhibitor of α-Synuclein Neurotoxicity in Vitro and in Vivo." Neurotherapeutics 2012; 9 (2), 464-476.

Sohn CH, Agnew HD, Lee JE, Sweredoski MJ, Graham RLJ, Smith GT, Hess S, Czerwieniec G, Loo JA, Heath JR, Deshaies RJ, Beauchamp JL. "Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions." Anal. Chem 2012; 84 (6), 2662–2669.

Sohn CH, Lee JE, Sweredoski MJ, Graham RLJ, Smith GT, Hess S, Czerwieniec G, Loo JA, Deshaies RJ, 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 (5), 2672–2680.

Sondej MA, Doran P, Loo JA, and Wanner I-B. "Sample Preparation of Primary Astrocyte Cellular and Released Proteins for 2-D Gel Elecrophoresis and Protein Identification by Mass Spectrometry." In Sample Preparation in Biological Mass Spectrometry, Ivanov A and Lazarev A, Eds., Springer: Dordrecht, Netherlands, 2011, pp 829-849.

Schneider RE, Brown MT, Shiflett AM, Dyall SD, Hayes RD, Xie Y, Loo JA, Johnson PJ. "The Trichomonas vaginalis Hydrogenosome Proteome is Highly Reduced Relative to Mitochondria, Yet Complex Compared with Mitosomes." Intl Jour Parasitology 2011, 41 (13-14), 1421-1434.

Sinha S, Lopes DHJ, Du Z, Pang ES, Shanmugam A, Lomakin A, Talbiersky P, Tennstaedt A, McDaniel K, Bakshi R, Kuo P-Y, Ehrmann M, Benedek GB, Loo JA, Klärner F-G, Schrader T, Wang C, Bitan G. "Lysine-Specific Molecular Tweezers Are Broad-Spectrum Inhibitors of Assembly and Toxicity of Amyloid Proteins." J Am Chem Soc 2011, 133 (42), 16958–16969.

Zhang L, Pang E, Ogorzalek Loo RR, Rao J, Go V-LW, Loo JA, 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 CN, Miao Z, Loo JA, Chen H. "Direct Ionization of Large Proteins and Protein Complexes by Desorption Electrospray Ionization-Mass Spectrometry." Anal Chem 2011, 83 (17), 6468–6473.

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.

Loo JA and Neff JL. "Editorial: Outstanding Reviewers of JASMS Reviewers, 2010–2011." J Am Soc Mass Spectrom 2011; 22: 2101-2102.

Ytterberg AJ, Dunsmore J, Lomeli SH, Thevis M, Xie Y, Ogorzalek Loo RR, and Loo JA.  “The Role Mass Spectrometry for Peptide, Protein, and Proteome Characterization.”  In Electrospray and MALDI Mass Spectrometry: Fundamentals, Instrumentation, Practicalities, and Biological Applications (2nd Ed.); Cole RB, Ed.; John Wiley & Sons, 2010, pp 685-721.

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.

Loo JA.  “Editorial:  Outstanding JASMS Manuscript Reviewers, 2009–2010.”  J Am Soc Mass Spectrom 2010; 21 (December): i-ii.

Loo JA.  “Focus in Honor of Dr. Neil Kelleher, Recipient of the 2009 Biemann Medal.”  J Am Soc Mass Spectrom 2010; 21: i-iii.

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 β-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.

Leary JA and Loo JA.  “Report of the 2008 ASMS Fall Workshop on Protein-Protein and Protein-Ligand Interactions.”  J Am Soc Mass Spectrom 2009; 20: R1-R2.

Loo JA.  “Rantings of an Associate Editor:  A Plea to Manuscript Reviewers (Editorial).”  J Am Soc Mass Spectrom 2009; 20:  i–ii.

Chatterjee D, Ytterberg AJ, Son S-U, Loo JA, and Garrell RL. “Integration of Protein Processing Steps on a Digital Microfluidics Platform for Analysis by MALDI-MS.”  In Micro Total Analysis Systems, 2008, Los Angeles.  Locascio L, Gaitan M, Paegel MN, Roos DJ, and Vreeland WN, Eds.  (Chemical and Biological Microsystems Society, San Diego, CA 2008) pp. 1072-1074.

Yan W, Yu W, Than S, Qiao R, Parker SD, Loo JA, and Wong DT.  “SPKB – A Salivary Proteome Knowledge Base.”  In Saliva Diagnostics, Wong DT, Ed.; Wiley-Blackwell: Ames, IA, 2008, pp 233-240.

Hu S, Hardt M, Fisher SJ, Wong DT, Yates JR, Melvin JE, and Loo JA.  “Human Salivary Proteomics.”  In Saliva Diagnostics, Wong DT, Ed.; Wiley-Blackwell: Ames, IA, 2008, pp 122-128.

Yin S and Loo JA.  “Mass Spectrometry Detection and Characterization of Noncovalent Protein Complexes.”  In Mass Spectrometry of Proteins and Peptides – Methods and Protocols, Methods in Molecular Biology, Volume 496, Lipton MS and Pasa-Tolic L, Eds., Humana Press, New York, New York, 2008, pp 273-282.

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.

Loo JA and Kaddis CS.  “Direct Characterization of Protein Complexes by Electrospray Ionization Mass Spectrometry and Ion Mobility Analysis.”  In Mass Spectrometry of Protein Interactions, Downard KM, Ed., Wiley, Hoboken, NJ, 2007, pp 1-23.

Kaddis CS and Loo JA. "Native Protein Mass Spectrometry and Ion Mobility: ESI and Large Flying Proteins." Anal Chem 2007; 79: 1779-1784. (cover article)

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.

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, Leong 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 (11), 3588–3600.

Hu S, Yu T, Xie Y, Yang Y, Li Y, Zhou X, Tsung S, Loo RR, Loo JA, Wong DT. "Discovery of Oral Fluid Biomarkers for Human Oral Cancer by Mass Spectrometry." Cancer Genomics & Proteomics 2007; 4 (2), 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, Loo JA. "Sizing Large Proteins and Protein Complexes by Electrospray Ionization Mass Spectrometry and Ion Mobility." J Am Soc Mass Spectrom 2007; 18 (7), 1206-1216.

Hu S, Loo JA, Wong DT. "Human Saliva Proteome Analysis." Annals NY Acad Sci 2007; 1098, 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, Shuai K. "Proinflammatory Stimuli Induce IKKα-Mediated Phosphorylation of PIAS1 to Restrict Inflammation and Immunity." Cell 2007; 129 (5), 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)

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.

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.

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

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.

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.

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.

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 JA, and Ping P. "The Murine Cardiac 26S Proteasome: An Organelle Awaiting Exploration." Ann NY Acad Sci 2005; 1047: 197-207.

Loo JA, Berhane BT, 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 Human Oral Fluid Proteins by Liquid Chromatography-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.

Loo JA. "Review of Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules (Kaltashov IA and Eyles SJ, authors; John Wiley & Sons, Hoboken, NJ, USA)." J Am Soc Mass Spectrom 2005; 16: 2057-2058.

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.

Xian M, Fatima Z, Zhang W, Fang J, Li H, Pei D, Loo JA, 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.

Loo JA and Gross ML. "Editorial: Focus in Honor of Carol V. Robinson, 2003 Biemann Medal Awardee." J Am Soc Mass Spectrom 2004; 15: 1379-1381.

Loo JA and Robinson CV. "Review of the 19th Asilomar Conference on Mass Spectrometry: Bimolecular Interactions: Identification and Characterization of Protein Complexes." J Am Soc Mass Spectrom 2004; 15: 759-761.

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.

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.

Loo JA. "Electrospray Ionization Mass Spectrometry: A Technology for Studying Noncovalent Macromolecular Complexes". Int J Mass Spectrom 2000; 200:175-186.

Loo JA. "Studying Noncovalent Protein Complexes by Electrospray Ionization Mass Spectrometry". Mass Spectrom Rev 1997;16:1-23.

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