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# Thomas A. Neubert, Ph.D.

Associate Professor; Director - Proteomics Core   
Department of Biochemistry and Molecular Pharmacology [1] and Structural Biology    
  


## Contact Info

**Address**  
540 First Avenue  
Floor 5 Room Lab 18  
Skirball Institute  
New York, NY 10016-6481

Phone: 212-263-7265   
Fax: 212-263-8214  
Email: Thomas.Neubert@med.nyu.edu   


### Education

1990 — Dr. Neubert received his Ph.D. in Immunology and Infectious Diseases from Johns Hopkins University, Graduate Education   
— Postdoctoral fellow with Dr. James B. Hurley in the Department of Biochemistry at the University of Washington (1990-1994) and with Dr. Lubert Stryer in the Department of Neurobiology at Stanford University (1995), PostDoctoral Training   
1990 — Johns Hopkins Univ, Medical Education   


### Research Summary

The main focus of our lab is the study of proteins and their roles in cellular signaling events. While great strides in understanding intracellular signal transduction have been made in recent years by using molecular biological techniques, we feel that a more complete understanding of the dynamics of intracellular decision-making processes can be gained only by studying the proteins directly. We use mass spectrometry as the main tool for our studies because of the wide variety of information about protein structure it can provide while requiring only small amounts of protein for analysis.<br><br>One goal of our research is to identify proteins that interact with each other during specific signaling events. Our lab has a special interest in the study of signal transduction in neurons, especially the ephrin signaling pathway. The basic strategy for these experiments is to isolate protein complexes by immunoprecipitation or affinity chromatography, separate the proteins by SDS-PAGE and then identify proteins of interest from the gel. We do this by excising the protein band from the gel, cleaving the protein with a specific protease such as trypsin, then determining the amino acid sequences of the peptides by Q-TOF tandem mass spectrometry. The masses and tandem mass spectra (containing peptide sequence information) of the peptides are then used to search genome databases to identify the proteins. To get more information about the relative amounts of each protein that participate in signaling complexes in the stimulated and nonstimulated states, we use stable isotope coding methods (for example, stable isotope labeling in cell culture, or SILAC). We also have used mass spectrometry to identify large numbers of proteins present in subcellular organelles. By first separating complex mixtures of peptides by nanoflow HPLC coupled directly to the Q-TOF mass spectrometer, we can identify many dozens of proteins at a time at low femtomolar levels, and many hundreds of proteins in a single experiment. In collaboration with Dr. Ed Ziff''s group, we have identified several hundred proteins in neuronal postsynaptic densities.<br> <br> Another focus of our work is to identify posttranslational modifications on proteins. An example of a common posttranslational modification with an important role in the regulation of protein activities is phosphorylation on serine, threonine or tyrosine residues. We have established a useful method for identifying potential phosphopeptides present at low levels in complex mixtures of nonphosphorylated peptides by comparison of MALDI-TOF mass spectra taken in both negative and positive ion modes (Figure 1). Another example of a useful method for identification of sites of posttranslational modification is shown in Figure 2. In this case the glycosylated asparagine residue of the urothelial protein uroplakin was partially labeled with 18O by cleaving the sugar residue with PNGase F in the presence of 50% 18O water. After cleaving the uroplakin with trypsin, the peptide containing the labeled asparagine was then identified on the basis of its isotopic mass distribution and sequenced by Q-TOF mass spectrometry.<br>. 

### Research Interests

Using mass spectrometry to study proteins and their posttranslational modifications. 

### Research Keywords

Mass spectrometry, proteins, posttranslational modifications, signal transduction, MALDI-TOF mass spectrometry, Q-TOF mass spectrometry, proteomics  


### Research Documents

Figure 1. MALDI-TOF mass spectrometry of phosphopeptides in positive and negative ion modes [8]

Figure 2. Identification of the partially 18O-labeled N-glycosylation site [9]

**Antipsychotics Activate mTORC1-Dependent Translation to Enhance Neuronal Morphological Complexity**  
 _Bowling, Heather; Zhang, Guoan; Bhattacharya, Aditi; Perez-Cuesta, Luis M; Deinhardt, Katrin; Hoeffer, Charles A; Neubert, Thomas A; Gan, Wen-Biao; Klann, Eric; Chao, Moses V_  
2014 ;7(308):ra4-ra4 ra4, Science signaling  
— id: 741242, year: 2014, vol: 7, page: ra4, stat: Journal Article, 

**Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture**  
 _Chalkley, Robert J; Bandeira, Nuno; Chambers, Matthew C; Clauser, Karl R; Cottrell, John S; Deutsch, Eric W; Kapp, Eugene A; Lam, Henry H N; McDonald, W Hayes; Neubert, Thomas A; Sun, Rui-Xiang_  
2014 Jan;13(1):360-371, Molecular & cellular proteomics  
— id: 781292, year: 2014, vol: 13, page: 360, stat: Journal Article, 

**Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics**  
 _Hoedt, Esthelle; Zhang, Guoan; Neubert, Thomas A_  
2014 ;806:93-106, Advances in experimental medicine & biology  
— id: 1050822, year: 2014, vol: 806, page: 93, stat: Journal Article, 

**DFG-out Mode of Inhibition by an Irreversible type-1 Inhibitor Capable of Overcoming Gate-Keeper Mutations in FGF Receptors**  
 _Huang, Zhifeng; Tan, Li; Wang, Huiyan; Liu, Yang; Blais, Steven; Deng, Jingjing; Neubert, Thomas A; Gray, Nathanael S; Li, Xiaokun; Mohammadi, Moosa_  
2014 Oct;:1-23, ACS chemical biology  
— id: 1310152, year: 2014, vol: , page: 1, stat: Journal Article, 

**Proteome analysis reveals roles of L-DOPA in response to oxidative stress in neurons**  
 _Jami, Mohammad-Saeid; Pal, Ramavati; Hoedt, Esthelle; Neubert, Thomas A; Larsen, Jan Petter; Moller, Simon Geir_  
2014 Jul;15(1):93-93, BMC neuroscience  
— id: 1090382, year: 2014, vol: 15, page: 93, stat: Journal Article, 

**gammaCaMKII Shuttles Ca(2+)/CaM to the Nucleus to Trigger CREB Phosphorylation and Gene Expression**  
 _Ma, Huan; Groth, Rachel D; Cohen, Samuel M; Emery, John F; Li, Boxing; Hoedt, Esthelle; Zhang, Guoan; Neubert, Thomas A; Tsien, Richard W_  
2014 Oct;159(2):281-294, Cell  
— id: 1300222, year: 2014, vol: 159, page: 281, stat: Journal Article, 

**Dephosphorylation of Tyrosine 393 in Argonaute 2 by Protein Tyrosine Phosphatase 1B Regulates Gene Silencing in Oncogenic RAS-Induced Senescence**  
 _Yang, Ming; Haase, Astrid D; Huang, Fang-Ke; Coulis, Gerald; Rivera, Keith D; Dickinson, Bryan C; Chang, Christopher J; Pappin, Darryl J; Neubert, Thomas A; Hannon, Gregory J; Boivin, Benoit; Tonks, Nicholas K_  
2014 Sep;55(5):782-790, Molecular cell  
— id: 1180612, year: 2014, vol: 55, page: 782, stat: Journal Article, 

**Overview of Peptide and protein analysis by mass spectrometry**  
 _Zhang, Guoan; Annan, Roland S; Carr, Steven A; Neubert, Thomas A_  
2014 ;108:10.21.1-10.21.30, Current protocols in molecular biology  
— id: 1282972, year: 2014, vol: 108, page: 10.21.1, stat: Journal Article, 

**In-depth Quantitative Proteomic Analysis of De Novo Protein Synthesis Induced by Brain-derived Neurotrophic Factor**  
 _Zhang, Guoan; Bowling, Heather; Hom, Nancy; Kirshenbaum, Kent; Klann, Eric; Chao, Moses V; Neubert, Thomas A_  
2014 Oct;:831-844, Journal of proteome research  
— id: 1282932, year: 2014, vol: , page: 831, stat: Journal Article, 

**Stable isotope labeling by amino acids in cultured primary neurons**  
 _Zhang, Guoan; Deinhardt, Katrin; Neubert, Thomas A_  
2014 ;1188:57-64, Methods in molecular biology  
— id: 1089482, year: 2014, vol: 1188, page: 57, stat: Journal Article, 

**Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)**  
_Abbatiello, Susan E; Mani, D R; Schilling, Birgit; Maclean, Brendan; Zimmerman, Lisa J; Feng, Xingdong; Cusack, Michael P; Sedransk, Nell; Hall, Steven C; Addona, Terri; Allen, Simon; Dodder, Nathan G; Ghosh, Mousumi; Held, Jason M; Hedrick, Victoria; Inerowicz, H Dorota; Jackson, Angela; Keshishian, Hasmik; Kim, Jong Won; Lyssand, John S; Riley, C Paige; Rudnick, Paul; Sadowski, Pawel; Shaddox, Kent; Smith, Derek; Tomazela, Daniela; Wahlander, Asa; Waldemarson, Sofia; Whitwell, Corbin A; You, Jinsam; Zhang, Shucha; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Borchers, Christoph H; Buck, Charles; Fisher, Susan J; Gibson, Bradford W; Liebler, Daniel; Maccoss, Michael; Neubert, Thomas A; Paulovich, Amanda; Regnier, Fred; Skates, Steven J; Tempst, Paul; Wang, Mu; Carr, Steven A_  
2013 Sep;12(9):2623-2639, Molecular & cellular proteomics  
— id: 557832, year: 2013, vol: 12, page: 2623, stat: Journal Article, 

**Ionotropic glutamate receptors IR64a and IR8a form a functional odorant receptor complex in vivo in Drosophila**  
 _Ai, Minrong; Blais, Steven; Park, Jin-Yong; Min, Soohong; Neubert, Thomas A; Suh, Greg S B_  
2013 Jun;33(26):10741-10749, Journal of neuroscience  
— id: 509072, year: 2013, vol: 33, page: 10741, stat: Journal Article, 

**Detection and correction of interference in SRM analysis**  
 _Bao, Y; Waldemarson, S; Zhang, G; Wahlander, A; Ueberheide, B; Myung, S; Reed, B; Molloy, K; Padovan, J C; Eriksson, J; Neubert, T A; Chait, B T; Fenyo, D_  
2013 Jun;61(3):299-303, Methods  
— id: 415052, year: 2013, vol: 61, page: 299, stat: Journal Article, 

**Comparison of commercially available target enrichment methods for next-generation sequencing**  
 _Bodi, K; Perera, A G; Adams, P S; Bintzler, D; Dewar, K; Grove, D S; Kieleczawa, J; Lyons, R H; Neubert, T A; Noll, A C; Singh, S; Steen, R; Zianni, M_  
2013 Jul;24(2):73-86, Journal of biomolecular techniques  
— id: 452232, year: 2013, vol: 24, page: 73, stat: Journal Article, 

**The N550K/H mutations in FGFR2 confer differential resistance to PD173074, dovitinib, and ponatinib ATP-competitive inhibitors**  
 _Byron, Sara A; Chen, Huaibin; Wortmann, Andreas; Loch, David; Gartside, Michael G; Dehkhoda, Farhad; Blais, Steven P; Neubert, Thomas A; Mohammadi, Moosa; Pollock, Pamela M_  
2013 Aug;15(8):975-988, Neoplasia  
— id: 575672, year: 2013, vol: 15, page: 975, stat: Journal Article, 

**Cracking the Molecular Origin of Intrinsic Tyrosine Kinase Activity through Analysis of Pathogenic Gain-of-Function Mutations**  
 _Chen, Huaibin; Huang, Zhifeng; Dutta, Kaushik; Blais, Steven; Neubert, Thomas A; Li, Xiaokun; Cowburn, David; Traaseth, Nathaniel J; Mohammadi, Moosa_  
2013 Jul;4(2):376-384, Cell reports  
— id: 463582, year: 2013, vol: 4, page: 376, stat: Journal Article, 

**Structural Mimicry of A-Loop Tyrosine Phosphorylation by a Pathogenic FGF Receptor 3 Mutation**  
 _Huang, Zhifeng; Chen, Huaibin; Blais, Steven; Neubert, Thomas A; Li, Xiaokun; Mohammadi, Moosa_  
2013 Oct;21(10):1889-1896, Structure  
— id: 573812, year: 2013, vol: 21, page: 1889, stat: Journal Article, 

**Comparative proteomic analysis of the ATP-sensitive K(+) channel complex in different tissue types**  
 _Kefaloyianni, Eirini; Lyssand, John S; Moreno, Cesar; Delaroche, Diane; Hong, Miyoun; Fenyo, David; Mobbs, Charles V; Neubert, Thomas A; Coetzee, William A_  
2013 Jan;13(2):368-378, Proteomics  
— id: 213632, year: 2013, vol: 13, page: 368, stat: Journal Article, 

**Brain-Derived Neurotrophic Factor Signaling Rewrites the Glucocorticoid Transcriptome via Glucocorticoid Receptor Phosphorylation**  
 _Lambert, W Marcus; Xu, Chong-Feng; Neubert, Thomas A; Chao, Moses V; Garabedian, Michael J; Jeanneteau, Freddy D_  
2013 Sep;33(18):3700-3714, Molecular & cellular biology  
— id: 540352, year: 2013, vol: 33, page: 3700, stat: Journal Article, 

**Brain-Derived Neurotrophic Factor Signaling Rewrites the Glucocorticoid Transcriptome via Glucocorticoid Receptor Phosphorylation (vol 33, pg 3700, 2013)**  
_Lambert, W. Marcus; Xu, Chong-Feng; Neubert, Thomas A.; Chao, Moses V.; Garabedian, Michael J.; Jeanneteau, Freddy D._  
2013 OCT;33(20):4138-4138, Molecular & cellular biology  
— id: 612042, year: 2013, vol: 33, page: 4138, stat: Journal Article, 

**Brain-derived neurotrophic factor signaling rewrites the glucocorticoid transcriptome via glucocorticoid receptor phosphorylation**  
 _Marcus, Lambert W; Xu, C -F; Neubert, T A; Chao, M V; Garabedian, M J; Jeanneteau, F D_  
2013 2013;33(20):4138-, Molecular & cellular biology  
— id: 612462, year: 2013, vol: 33, page: 4138, stat: Journal Article, 

**Development of a biosensor for detection of pleural mesothelioma cancer biomarker using surface imprinting**  
 _Mathur, Aabhas; Blais, Steven; Goparaju, Chandra M V; Neubert, Thomas; Pass, Harvey; Levon, Kalle_  
2013 ;8(3):e57681-e57681 e57681, PLoS one  
— id: 753322, year: 2013, vol: 8, page: e57681, stat: Journal Article, 

**Exploring the role of conformational heterogeneity in the V1/V2 domain of HIV-1 gp120 on the immunological properties of Env immunogens**  
 _Pinter, Abraham; Neubert, Thomas; Burkhart, Michael; Irene, Carmela; Reichman, Charles; Honnen, William J._  
2013 APR;62 1 1:53-53, Journal of acquired immune deficiency syndromes. JAIDS  
— id: 833572, year: 2013, vol: 62 1 1, page: 53, stat: Journal Article, 

**The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule**  
 _Cross, Benedict C S; Bond, Peter J; Sadowski, Pawel G; Jha, Babal Kant; Zak, Jaroslav; Goodman, Jonathan M; Silverman, Robert H; Neubert, Thomas A; Baxendale, Ian R; Ron, David; Harding, Heather P_  
2012 Apr;109(15):E869-E878, Proceedings of the National Academy of Sciences of the United States of America  
— id: 165427, year: 2012, vol: 109, page: E869, stat: Journal Article, 

**Calpastatin modulates APP processing in the brains of beta-amyloid depositing but not wild-type mice**  
 _Morales-Corraliza, Jose; Berger, Jason D; Mazzella, Matthew J; Neubert, Thomas A; Ghiso, Jorge; Rao, Mala V; Staufenbiel, Matthias; Nixon, Ralph A; Mathews, Paul M_  
2012 Jun;33(6):1125.e9-1125.18, Neurobiology of aging  
— id: 164336, year: 2012, vol: 33, page: 1125.e9, stat: Journal Article, 

**Conformational heterogeneity in V1/V2 domain affects the immunological properties of this region**  
 _Pinter, A.; Wu, A. Z.; Neubert, T.; Burkhart, M. D.; Honnen, W. J._  
2012 SEP 13;9 2 2:-, Retrovirology  
— id: 181492, year: 2012, vol: 9 2 2, page: , stat: Journal Article, 

**Comparison of cardiolipins from Drosophila strains with mutations in putative remodeling enzymes**  
 _Schlame, Michael; Blais, Steven; Edelman-Novemsky, Irit; Xu, Yang; Montecillo, Fleurise; Phoon, Colin K L; Ren, Mindong; Neubert, Thomas A_  
2012 Jul;165(5):512-519, Chemistry & physics of lipids  
— id: 175766, year: 2012, vol: 165, page: 512, stat: Journal Article, 

**MIRG Survey 2011: Snapshot of Rapidly Evolving Label-Free Technologies Used for Characterizing Molecular Interactions**  
 _Yadav, Satya P; Bergqvist, Simon; Doyle, Michael L; Neubert, Thomas A; Yamniuk, Aaron P_  
2012 Sep;23(3):94-100, Journal of biomolecular techniques  
— id: 179193, year: 2012, vol: 23, page: 94, stat: Journal Article, 

**RNA binding proteins accumulate at the postsynaptic density with synaptic activity**  
 _Zhang, Guoan; Neubert, Thomas A; Jordan, Bryen A_  
2012 Jan 11;32(2):599-609, Journal of neuroscience  
— id: 149813, year: 2012, vol: 32, page: 599, stat: Journal Article, 

**MAL facilitates the incorporation of exocytic uroplakin-delivering vesicles into the apical membrane of urothelial umbrella cells**  
 _Zhou, G; Liang, FX; Romih, R; Wang, Z; Liao, Y; Ghiso, J; Luque-Garcia, JL; Neubert, TA; Kreibich, G; Alonso, MA; Schaeren-Wiemers, N; Sun, TT_  
2012 Apr;23(7):1354-1366, Molecular biology of the cell  
— id: 165440, year: 2012, vol: 23, page: 1354, stat: Journal Article, 

**Intercellular cancer collisions generate an ejected crystal comet tail effect with fractal interface embryoid body reassembly transformation**  
 _Bushnell, Philip J.; Strupp, Barbara J.; Rice, Margaret E.; Avshalumov, Marat V.; Patel, Jyoti C.; Hrabetova, Sabina; Nicholson, Charles; Jordan, Bryen A.; Fernholz, Brian D.; Neubert, Thomas A.; Ziff, Edward B.; Faltz, Lawrence L; Morley, John N; Flink, Ellen; Dameron, Peg DeHont; Al-Ibrahim, Mohamed S.; Gross, Joyce Y.; Mobasheri, Ali; Barrett-Jolley, Richard; Shakibaei, Mehdi; Canessa, Cecilia M.; Martin-Vasallo, Pablo; Mobasheri, Ali; Barrett-Jolley, Richard; Carter, Stuart D.; Martin-Vasallo, Pablo; Schulze-Tanzil, Gundula; Shakibaei, Mehdi; Albertson, Donna G; Rose, Ann M; Villeneuve, Anne M; Diaz, Jairo A; Murillo, Mauricio F; Barrero, Alvaro_  
2011 Aug;3:143-155, Cancer management & research  
— id: 995532, year: 2011, vol: 3, page: 143, stat: Journal Article, 

**Identifying transient protein-protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry**  
 _Darie, Costel C; Deinhardt, Katrin; Zhang, Guoan; Cardasis, Helene S; Chao, Moses V; Neubert, Thomas A_  
2011 Dec;11(23):4514-4528, Proteomics  
— id: 145796, year: 2011, vol: 11, page: 4514, stat: Journal Article, 

**Neuronal growth cone retraction relies on proneurotrophin receptor signaling through rac**  
 _Deinhardt, Katrin; Kim, Taeho; Spellman, Daniel S; Mains, Richard E; Eipper, Betty A; Neubert, Thomas A; Chao, Moses V; Hempstead, Barbara L_  
2011 ;4(202):ra82-ra82, Science signaling  
— id: 146263, year: 2011, vol: 4, page: ra82, stat: Journal Article, 

**Cardiac ATP-sensitive K+ channel associates with the glycolytic enzyme complex**  
 _Hong, Miyoun; Kefaloyianni, Eirini; Bao, Li; Malester, Brian; Delaroche, Diane; Neubert, Thomas A; Coetzee, William A_  
2011 Jul;25(7):2456-2467, FASEB journal  
— id: 134908, year: 2011, vol: 25, page: 2456, stat: Journal Article, 

**iPRG 2011: A study on the identification of electron transfer dissociation (ETD) mass spectra**  
 _Martens, L; Askenazi, M; Bandeira, N; Chalkley, R J; Clauser, K R; Deutsch, E; Lam, H H N; McDonald, W H; Neubert, T; Rudnick, P A_  
2011 October 2011;22:S20-S20, Journal of biomolecular techniques  
— id: 164439, year: 2011, vol: 22, page: S20, stat: Journal Article, 

**Catabolism of Alzheimer's amyloid-b: Implications for brain clearance and plaque deposition**  
 _McIntee F.L.; Giannoni P.; Blais S.; Neubert T.; Mathews P.; Rostagno A.; Ghiso J._  
2011 ;8:?-?, Neuro-degenerative diseases  
— id: 136531, year: 2011, vol: 8, page: ?, stat: Journal Article, 

**The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling**  
 _Ungureanu, Daniela; Wu, Jinhua; Pekkala, Tuija; Niranjan, Yashavanthi; Young, Clifford; Jensen, Ole N; Xu, Chong-Feng; Neubert, Thomas A; Skoda, Radek C; Hubbard, Stevan R; Silvennoinen, Olli_  
2011 ;18(9):971-976, Nature structural & molecular biology  
— id: 137017, year: 2011, vol: 18, page: 971, stat: Journal Article, 

**Conclusions from the MIRG 2010 benchmark study: Molecular interactions in a three component system and presentation of 2011 survey results on label-free technologies**  
 _Yamniuk, A P; Yadav, S P; Bergqvist, S; Doyle, M L; Eisenstein, E; Robinson, M K; Neubert, T_  
2011 October 2011;22:S23-S24, Journal of biomolecular techniques  
— id: 164438, year: 2011, vol: 22, page: S23, stat: Journal Article, 

**A Novel Transcription Complex That Selectively Modulates Apoptosis of Breast Cancer Cells through Regulation of FASTKD2**  
 _Yeung, Kay T; Das, Sharmistha; Zhang, Jin; Lomniczi, Alejandro; Ojeda, Sergio R; Xu, Chong-Feng; Neubert, Thomas A; Samuels, Herbert H_  
2011 Jun;31(11):2287-2298, Molecular & cellular biology  
— id: 132312, year: 2011, vol: 31, page: 2287, stat: Journal Article, 

**Study of Neurotrophin-3 Signaling in Primary Cultured Neurons using Multiplex Stable Isotope Labeling with Amino Acids in Cell Culture**  
 _Zhang, Guoan; Deinhardt, Katrin; Chao, Moses V; Neubert, Thomas A_  
2011 May 6;10(5):2546-2554, Journal of proteome research  
— id: 132309, year: 2011, vol: 10, page: 2546, stat: Journal Article, 

**Comparison of three quantitative phosphoproteomic strategies to study receptor tyrosine kinase signaling**  
 _Zhang, Guoan; Neubert, Thomas A_  
2011 Dec 2;10(12):5454-5462, Journal of proteome research  
— id: 145751, year: 2011, vol: 10, page: 5454, stat: Journal Article, 

**Recombinant derivatives of botulinum neurotoxin A engineered for trafficking studies and neuronal delivery**  
 _Band, Philip A; Blais, Steven; Neubert, Thomas A; Cardozo, Timothy J; Ichtchenko, Konstantin_  
2010 May;71(1):62-73, Protein expression & purification  
— id: 107925, year: 2010, vol: 71, page: 62, stat: Journal Article, 

**Canonical and alternate functions of the microRNA biogenesis machinery**  
 _Chong, Mark M W; Zhang, Guoan; Cheloufi, Sihem; Neubert, Thomas A; Hannon, Gregory J; Littman, Dan R_  
2010 Sep 1;24(17):1951-1960, Genes & development  
— id: 112041, year: 2010, vol: 24, page: 1951, stat: Journal Article, 

**Dok-7 regulates neuromuscular synapse formation by recruiting Crk and Crk-L**  
 _Hallock, Peter T; Xu, Chong-Feng; Park, Tae-Ju; Neubert, Thomas A; Curran, Tom; Burden, Steven J_  
2010 Nov 1;24(21):2451-2461, Genes & development  
— id: 114184, year: 2010, vol: 24, page: 2451, stat: Journal Article, 

**The matrix peptide exporter HAF-1 signals a mitochondrial UPR by activating the transcription factor ZC376.7 in C. elegans**  
 _Haynes, Cole M; Yang, Yun; Blais, Steven P; Neubert, Thomas A; Ron, David_  
2010 Feb 26;37(4):529-540, Molecular cell  
— id: 107928, year: 2010, vol: 37, page: 529, stat: Journal Article, 

**Matrix metalloproteinase 2 (MMP-2) degrades soluble vasculotropic amyloid-beta E22Q and L34V mutants, delaying their toxicity for human brain microvascular endothelial cells**  
 _Hernandez-Guillamon, Mar; Mawhirt, Stephanie; Fossati, Silvia; Blais, Steven; Pares, Mireia; Penalba, Anna; Boada, Merce; Couraud, Pierre-Olivier; Neubert, Thomas A; Montaner, Joan; Ghiso, Jorge; Rostagno, Agueda_  
2010 Aug 27;285(35):27144-27158, Journal of biological chemistry  
— id: 112035, year: 2010, vol: 285, page: 27144, stat: Journal Article, 

**Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA**  
 _Kaneko, Syuzo; Li, Gang; Son, Jinsook; Xu, Chong-Feng; Margueron, Raphael; Neubert, Thomas A; Reinberg, Danny_  
2010 Dec 1;24(23):2615-2620, Genes & development  
— id: 114862, year: 2010, vol: 24, page: 2615, stat: Journal Article, 

**Catabolism of Alzheimer's amyloid-beta: Implications for brain clearance and plaque deposition**  
 _McIntee F.L.; Neubert T.; Blais S.; Ghiso J._  
2010 ;3(2):S47-S47, Clinical & translational science  
— id: 111407, year: 2010, vol: 3, page: S47, stat: Journal Article, 

**Super-SILAC for tumors and tissues**  
 _Neubert, Thomas A; Tempst, Paul_  
2010 May;7(5):361-362, Nature methods  
— id: 967912, year: 2010, vol: 7, page: 361, stat: Journal Article, 

**Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance**  
 _Paulovich, Amanda G; Billheimer, Dean; Ham, Amy-Joan L; Vega-Montoto, Lorenzo; Rudnick, Paul A; Tabb, David L; Wang, Pei; Blackman, Ronald K; Bunk, David M; Cardasis, Helene L; Clauser, Karl R; Kinsinger, Christopher R; Schilling, Birgit; Tegeler, Tony J; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R; Zimmerman, Lisa J; Fenyo, David; Carr, Steven A; Fisher, Susan J; Gibson, Bradford W; Mesri, Mehdi; Neubert, Thomas A; Regnier, Fred E; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E; Tempst, Paul; Liebler, Daniel C_  
2010 Feb;9(2):242-254, Molecular & cellular proteomics  
— id: 114127, year: 2010, vol: 9, page: 242, stat: Journal Article, 

**Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses**  
 _Rudnick, Paul A; Clauser, Karl R; Kilpatrick, Lisa E; Tchekhovskoi, Dmitrii V; Neta, Pedatsur; Blonder, Niksa; Billheimer, Dean D; Blackman, Ronald K; Bunk, David M; Cardasis, Helene L; Ham, Amy-Joan L; Jaffe, Jacob D; Kinsinger, Christopher R; Mesri, Mehdi; Neubert, Thomas A; Schilling, Birgit; Tabb, David L; Tegeler, Tony J; Vega-Montoto, Lorenzo; Variyath, Asokan Mulayath; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R; Zimmerman, Lisa J; Carr, Steven A; Fisher, Susan J; Gibson, Bradford W; Paulovich, Amanda G; Regnier, Fred E; Rodriguez, Henry; Spiegelman, Cliff; Tempst, Paul; Liebler, Daniel C; Stein, Stephen E_  
2010 Feb;9(2):225-241, Molecular & cellular proteomics  
— id: 967902, year: 2010, vol: 9, page: 225, stat: Journal Article, 

**Myristoylation of the dual-specificity phosphatase c-JUN N-terminal kinase (JNK) stimulatory phosphatase 1 is necessary for its activation of JNK signaling and apoptosis**  
 _Schwertassek, Ulla; Buckley, Deirdre A; Xu, Chong-Feng; Lindsay, Andrew J; McCaffrey, Mary W; Neubert, Thomas A; Tonks, Nicholas K_  
2010 Jun;277(11):2463-2473, FEBS journal  
— id: 967922, year: 2010, vol: 277, page: 2463, stat: Journal Article, 

**Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry**  
 _Tabb, David L; Vega-Montoto, Lorenzo; Rudnick, Paul A; Variyath, Asokan Mulayath; Ham, Amy-Joan L; Bunk, David M; Kilpatrick, Lisa E; Billheimer, Dean D; Blackman, Ronald K; Cardasis, Helene L; Carr, Steven A; Clauser, Karl R; Jaffe, Jacob D; Kowalski, Kevin A; Neubert, Thomas A; Regnier, Fred E; Schilling, Birgit; Tegeler, Tony J; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R; Zimmerman, Lisa J; Fisher, Susan J; Gibson, Bradford W; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E; Tempst, Paul; Paulovich, Amanda G; Liebler, Daniel C; Spiegelman, Cliff_  
2010 Feb 5;9(2):761-776, Journal of proteome research  
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**Iowa variant of familial Alzheimer's disease: accumulation of posttranslationally modified AbetaD23N in parenchymal and cerebrovascular amyloid deposits**  
 _Tomidokoro, Yasushi; Rostagno, Agueda; Neubert, Thomas A; Lu, Yun; Rebeck, G William; Frangione, Blas; Greenberg, Steven M; Ghiso, Jorge_  
2010 Apr;176(4):1841-1854, American journal of pathology  
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**Overview of peptide and protein analysis by mass spectrometry**  
 _Zhang, Guoan; Annan, Roland S; Carr, Steven A; Neubert, Thomas A_  
2010 Nov;Chapter 16:Unit16.1-Unit16.1, Current protocols in protein science  
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**Protein quantitation using mass spectrometry**  
 _Zhang, Guoan; Ueberheide, Beatrix M; Waldemarson, Sofia; Myung, Sunnie; Molloy, Kelly; Eriksson, Jan; Chait, Brian T; Neubert, Thomas A; Fenyo, David_  
2010 ;673:211-222, Methods in molecular biology  
— id: 112434, year: 2010, vol: 673, page: 211, stat: Journal Article, 

**Oxidative protein folding by an endoplasmic reticulum-localized peroxiredoxin**  
 _Zito, Ester; Melo, Eduardo Pinho; Yang, Yun; Wahlander, Asa; Neubert, Thomas A; Ron, David_  
2010 Dec 10;40(5):787-797, Molecular cell  
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**Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma**  
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2009 Jul;27(7):633-641, Nature biotechnology  
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**Identification and characterization of a novel nuclear protein complex Involved In nuclear hormone receptor-mediated gene regulation**  
 _Garapaty, Shivani; Xu, Chong-Feng; Trojer, Patrick; Mahajan, Muktar A; Neubert, Thomas A; Samuels, Herbert H_  
2009 Mar 20;284(12):7542-7552, Journal of biological chemistry  
— id: 95312, year: 2009, vol: 284, page: 7542, stat: Journal Article, 

**Crystal structure of a fibroblast growth factor homologous factor (FHF) defines a conserved surface on FHFs for binding and modulation of voltage-gated sodium channels**  
 _Goetz, Regina; Dover, Katarzyna; Laezza, Fernanda; Shtraizent, Nataly; Huang, Xiao; Tchetchik, Dafna; Eliseenkova, Anna V; Xu, Chong-Feng; Neubert, Thomas A; Ornitz, David M; Goldfarb, Mitchell; Mohammadi, Moosa_  
2009 Jun 26;284(26):17883-17896, Journal of biological chemistry  
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**Homodimerization controls the fibroblast growth factor 9 subfamily's receptor binding and heparan sulfate-dependent diffusion in the extracellular matrix**  
 _Kalinina, Juliya; Byron, Sara A; Makarenkova, Helen P; Olsen, Shaun K; Eliseenkova, Anna V; Larochelle, William J; Dhanabal, Mohanraj; Blais, Steven; Ornitz, David M; Day, Loren A; Neubert, Thomas A; Pollock, Pamela M; Mohammadi, Moosa_  
2009 Sep;29(17):4663-4678, Molecular & cellular biology  
— id: 156085, year: 2009, vol: 29, page: 4663, stat: Journal Article, 

**Dissociation of the subunits of the calcium-independent receptor of alpha-latrotoxin as a result of two-step proteolysis**  
 _Krasnoperov, Valery; Deyev, Igor E; Serova, Oxana V; Xu, Chongfeng; Lu, Yun; Buryanovsky, Leonid; Gabibov, Alexander G; Neubert, Thomas A; Petrenko, Alexander G_  
2009 Apr 14;48(14):3230-3238, Biochemistry  
— id: 98778, year: 2009, vol: 48, page: 3230, stat: Journal Article, 

**The target of the NSD family of histone lysine methyltransferases depends on the nature of the substrate**  
 _Li, Yan; Trojer, Patrick; Xu, Chong-Feng; Cheung, Peggie; Kuo, Alex; Drury, William J 3rd; Qiao, Qi; Neubert, Thomas A; Xu, Rui-Ming; Gozani, Or; Reinberg, Danny_  
2009 Dec 4;284(49):34283-34295, Journal of biological chemistry  
— id: 105498, year: 2009, vol: 284, page: 34283, stat: Journal Article, 

**On-membrane tryptic digestion of proteins for mass spectrometry analysis**  
 _Luque-Garcia, Jose L; Neubert, Thomas A_  
2009 ;536:331-341, Methods in molecular biology  
— id: 99320, year: 2009, vol: 536, page: 331, stat: Journal Article, 

**Characterization of novel oxidation products of cysteine in an active site motif peptide of PTP1B**  
 _Shetty, Vivekananda; Neubert, Thomas A_  
2009 Aug;20(8):1540-1548, Journal of the American Society for Mass Spectrometry  
— id: 101283, year: 2009, vol: 20, page: 1540, stat: Journal Article, 

**Thioredoxin-related Protein 32 Is an Arsenite-regulated Thiol Reductase of the Proteasome 19 S Particle**  
 _Wiseman, R Luke; Chin, King-Tung; Haynes, Cole M; Stanhill, Ariel; Xu, Chong-Feng; Roguev, Assen; Krogan, Nevan J; Neubert, Thomas A; Ron, David_  
2009 May 29;284(22):15233-15245, Journal of biological chemistry  
— id: 99210, year: 2009, vol: 284, page: 15233, stat: Journal Article, 

**Characterization of tafazzin splice variants from humans and fruit flies**  
 _Xu, Yang; Zhang, Shali; Malhotra, Ashim; Edelman-Novemsky, Irit; Ma, Jinping; Kruppa, Antonina; Cernicica, Carolina; Blais, Steven; Neubert, Thomas A; Ren, Mindong; Schlame, Michael_  
2009 Oct 16;284(42):29230-29239, Journal of biological chemistry  
— id: 104345, year: 2009, vol: 284, page: 29230, stat: Journal Article, 

**Evaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope Labeling by Amino Acids in Cell Culture**  
 _Zhang, Guoan; Fenyo, David; Neubert, Thomas A_  
2009 Mar;8(3):1285-1292, Journal of proteome research  
— id: 96814, year: 2009, vol: 8, page: 1285, stat: Journal Article, 

**Use of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Phosphotyrosine Protein Identification and Quantitation**  
 _Zhang, Guoan; Neubert, Thomas A_  
2009 ;527:409-416, Methods in molecular biology  
— id: 96813, year: 2009, vol: 527, page: 409, stat: Journal Article, 

**Isoflurane inhibits cyclic adenosine monophosphate response element-binding protein phosphorylation and calmodulin translocation to the nucleus of SH-SY5Y cells**  
 _Zhang, Jin; Sutachan, Jhon-Jairo; Montoya-Gacharna, Jose; Xu, Chong-Feng; Xu, Fang; Neubert, Thomas A; Recio-Pinto, Esperanza; Blanck, Thomas J J_  
2009 Oct;109(4):1127-1134, Anesthesia & analgesia  
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**A crystallographic snapshot of tyrosine trans-phosphorylation in action**  
 _Chen, Huaibin; Xu, Chong-Feng; Ma, Jinghong; Eliseenkova, Anna V; Li, Wanqing; Pollock, Pamela M; Pitteloud, Nelly; Miller, W Todd; Neubert, Thomas A; Mohammadi, Moosa_  
2008 Dec 16;105(50):19660-19665, Proceedings of the National Academy of Sciences of the United States of America  
— id: 90927, year: 2008, vol: 105, page: 19660, stat: Journal Article, 

**Blue native page and mass spectrometry analysis of ephrin stimulation-dependent protein-protein interactions in NG108-EphB2 cells**  
 _Darie, CC; Shetty, V; Spellman, DS; Zhang, G; Xu, C; Cardasis, HL; Blais, S; Fenyo, D; Neubert, TA_  
2008 ;:3-22, NATO Science for Peace & Security. Series A: Chemistry & Biology  
— id: 653052, year: 2008, vol: , page: 3, stat: Journal Article, 

**ABRF-PRG05: de novo peptide sequence determination**  
 _Falick, Arnold M; Kowalak, Jeffrey A; Lane, William S; Phinney, Brett S; Turck, Christoph W; Weintraub, Susan T; West, Karen A; Neubert, Thomas A_  
2008 Sep;19(4):251-257, Journal of biomolecular techniques  
— id: 96815, year: 2008, vol: 19, page: 251, stat: Journal Article, 

**Analysis of electroblotted proteins by mass spectrometry: protein identification after Western blotting**  
 _Luque-Garcia, Jose L; Zhou, Ge; Spellman, Daniel S; Sun, Tung-Tien; Neubert, Thomas A_  
2008 Feb;7(2):308-314, Molecular & cellular proteomics  
— id: 76651, year: 2008, vol: 7, page: 308, stat: Journal Article, 

**Human Proteinpedia enables sharing of human protein data**  
 _Mathivanan, Suresh; Ahmed, Mukhtar; Ahn, Natalie G; Alexandre, Hainard; Amanchy, Ramars; Andrews, Philip C; Bader, Joel S; Balgley, Brian M; Bantscheff, Marcus; Bennett, Keiryn L; Bjorling, Erik; Blagoev, Blagoy; Bose, Ron; Brahmachari, Samir K; Burlingame, Alma S; Bustelo, Xose R; Cagney, Gerard; Cantin, Greg T; Cardasis, Helene L; Celis, Julio E; Chaerkady, Raghothama; Chu, Feixia; Cole, Philip A; Costello, Catherine E; Cotter, Robert J; Crockett, David; DeLany, James P; De Marzo, Angelo M; DeSouza, Leroi V; Deutsch, Eric W; Dransfield, Eric; Drewes, Gerard; Droit, Arnaud; Dunn, Michael J; Elenitoba-Johnson, Kojo; Ewing, Rob M; Van Eyk, Jennifer; Faca, Vitor; Falkner, Jayson; Fang, Xiangming; Fenselau, Catherine; Figeys, Daniel; Gagne, Pierre; Gelfi, Cecilia; Gevaert, Kris; Gimble, Jeffrey M; Gnad, Florian; Goel, Renu; Gromov, Pavel; Hanash, Samir M; Hancock, William S; Harsha, H C; Hart, Gerald; Hays, Faith; He, Fuchu; Hebbar, Prashantha; Helsens, Kenny; Hermeking, Heiko; Hide, Winston; Hjerno, Karin; Hochstrasser, Denis F; Hofmann, Oliver; Horn, David M; Hruban, Ralph H; Ibarrola, Nieves; James, Peter; Jensen, Ole N; Jensen, Pia Honnerup; Jung, Peter; Kandasamy, Kumaran; Kheterpal, Indu; Kikuno, Reiko F; Korf, Ulrike; Korner, Roman; Kuster, Bernhard; Kwon, Min-Seok; Lee, Hyoung-Joo; Lee, Young-Jin; Lefevre, Michael; Lehvaslaiho, Minna; Lescuyer, Pierre; Levander, Fredrik; Lim, Megan S; Lobke, Christian; Loo, Joseph A; Mann, Matthias; Martens, Lennart; Martinez-Heredia, Juan; McComb, Mark; McRedmond, James; Mehrle, Alexander; Menon, Rajasree; Miller, Christine A; Mischak, Harald; Mohan, S Sujatha; Mohmood, Riaz; Molina, Henrik; Moran, Michael F; Morgan, James D; Moritz, Robert; Morzel, Martine; Muddiman, David C; Nalli, Anuradha; Navarro, J Daniel; Neubert, Thomas A; Ohara, Osamu; Oliva, Rafael; Omenn, Gilbert S; Oyama, Masaaki; Paik, Young-Ki; Pennington, Kyla; Pepperkok, Rainer; Periaswamy, Balamurugan; Petricoin, Emanuel F; Poirier, Guy G; Prasad, T S Keshava; Purvine, Samuel O; Rahiman, B Abdul; Ramachandran, Prasanna; Ramachandra, Y L; Rice, Robert H; Rick, Jens; Ronnholm, Ragna H; Salonen, Johanna; Sanchez, Jean-Charles; Sayd, Thierry; Seshi, Beerelli; Shankari, Kripa; Sheng, Shi Jun; Shetty, Vivekananda; Shivakumar, K; Simpson, Richard J; Sirdeshmukh, Ravi; Siu, K W Michael; Smith, Jeffrey C; Smith, Richard D; States, David J; Sugano, Sumio; Sullivan, Matthew; Superti-Furga, Giulio; Takatalo, Maarit; Thongboonkerd, Visith; Trinidad, Jonathan C; Uhlen, Mathias; Vandekerckhove, Joel; Vasilescu, Julian; Veenstra, Timothy D; Vidal-Taboada, Jose-Manuel; Vihinen, Mauno; Wait, Robin; Wang, Xiaoyue; Wiemann, Stefan; Wu, Billy; Xu, Tao; Yates, John R; Zhong, Jun; Zhou, Ming; Zhu, Yunping; Zurbig, Petra; Pandey, Akhilesh_  
2008 Feb;26(2):164-167, Nature biotechnology  
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**Calsyntenins Are Secretory Granule Proteins in Anterior Pituitary Gland and Pancreatic Islet {alpha} Cells**  
 _Rindler, Michael J; Xu, Chong-Feng; Gumper, Iwona; Cen, Chuan; Sonderegger, Peter; Neubert, Thomas A_  
2008 Apr;56(4):381-388, Journal of histochemistry & cytochemistry  
— id: 76650, year: 2008, vol: 56, page: 381, stat: Journal Article, 

**Stable isotopic labeling of amino acids in cultured primary neurons: Application to BDNF-dependent phosphotyrosine-associated signaling**  
 _Spellman, Daniel S; Deinhardt, Katrin; Darie, Costel C; Chao, Moses V; Neubert, Thomas A_  
2008 Jun;7(6):1067-1076, Molecular & cellular proteomics  
— id: 76648, year: 2008, vol: 7, page: 1067, stat: Journal Article, 

**Guidelines for reporting the use of mass spectrometry in proteomics**  
 _Taylor, Chris F; Binz, Pierre-Alain; Aebersold, Ruedi; Affolter, Michel; Barkovich, Robert; Deutsch, Eric W; Horn, David M; Huhmer, Andreas; Kussmann, Martin; Lilley, Kathryn; Macht, Marcus; Mann, Matthias; Muller, Dieter; Neubert, Thomas A; Nickson, Janice; Patterson, Scott D; Raso, Roberto; Resing, Kathryn; Seymour, Sean L; Tsugita, Akira; Xenarios, Ioannis; Zeng, Rong; Julian, Randall K Jr_  
2008 Aug;26(8):860-861, Nature biotechnology  
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**Phosphorylation of liver X receptor alpha selectively regulates target gene expression in macrophages**  
 _Torra, Ines Pineda; Ismaili, Naima; Feig, Jonathan E; Xu, Chong-Feng; Cavasotto, Claudio; Pancratov, Raluca; Rogatsky, Inez; Neubert, Thomas A; Fisher, Edward A; Garabedian, Michael J_  
2008 Apr;28(8):2626-2636, Molecular & cellular biology  
— id: 76646, year: 2008, vol: 28, page: 2626, stat: Journal Article, 

**Histoplasma capsulatum proteome response to decreased iron availability**  
 _Winters, Michael S; Spellman, Daniel S; Chan, Qilin; Gomez, Francisco J; Hernandez, Margarita; Catron, Brittany; Smulian, Alan G; Neubert, Thomas A; Deepe, George S Jr_  
2008 ;6:36-36, Proteome science  
— id: 96816, year: 2008, vol: 6, page: 36, stat: Journal Article, 

**Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2**  
 _Wu, Jinhua; Tseng, Yolanda D; Xu, Chong-Feng; Neubert, Thomas A; White, Morris F; Hubbard, Stevan R_  
2008 Mar;15(3):251-258, Nature structural & molecular biology  
— id: 76468, year: 2008, vol: 15, page: 251, stat: Journal Article, 

**Proteasomal adaptation to environmental stress links resistance to proteotoxicity with longevity in Caenorhabditis elegans**  
 _Yun, Chi; Stanhill, Ariel; Yang, Yun; Zhang, Yuhong; Haynes, Cole M; Xu, Chong-Feng; Neubert, Thomas A; Mor, Adam; Philips, Mark R; Ron, David_  
2008 May 13;105(19):7094-7099, Proceedings of the National Academy of Sciences of the United States of America  
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**Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer**  
 _Zhang, Guoan; Fenyo, David; Neubert, Thomas A_  
2008 Nov;7(11):4715-4726, Journal of proteome research  
— id: 91446, year: 2008, vol: 7, page: 4715, stat: Journal Article, 

**Use of DNA ladders for reproducible protein fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) for quantitative proteomics**  
 _Zhang, Guoan; Fenyo, David; Neubert, Thomas A_  
2008 Feb;7(2):678-686, Journal of proteome research  
— id: 76649, year: 2008, vol: 7, page: 678, stat: Journal Article, 

**ABRF-PRG04: differentiation of protein isoforms**  
 _Arnott, David; Gawinowicz, Mary Ann; Kowalak, Jeffrey A; Lane, William S; Speicher, Kaye D; Turck, Christoph W; West, Karen A; Neubert, Thomas A_  
2007 Apr;18(2):124-134, Journal of biomolecular techniques  
— id: 72970, year: 2007, vol: 18, page: 124, stat: Journal Article, 

**A molecular brake in the kinase hinge region regulates the activity of receptor tyrosine kinases**  
 _Chen, Huaibin; Ma, Jinghong; Li, Wanqing; Eliseenkova, Anna V; Xu, Chongfeng; Neubert, Thomas A; Miller, W Todd; Mohammadi, Moosa_  
2007 Sep 7;27(5):717-730, Molecular cell  
— id: 73939, year: 2007, vol: 27, page: 717, stat: Journal Article, 

**Molecular insights into the klotho-dependent, endocrine mode of action of fibroblast growth factor 19 subfamily members**  
 _Goetz, Regina; Beenken, Andrew; Ibrahimi, Omar A; Kalinina, Juliya; Olsen, Shaun K; Eliseenkova, Anna V; Xu, ChongFeng; Neubert, Thomas A; Zhang, Fuming; Linhardt, Robert J; Yu, Xijie; White, Kenneth E; Inagaki, Takeshi; Kliewer, Steven A; Yamamoto, Masaya; Kurosu, Hiroshi; Ogawa, Yasushi; Kuro-o, Makoto; Lanske, Beate; Razzaque, Mohammed S; Mohammadi, Moosa_  
2007 May;27(9):3417-3428, Molecular & cellular biology  
— id: 71392, year: 2007, vol: 27, page: 3417, stat: Journal Article, 

**Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry**  
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2007 Jun 15;1153(1-2):259-276, Journal of chromatography  
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**Using SILAC to Study Cell Signaling in Neurons**  
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**Proteomic analysis of exfoliation deposits**  
 _Ovodenko, Boris; Rostagno, Agueda; Neubert, Thomas A; Shetty, Vivekananda; Thomas, Stefani; Yang, Austin; Liebmann, Jeffrey; Ghiso, Jorge; Ritch, Robert_  
2007 Apr;48(4):1447-1457, Investigative ophthalmology & visual science. IOVS  
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**Proteomic Analysis of Pancreatic Zymogen Granules: Identification of New Granule Proteins**  
 _Rindler, Michael J; Xu, Chong-Feng; Gumper, Iwona; Smith, Nora N; Neubert, Thomas A_  
2007 Aug;6(8):2978-2992, Journal of proteome research  
— id: 72969, year: 2007, vol: 6, page: 2978, stat: Journal Article, 

**Characterization by tandem mass spectrometry of stable cysteine sulfenic acid in a cysteine switch peptide of matrix metalloproteinases**  
 _Shetty, Vivekananda; Spellman, Daniel S; Neubert, Thomas A_  
2007 Aug;18(8):1544-1551, Journal of the American Society for Mass Spectrometry  
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**The minimum information about a proteomics experiment (MIAPE)**  
_Taylor, Chris F; Paton, Norman W; Lilley, Kathryn S; Binz, Pierre-Alain; Julian, Randall K Jr; Jones, Andrew R; Zhu, Weimin; Apweiler, Rolf; Aebersold, Ruedi; Deutsch, Eric W; Dunn, Michael J; Heck, Albert J R; Leitner, Alexander; Macht, Marcus; Mann, Matthias; Martens, Lennart; Neubert, Thomas A; Patterson, Scott D; Ping, Peipei; Seymour, Sean L; Souda, Puneet; Tsugita, Akira; Vandekerckhove, Joel; Vondriska, Thomas M; Whitelegge, Julian P; Wilkins, Marc R; Xenarios, Ioannnis; Yates, John R 3rd; Hermjakob, Henning_  
2007 Aug;25(8):887-893, Nature biotechnology  
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**Selective enrichment and fractionation of phosphopeptides from peptide mixtures by isoelectric focusing after methyl esterification**  
 _Xu, Chong-Feng; Wang, Huaibin; Li, Daming; Kong, Xiang-Peng; Neubert, Thomas A_  
2007 Mar 1;79(5):2007-2014, Analytical chemistry  
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**New tricks for an old dog: proteomics of the PSD**  
 _Jordan, BA; Fernholz, BD; Neubert, TA; Ziff, EB_  
The dynamic synapse : molecular methods in ionotropic receptor biology Boca Raton, FL : CRC/Taylor & Francis, 2006,   
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**Use of nitrocellulose membranes for protein characterization by matrix-assisted laser desorption/ionization mass spectrometry**  
 _Luque-Garcia, Jose L; Zhou, Ge; Sun, Tung-Tien; Neubert, Thomas A_  
2006 Jul 15;78(14):5102-5108, Analytical chemistry  
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**Automated comparative proteomics based on multiplex tandem mass spectrometry and stable isotope labeling**  
 _Zhang, Guoan; Neubert, Thomas A_  
2006 Feb;5(2):401-411, Molecular & cellular proteomics  
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**Use of detergents to increase selectivity of immunoprecipitation of tyrosine phosphorylated peptides prior to identification by MALDI quadrupole-TOF MS**  
 _Zhang, Guoan; Neubert, Thomas A_  
2006 Jan;6(2):571-578, Proteomics  
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**Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture (SILAC)**  
_Zhang, Guoan; Spellman, Daniel S; Skolnik, Edward Y; Neubert, Thomas A_  
2006 Mar;5(3):581-588, Journal of proteome research  
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**Familial Danish dementia: co-existence of Danish and Alzheimer amyloid subunits (ADan AND A{beta}) in the absence of compact plaques**  
 _Tomidokoro, Yasushi; Lashley, Tammaryn; Rostagno, Agueda; Neubert, Thomas A; Bojsen-Moller, Marie; Braendgaard, Hans; Plant, Gordon; Holton, Janice; Frangione, Blas; Revesz, Tamas; Ghiso, Jorge_  
2005 Nov 4;280(44):36883-36894, Journal of biological chemistry  
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**Identification of phosphopeptides by MALDI Q-TOF mass spectrometry in positive and negative ion modes after methyl esterification**  
 _Xu, Chong-Feng; Lu, Yun; Ma, Jinghong; Mohammadi, Moosa; Neubert, Thomas A_  
2005 Jun;4(6):809-818, Molecular & cellular proteomics  
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**Cleavage of p75 Neurotrophin Receptor by {alpha}-Secretase and {gamma}-Secretase Requires Specific Receptor Domains**  
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2005 Apr 15;280(15):14563-14571, Journal of biological chemistry  
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**Identification and verification of novel rodent postsynaptic density proteins**  
 _Jordan, Bryen A; Fernholz, Brian D; Boussac, Muriel; Xu, Chongfeng; Grigorean, Gabriela; Ziff, Edward B; Neubert, Thomas A_  
2004 Sep;3(9):857-871, Molecular & cellular proteomics  
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**The N-terminal SH4 region of the Src family kinase Fyn is modified by methylation and heterogeneous fatty acylation: role in membrane targeting, cell adhesion, and spreading**  
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2004 Feb 27;279(9):8133-8139, Journal of biological chemistry  
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**ABRF-PRG03: phosphorylation site determination**  
 _Arnott, David; Gawinowicz, Mary Ann; Grant, Raymond A; Neubert, Thomas A; Packman, Len C; Speicher, Kaye D; Stone, Kathryn; Turck, Christoph W_  
2003 Sep;14(3):205-215, Journal of biomolecular techniques  
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**Facilitated forward chemical genetics using a tagged triazine library and zebrafish embryo screening**  
 _Khersonsky, Sonya M; Jung, Da-Woon; Kang, Tae-Wook; Walsh, Daniel P; Moon, Ho-Sang; Jo, Hakryul; Jacobson, Eric M; Shetty, Vivekananda; Neubert, Thomas A; Chang, Young-Tae_  
2003 Oct 1;125(39):11804-11805, Journal of the American Chemical Society  
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**The CD26-related dipeptidyl aminopeptidase-like protein DPPX is a critical component of neuronal A-type K+ channels**  
 _Nadal, Marcela S; Ozaita, Andres; Amarillo, Yimy; Vega-Saenz de Miera, Eleazar; Ma, Yuliang; Mo, Wenjun; Goldberg, Ethan M; Misumi, Yoshio; Ikehara, Yukio; Neubert, Thomas A; Rudy, Bernardo_  
2003 Feb 6;37(3):449-461, Neuron  
— id: 38424, year: 2003, vol: 37, page: 449, stat: Journal Article, 

**Could TCR antagonism explain associations between MHC genes and disease?**  
_Vukmanovic, Stanislav; Neubert, Thomas A; Santori, Fabio R_  
2003 Apr;9(4):139-146, Trends in molecular medicine  
— id: 34691, year: 2003, vol: 9, page: 139, stat: Journal Article, 

**Protein-tyrosine Phosphatase-sigma Is a Novel Member of the Functional Family of alpha -Latrotoxin Receptors**  
 _Krasnoperov, Valery; Bittner, Mary A; Mo, Wenjun; Buryanovsky, Leonid; Neubert, Thomas A; Holz, Ronald W; Ichtchenko, Konstantin; Petrenko, Alexander G_  
2002 Sep 27;277(39):35887-35895, Journal of biological chemistry  
— id: 32497, year: 2002, vol: 277, page: 35887, stat: Journal Article, 

**Post-translational proteolytic processing of the calcium-independent receptor of alpha-latrotoxin (CIRL), a natural chimera of the cell adhesion protein and the G protein-coupled receptor. Role of the G protein-coupled receptor proteolysis site (GPS) motif**  
 _Krasnoperov, Valery; Lu, Yun; Buryanovsky, Leonid; Neubert, Thomas A; Ichtchenko, Konstantin; Petrenko, Alexander G_  
2002 Nov 29;277(48):46518-46526, Journal of biological chemistry  
— id: 33173, year: 2002, vol: 277, page: 46518, stat: Journal Article, 

**Mass Spectrometric Analysis of GAP-43/Neuromodulin Reveals the Presence of a Variety of Fatty Acylated Species**  
 _Liang, Xiquan; Lu, Yun; Neubert, Thomas A; Resh, Marilyn D_  
2002 Sep 6;277(36):33032-33040, Journal of biological chemistry  
— id: 32498, year: 2002, vol: 277, page: 33032, stat: Journal Article, 

**Rare, structurally homologous self-peptides promote thymocyte positive selection**  
 _Santori, Fabio R; Kieper, William C; Brown, Stuart M; Lu, Yun; Neubert, Thomas A; Johnson, Kenneth L; Naylor, Stephen; Vukmanovic, Stanislav; Hogquist, Kristin A; Jameson, Stephen C_  
2002 Aug;17(2):131-142, Immunity  
— id: 32496, year: 2002, vol: 17, page: 131, stat: Journal Article, 

**Crystal Structure of the MuSK Tyrosine Kinase. Insights into Receptor Autoregulation**  
 _Till, Jeffrey H; Becerra, Manuel; Watty, Anke; Lu, Yun; Ma, Yuliang; Neubert, Thomas A; Burden, Steven J; Hubbard, Stevan R_  
2002 Sep;10(9):1187-1196, Structure  
— id: 32906, year: 2002, vol: 10, page: 1187, stat: Journal Article, 

**Definitive Identification of Mammalian 5-Hydroxymethyluracil DNA N-Glycosylase Activity as SMUG1**  
 _Boorstein RJ; Cummings A Jr; Marenstein DR; Chan MK; Ma Y; Neubert TA; Brown SM; Teebor GW_  
2001 Nov 9;276(45):41991-41997, Journal of biological chemistry  
— id: 23928, year: 2001, vol: 276, page: 41991, stat: Journal Article, 

**Systemic Amyloid Deposits in Familial British Dementia**  
 _Ghiso JA; Holton J; Miravalle L; Calero M; Lashley T; Vidal R; Houlden H; Wood N; Neubert TA; Rostagno A; Plant G; Revesz T; Frangione B_  
2001 Nov 23;276(47):43909-43914, Journal of biological chemistry  
— id: 23926, year: 2001, vol: 276, page: 43909, stat: Journal Article, 

**Characterization of phosphopeptides from protein digests using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nanoelectrospray quadrupole time-of-flight mass spectrometry**  
 _Ma Y; Lu Y; Zeng H; Ron D; Mo W; Neubert TA_  
2001 ;15(18):1693-1700, Rapid communications in mass spectrometry  
— id: 23927, year: 2001, vol: 15, page: 1693, stat: Journal Article, 

**Cutting Edge: Positive Selection Induced by a Self-Peptide with TCR Antagonist Activity**  
 _Santori FR; Brown SM; Lu Y; Neubert TA; Vukmanovic S_  
2001 Dec 1;167(11):6092-6095, Journal of immunology (1950)  
— id: 23925, year: 2001, vol: 167, page: 6092, stat: Journal Article, 

**Uroplakin Ia is the urothelial receptor for uropathogenic Escherichia coli: evidence from in vitro FimH binding**  
 _Zhou G; Mo WJ; Sebbel P; Min G; Neubert TA; Glockshuber R; Wu XR; Sun TT; Kong XP_  
2001 Nov;114(Pt 22):4095-4103, Journal of cell science  
— id: 26903, year: 2001, vol: 114, page: 4095, stat: Journal Article, 

**Sequencing of oxidized methionine-containing peptides for protein identification**  
 _Mo W; Ma Y; Takao T; Neubert TA_  
2000 ;14(21):2080-2081, Rapid communications in mass spectrometry  
— id: 23929, year: 2000, vol: 14, page: 2080, stat: Journal Article,