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Saturday, December 21, 2024

LABORATORY OF MASS SPECTROMETRY AND GASEOUS ION CHEMISTRY

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Publications

2024

N. Gao, D. Mazzoletti, A. Peng, P.D.B. Olinares, C. Morrone, A. Garavaglia, N. Gouda, S. Tsoy, A. Mendoza, A. Chowdhury, A. Cerullo, H. Bhavsar, F. Rossi, M. Rizzi, B.T. Chait, R. Miggiano, D. Jeruzalmi. “DnaB and DciA: Mechanisms of Helicase Loading and Translocation on ssDNA”, bioRxiv. 2024.11.09.622779. [PMID: 39574654]

L.E. Vostal, N.E. Dahan, W. Zhang, M.J. Reynolds, B.T. Chait, T.M. Kapoor. “Distinct modes of coupling between VCP, an essential unfoldase, and deubiquitinases”, bioRxiv. 2024.09.08.611915. [PMID: 39314330]

G.N.L. Chua, J.W. Watters, P.D.B. Olinares, M. Begum, L.E. Vostal, J.A. Luo, B.T. Chait, S. Liu. “Differential dynamics specify MeCP2 function at nucleosomes and methylated DNA”, Nat Struct Mol Biol. 2024 Aug 20. Online ahead of print. [PMID: 39164525]

D. Singh, N. Soni, J. Hutchings, I. Echeverria, F. Shaikh, M. Duquette, S. Suslov, Z. Li, T. van Eeuwen, K. Molloy, Y. Shi, J. Wang, Q. Guo, B. T. Chait, J. Fernandez-Martinez, M. P. Rout, A. Sali, E. Villa. "The Molecular Architecture of the Nuclear Basket", Cell. 2024 Aug 5. Online ahead of print. [PMID: 39127037]

P.C. Fridy, R.J. Farrell, K.R. Molloy, S. Keegan, J. Wang, E.Y. Jacobs, Y. Li, J. Trivedi, V. Sehgal, D. Fenyö, Z. Wu, B.T. Chait, M.P. Rout. “A new generation of nanobody research tools using improved mass spectrometry-based discovery methods”, J Biol Chem. 2024 Aug 2. Online ahead of print. [PMID: 39098531]

T. Ge, D.G. Brickner, K. Zehr, D.J. VanBelzen, W. Zhang, C. Caffalette, S. Ungerleider, N. Marcou, B. Chait, M.P. Rout, J.H. Brickner. “Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex”, bioRxiv. 2024.05.09.593355. [PMID: 38798450]

N.E. Ketaren, F.D. Mast, P.C. Fridy, J.P. Olivier, T. Sanyal, A. Sali, B.T. Chait, M.P. Rout, J.D. Aitchison. "Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus", Elife. 2024 May 7;12:RP89423. [PMID: 38712823]

E.R. Butterfield, S.O. Obado, S.R. Scutts, W. Zhang, B.T. Chait, M.P. Rout, M.C. Field. “A lineage-specific protein network at the trypanosome nuclear envelope”, Nucleus. 2024 Dec;15(1):2310452. Epub 2024 Apr 11. [PMID: 38605598]

J.R. Ramsey, P.M.M. Shelton, T.K. Heiss, P.D.B. Olinares, L.E. Vostal, H. Soileau, M. Grasso, S.W. Casebeer, S. Adaniya, M. Miller, S. Sun, D.J. Huggins, R.W. Myers, B.T. Chait, E.V. Vinogradova, T.M. Kapoor. “Using a function-first 'scout fragment'-based approach to develop allosteric covalent inhibitors of conformationally dynamic helicase mechanoenzymes”, J Am Chem Soc. 2024 Jan 10;146(1):62-67. [PMID: 38134034]

2023

G.I. Small, O. Fedorova, P.D.B. Olinares, J. Chandanani, A. Banerjee, Y.J. Choi, H. Molina, B.T. Chait, S.A. Darst, E.A. Campbell. “Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain”, Mol Cell. 2023 Oct 24. [PMID: 37890482]

C.W. Akey, I. Echeverria, C. Ouch, I. Nudelman, Y. Shi, J. Wang, B.T. Chait, A. Sali, J. Fernandez-Martinez, M.P. Rout. “Implications of a multiscale structure of the yeast nuclear pore complex”, Mol Cell. 2023 Sep 21; 83(18):3283-3302. [PMID: 37738963]

Taylor MS, Wu C, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cajuso T, Cheng WC, Heaps JD, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Chait BT, Goggins MG, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Fairman JE, Jung E, Arora KS, Yilmaz OH, Cohen S, Sharova T, Chi G, Norden BL, Song Y, Nieman LT, Pappas L, Parikh AR, Strickland MR, Corcoran RB, Mustelin T, Eng G, Yilmaz OH, Matulonis UA, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. “Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker”, Cancer Discovery. 2023 Sep 12. Online ahead of print. [PMID: 37698949]

T. Kozai, J. Fernandez-Martinez, T. van Eeuwen, P. Gallardo, L.E. Kapinos, A. Mazur, W. Zhang, J. Tempkin, R. Panatala, M. Delgado-Izquierdo, B. Raveh, A. Sali, B.T. Chait, L.M. Veenhoff, M.P. Rout, R.Y.H. Lim. “Dynamic molecular mechanism of the nuclear pore complex permeability barrier”, bioRxiv. 2023 Apr 14: 2023.03.31.535055. Preprint. [PMID: 37066338]

A. Gkeka, F. Aresta-Branco, G. Triller, E.P. Vlachou, M. van Straaten, M. Lilic, P.D.B. Olinares, K. Perez, B.T. Chait, R. Blatnik, T. Ruppert, J.P. Verdi, C.E. Stebbins, F.N. Papavasiliou. “Immunodominant surface epitopes power immune evasion in the African trypanosome”, Cell Rep. 2023 Mar 20. Online ahead of print. [PMID: 36943866]

Y. Udi, W. Zhang, M.E. Stein, I. Ricardo-Lax, H.A. Pasolli, B.T. Chait, M.P. Rout. “A general method for quantitative fractionation of mammalian cells”, J Cell Biol. Epub 2023 Mar 15. [PMID: 36920247]

B.F. Malone, J.K. Perry, P.D.B. Olinares, H.W. Lee, J. Chen, T.C. Appleby, J.Y. Feng, J.P. Bilello, H. Ng, J. Sotiris, M. Ebrahim, E.Y.D. Chua, J.H. Mendez, E.T. Eng, R. Landick, M. Götte, B.T. Chait, E.A. Campbell, S.A. Darst. “Structural basis for substrate selection by the SARS-CoV-2 replicase”, Nature. 2023 Feb 1. Online ahead of print. [PMID: 36725929]

F.R. Cross, P. Fridy, N. Ketaren, F. Mast, S. Li, P. Olivier, K. Pecani, B.T. Chait, J.D. Aitchison, M.P. Rout. “Expanding and Improving Nanobody Repertoires Using a Yeast Display Method: Targeting SARS-CoV-2”, J Biol Chem. 2023 Jan 28. Online ahead of print. [PMID: 36720309]

A.Y. Berman, M. Wieczorek, A. Aher, P.D.B. Olinares, B.T. Chait, T.M. Kapoor. “A nucleotide binding-independent role for γ-tubulin in microtubule capping and cell division”, J Cell Biol. 2023 Mar 6. Epub 2023 Jan 25. [PMID: 36695784]

2022

S. Hwang, P.D.B. Olinares, J. Lee, J. Kim, B.T. Chait, R.A. King, J.Y. Kang. “Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA”, Nat Commun. 2022 Aug 15. [Epub ahead of print] [PMID: 35970830]

J. Du, V.G. Vandavasi, K.R. Molloy, H. Yang, L.N. Massenburg, A. Singh, A.L. Kwansa, Y.G. Yingling, H. O'Neill, B.T. Chait, M. Kumar, B.T. Nixon. “Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes”, Biomacromolecules. 2022 Aug 10. [Online ahead of print] [PMID: 35948425]

J.C. Zinder, P.D.B. Olinares, V. Svetlov, M.W. Bush, E. Nudler, B.T. Chait, T. Walz, T. de Lange. “Shelterin is a dimeric complex with extensive structural heterogeneity”, Proc Natl Acad Sci U S A. 2022 Aug 2. 119 (31):e2201662119. [PMID: 35881804]

S. Balasubramanian, M. Andreani, J.G. Andrade, T. Saha, D. Sundaravinayagam, J. Garzón, W. Zhang, O. Popp, S.I. Hiraga, A. Rahjouei, D.B. Rosen, P. Mertins, B.T. Chait, A.D. Donaldson, M. Di Virgilio. “Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region”, Elife. 2022 Apr 13;11:e75047. [PMID: 35416772]

A.A. Serganov, Y. Udi, M.E. Stein, V. Patel, P.C. Fridy, C.M. Rice, M. Saeed, E.Y. Jacobs, B.T. Chait, M.P. Rout. “Proteomic elucidation of the targets and primary functions of the picornavirus 2A protease”, J Biol Chem. 2022 Mar 30. [Epub ahead of print] [PMID: 35367208]

K.J. Mickolajczyk, P.D.B. Olinares, B.T. Chait, S. Liu, T.M. Kapoor. “The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates”, Elife. 2022 Feb 11;11:e73534. [PMID: 35147499] 

2021

C.W. Akey, D. Singh, C. Ouch, I. Echeverria, I. Nudelman, J.M. Varberg, Z. Yu, F. Fang, Y. Shi, J. Wang, D. Salzberg, K. Song, C. Xu, J.C. Gumbart, S. Suslov, J. Unruh, S.L. Jaspersen, B.T. Chait, A. Sali, J. Fernandez-Martinez, S.J. Ludtke, E. Villa, M.P. Rout. “Comprehensive structure and functional adaptations of the yeast nuclear pore complex”, Cell. 2021 Dec 29. [Epub ahead of print] [PMID: 34982960]

F.D. Mast, P.C. Fridy, N.E. Ketaren, J. Wang, E.Y. Jacobs, J.P. Olivier, T. Sanyal, K.R. Molloy, F. Schmidt, M. Rutkowska, Y. Weisblum, L.M. Rich, E.R. Vanderwall, N. Dambrauskas, V. Vigdorovich, S. Keegan, J.B. Jiler, M.E. Stein, P.D.B. Olinares, L. Herlands, T. Hatziioannou, D.N. Sather, J.S. Debley, D. Fenyö, A. Sali, P.D. Bieniasz, J.D. Aitchison, B.T. Chait, M.P. Rout. “Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape”, Elife. 2021 Dec 7;10:e73027. [PMID: 34874007]

Z. Hakhverdyan, K.R. Molloy, R.I. Subbotin, J. Fernandez-Martinez, B.T. Chait, M.P. Rout. “Measuring in vivo protein turnover and exchange in yeast macromolecular assemblies”, STAR Protoc. 2021 Sep 8. [PMID: 34527957]

Y. Niu, X. Tao, G. Vaisey, P.D.B. Olinares, H. Alwaseem, B. Chait, R. MacKinnon. “Analysis of the Mechanosensor Channel Functionality of TACAN”, Elife. 2021 Aug 10;10:e71188. [PMID: 34374644]

B. Bosch, M.A. DeJesus, N.C. Poulton, W. Zhang, C.A. Engelhart, A. Zaveri, S. Lavalette, N. Ruecker, C. Trujillo, J.B. Wallach, S. Li, S. Ehrt, B.T. Chait, D. Schnappinger, J.M. Rock. “Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis”, Cell. 2021 Jul 16. [Epub ahead of print] [PMID: 34297925]

B. Malone, J. Chen, Q. Wang, E. Llewellyn, Y.J. Choi, P.D.B. Olinares, X. Cao, C. Hernandez, E.T. Eng, B.T. Chait, D.E. Shaw, R. Landick, S.A. Darst, E.A. Campbell. “Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex”, Proc Natl Acad Sci U S A. 2021 May 11. [PMID: 33883267]

M. Wieczorek, S.C. Ti, L. Urnavicius, K.R. Molloy, A. Aher, B.T. Chait, T.M. Kapoor. "Biochemical reconstitutions reveal principles of human γ-TuRC assembly and function.", J Cell Biol. 2021 Mar 1;220(3):e202009146. [PMID: 33496729]

J. Merkenschlager, S. Finkin, V. Ramos, J. Kraft, M. Cipolla, C.R. Nowosad, H. Hartweger, W. Zhang, P.D.B. Olinares, A. Gazumyan, T.Y. Oliveira, B.T. Chait, M.C. Nussenzweig. “Dynamic regulation of T_FHselection during the germinal centre reaction.”, Nature. 2021 Feb 3. doi: 10.1038/s41586-021-03187-x. [PMID: 33536617]

J.Y. Kang, E. Llewellyn, J. Chen, P.D.B. Olinares, J. Brewer, B.T. Chait, E.A. Campbell, S.A. Darst. “Structural basis for transcription complex disruption by the Mfd translocase.”, Elife. 2021 Jan 22;10:e62117. [PMID: 33480355]

J. Xu, X. Zhao, F. Mao, V. Basrur, B. Ueberheide, B.T. Chait, C.D. Allis, S.D. Taverna, S. Gao, W. Wang, Y. Liu. “A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies.”, Nucleic Acids Res. 2021 Jan 8:gkaa1262. [PMID: 33412588]

M.A. Schureck, J.E. Darling, A. Merk, J. Shao, G. Daggupati, P. Srinivasan, P.D.B. Olinares, M.P. Rout, B.T. Chait, K. Wollenberg, S. Subramaniam, S.A. Desai. “Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake.”, Elife. 2021 Jan 4;10:e65282. [PMID: 33393463]

2020

Z. Hakhverdyan, K.R. Molloy, S. Keegan, T. Herricks, D.M. Lepore, M. Munson, R.I. Subbotin, D. Fenyö, J.D. Aitchison, J. Fernandez-Martinez, B.T. Chait, M.P. Rout. “Dissecting the structural dynamics of the nuclear pore complex.” Mol Cell. 2020 Dec 8:S1097-2765(20)30832-7. [PMID: 33333016]

P.D.B. Olinares, J.Y. Kang, E. Llewellyn, C. Chiu, J. Chen, B. Malone, R.M. Saecker, E.A. Campbell, S.A. Darst, B.T. Chait. “Native mass spectrometry-based screening for optimal sample preparation in single-particle cryo-EM.” Structure. 2020 Nov 17:S0969-2126(20)30413-5. [PMID: 33217329]

F.D. Mast, A.T. Navare, A.M. van der Sloot, J. Coulombe-Huntington, M.P. Rout, N.S. Baliga, A. Kaushansky, B.T. Chait, A. Aderem, C.M. Rice, A. Sali, M. Tyers, J.D. Aitchison. "Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality", J Cell Biol. 2020 Oct 5. 219 (10): e202006159. [PMID: 32785687]

Y. Dou, I. Barbosa, H. Jiang, C. Iasillo, K.R. Molloy, W.M. Schulze, S. Cusack, M. Schmid, H. Le Hir, J. LaCava, T.H. Jensen. “NCBP3 positively impacts mRNA biogenesis”, Nucleic Acids Res. 2020 Oct 9. [PMID: 32960271]

Y. Dou, S. Kalmykova, M. Pashkova, M. Oghbaie, H. Jiang, K.R. Molloy, B.T. Chait, M.P. Rout, D. Fenyö, T.H. Jensen, I. Altukhov, J. LaCava. "Affinity proteomic dissection of the human nuclear cap-binding complex interactome", Nucleic Acids Res. 2020 Sep 22:gkaa743. [PMID: 32960270]

J. Chen, B. Malone, E. Llewellyn, M. Grasso, P.M.M. Shelton, P.D.B. Olinares, K. Maruthi, E. Eng, H. Vatandaslar, B.T. Chait, T. Kapoor, S.A. Darst, E.A. Campbell. “Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex”, Cell. 2020 Sep 17;182(6):1560-1573.e13. [PMID: 32783916]

K.J. Mickolajczyk, P.D.B. Olinares, Y. Niu, N. Chen, S.E. Warrington, Y. Sasaki, T. Walz, B.T. Chait, T.M. Kapoor. “Long-range intramolecular allostery and regulation in the dynein-like AAA protein Mdn1”, Proc Natl Acad Sci U S A. 2020 Aug 4;117(31):18459-18469. [PMID: 32694211]

J.M. Manning, L.R. Manning, A. Dumoulin, J.C. Padovan, B.T. Chait. “Embryonic and fetal human hemoglobins: structures, oxygen binding, and physiological roles”, Subcell Biochem. 2020;94:275-296. [PMID: 32189304]

J. Kagan, R.L. Moritz, R. Mazurchuk, J.H. Lee, P.V. Kharchenko, O. Rozenblatt-Rosen, E. Ruppin, F. Edfors, F. Ginty, Y. Goltsev, J.A. Wells, J. LaCava, J.L. Riesterer, R.N. Germain, T. Shi, M.S. Chee, B.A. Budnik, J.R. Yates 3rd, B.T. Chait, J.R. Moffitt, R.D. Smith, S. Srivastava . “National Cancer Institute Think-Tank Meeting Report on proteomic cartography and biomarkers at the single-cell level: interrogation of premalignant lesions”, J Proteome Res. 2020 May 1;19(5):1900-1912. [PMID: 32163288]

S.J. Ganesan, M.J. Feyder, I.E. Chemmama, F. Fang, M.P. Rout, B.T. Chait, Y. Shi, M. Munson, A. Sali. “Integrative structure and function of the yeast exocyst complex”, Protein Sci. 2020 Jun;29(6):1486-1501. [PMID: 32239688]

J. Chen, C. Chiu, S. Gopalkrishnan, A.Y. Chen, P.D.B. Olinares, R.M. Saecker, J.T. Winkelman, M.F. Maloney, B.T. Chait, W. Ross, R.L. Gourse, E.A. Campbell, S.A. Darst. “Stepwise Promoter Melting by Bacterial RNA Polymerase”, Mol Cell. 2020 Mar 2. [Epub ahead of print] [PMID: 32160514]

V. Kieuvongngam, P.D.B. Olinares, A. Palillo, M.L. Oldham, B.T. Chait, J. Chen. “Structural basis of substrate recognition by a polypeptide processing and secretion transporter”, Elife. 2020 Jan 14. [PMID: 31934861]

P.D.B. Olinares, B.T. Chait. “Native Mass Spectrometry Analysis of Affinity-Captured Endogenous Yeast RNA Exosome Complexes”, Methods Mol Biol. 2062 (2020) 357-382. [PMID: 31768985]

2019

D. Ardeljan, X. Wang, M. Oghbaie, M.S. Taylor, D. Husband, V. Deshpande, J.P. Steranka, M. Gorbounov, W.R. Yang, B. Sie, H.B. Larman, H. Jiang, K.R. Molloy, I. Altukhov, Z. Li, W. McKerrow, D. Fenyö, K.H. Burns, J. LaCava. “LINE-1 ORF2p expression is nearly imperceptible in human cancers”, Mob DNA. 2019 Dec 31. [PMID: 31892958]

M. Wieczorek, L. Urnavicius, S.C. Ti, K.R. Molloy, B.T. Chait, T.M. Kapoor. “Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex”, Cell. 2019 Dec 13. [PMID: 31862189] [Epub ahead of print]

S. Presslee, G.J. Slater, F. Pujos, A.M. Forasiepi, R. Fischer, K. Molloy, M. Mackie, J.V. Olsen, A. Kramarz, M. Taglioretti, F. Scaglia, M. Lezcano, J. L. Lanata, J. Southon, R. Feranec, J. Bloch, A. Hajduk, F.M. Martin, R. Salas Gismondi, M. Reguero, C. de Muizon, A. Greenwood, B.T. Chait, K. Penkman, M. Collins, R.D.E. MacPhee. “Palaeoproteomics resolves sloth relationships”, Nat Ecol Evol. 2019 Jun 6. [Epub ahead of print] [PMID: 31171860]

R. Hayama, M. Sorci, J.J. Keating IV, L.M. Hecht, J.L. Plawsky, G. Belfort, B.T. Chait, M.P. Rout. “Interactions of nuclear transport factors and surface-conjugated FG nucleoporins: Insights and limitations”, PLoS One. 2019 Jun 6. e0217897. [PMID: 31170242]

H. Jiang, M.S. Taylor, K.R. Molloy, I. Altukhov, J. LaCava. “Identification of RNase-sensitive LINE-1 Ribonucleoprotein Interactions by Differential Affinity Immobilization”, Bio Protoc. 2019 Apr 5. [PMID: 31106238]

2018

• R. Mayle, L. Langston, K.R. Molloy, D. Zhang, B.T. Chait, M.E. O'Donnell. “Mcm10 has potent strand-annealing activity and limits translocase-mediated fork regression”, Proc Natl Acad Sci U S A. 2018 Dec 31. [Epub ahead of print] [PMID: 30598452]
• J. Chase, A. Catalano, A.J. Noble, E.T. Eng, P.D.B. Olinares, K. Molloy, D. Pakotiprapha, M. Samuels, B. Chait, A. des Georges, D. Jeruzalmi. “Mechanisms of opening and closing of the bacterial replicative helicase”, Elife. 2018 Dec 24. [Epub ahead of print] [PMID: 30582519]
• V. Delgado-Benito, D.B. Rosen, Q. Wang, A. Gazumyan, J.A. Pai, T.Y. Oliveira, D. Sundaravinayagam, W. Zhang, M. Andreani, L. Keller, K.R. Kieffer-Kwon, A. Pekowska, S. Jung, M. Driesner, R.I. Subbotin, R. Casellas, B.T. Chait, M.C. Nussenzweig, M. Di Virgilio. “The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination”, Mol Cell. 2018 Sep 26. [Epub ahead of print] [PMID: 30293785]
• M. Jishage, X. Yu, Y. Shi, S.J. Ganesan, W.Y. Chen, A. Sali, B.T. Chait, F.J. Asturias, R.G. Roeder. “Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1", Nat Struct Mol Biol. 2018 Sep. 25 (9) 859-867. [PMID: 30190596]

• B.R. Schrank, T. Aparicio, Y. Li, W. Chang, B.T. Chait, G.G. Gundersen, M.E. Gottesman, J. Gautier. “Nuclear ARP2/3 drives DNA break clustering for homology-directed repair”, Nature. 2018 Jun 20. [Epub ahead of print] [PMID: 29925947]

  S.J. Kim, J. Fernandez-Martinez, I. Nudelman, Y. Shi, W. Zhang, B. Raveh, T. Herricks, B.D. Slaughter, J.A. Hogan, P. Upla, I.E. Chemmama, R. Pellarin, I. Echeverria, M. Shivaraju, A.S. Chaudhury, J. Wang, R. Williams, J.R. Unruh, C.H. Greenberg, E.Y. Jacobs, Z. Yu, M.J. de la Cruz, R. Mironska, D.L. Stokes, J.D. Aitchison, M.F. Jarrold, J.L. Gerton, S.J. Ludtke, C.W. Akey, B.T. Chait, A. Sali, M.P. Rout. “Integrative structure and functional anatomy of a nuclear pore complex”, Nature. 2018 Mar 14. [Epub ahead of print] [PMID: 29539637]

  Z.A. Sanghai, L. Miller, K.R. Molloy, J. Barandun, M. Hunziker, M. Chaker-Margot, J. Wang, B.T. Chait, S. Klinge. “Modular assembly of the nucleolar pre-60S ribosomal subunit”, Nature. 2018 Mar 5. [Epub ahead of print] [PMID: 29512650]

  J.M. Holden, L. Koreny, S. Obado, A.V. Ratushny, W.M. Chen, J.M. Bart, M. Navarro, B.T. Chait, J.D. Aitchison, M.P. Rout, M.C. Field. “Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes”, Mol Biol Cell. 2018 Mar 1. [Epub ahead of print] [PMID: 29496964]

  M.S. Taylor, I. Altukhov, K.R. Molloy, P. Mita, H. Jiang, E.M. Adney, A. Wudzinska, S. Badri, D. Ischenko, G. Eng, K.H. Burns, D. Fenyö, B.T. Chait, D. Alexeev, M.P. Rout, J.D. Boeke, J. LaCava. "Dissection of affinity captured LINE-1 macromolecular complexes", Elife. 2018 Jan 8. [Epub ahead of print] [PMID: 29309035]

  K. Winczura, M. Schmid, C. Iasillo, K.R. Molloy, L.M. Harder, J.S. Andersen, J. LaCava, T.H. Jensen. "Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions", Cell Rep. 2018 Jan 2. [PMID: 29298432]

2017

• A. Santanach, E. Blanco, H. Jiang, K.R. Molloy, M. Sansó, J. LaCava, L. Morey, L. Di Croce."The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity", Nat Commun. 2017 Nov 1. [PMID: 29089522]

• R.E. Kleiner, L.E. Hang, K.R. Molloy, B.T. Chait, T.M. Kapoor. "A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells", Cell Chem Biol. 2017 Oct 25. [Epub ahead of print] [PMID: 29104064]

• J. Barandun, M. Chaker-Margot, M. Hunziker, K.R. Molloy, B.T. Chait, S. Klinge. "The complete structure of the small-subunit processome", Nat Struct Mol Biol. 2017 Sep 25. [Epub ahead of print] [PMID: 28945246]

• J.Y. Kang, P.D. Olinares, J. Chen, E.A. Campbell, A. Mustaev, B.T. Chait, M.E. Gottesman, S.A. Darst. “Structural basis of transcription arrest by coliphage HK022 nun in an Escherichia coli RNA polymerase elongation complex”, Elife. 2017 Mar 20. [Epub ahead of print] [PMID: 28318486]

  P.T. Manna, S.O. Obado, C. Boehm, C. Gadelha, A. Sali, B.T. Chait, M.P. Rout, M.C. Field. “Lineage-specific proteins essential for endocytosis in trypanosomes”, J Cell Sci. 2017 Feb 23. [Epub ahead of print] [PMID: 28232524]

  C.M. Boehm, S. Obado, C. Gadelha, A. Kaupisch, P.T. Manna, G.W. Gould, M. Munson, B.T. Chait, M.P. Rout, M.C. Field. “The Trypanosome Exocyst: A Conserved Structure Revealing a New Role in Endocytosis”, PLoS Pathog. 2017 Jan 23. [PMID: 28114397]  

2016

• B. Wang, A. Zhao, Q. Xie, P.D. Olinares, B.T. Chait, R.P. Novick, T.W. Muir. “Functional Plasticity of the AgrC Receptor Histidine Kinase Required for Staphylococcal Virulence”, Cell Chem Biol. 2016 Dec 30. [Epub ahead of print] [PMID: 28065658]
• N. Orlova, M. Gerding, O. Ivashkiv, P.D. Olinares, B.T. Chait, M.K. Waldor, D. Jeruzalmi. “The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators”, Nucleic Acids Res. 2016 Dec 27. [Epub ahead of print] [PMID: 28031373]

• L.R. Manning, A.M. Popowicz, J.C. Padovan, B.T. Chait, J.M. Manning. “Gel filtration of dilute human embryonic hemoglobins reveals basis for their increased oxygen binding”, Anal Biochem. 2016 Dec 10. [Epub ahead of print] [PMID: 27965062]

  J. Fernandez-Martinez, S.J. Kim, Y. Shi, P. Upla, R. Pellarin, M. Gagnon, I.E. Chemmama, J. Wang, I. Nudelman, W. Zhang, R. Williams, W.J. Rice, D.L. Stokes, D. Zenklusen, B.T. Chait, A. Sali, M.P. Rout. “Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform”, Cell. 2016 Nov 9. [Epub ahead of print] [PMID: 27839866]
• L. Maishman, S.O. Obado, S. Alsford, J.M. Bart, W.M. Chen, A.V. Ratushny, M. Navarro, D. Horn, J.D. Aitchison, B.T. Chait, M.P. Rout, M.C. Field. “Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression”, Nucleic Acids Res. 2016 Sep 12. [Epub ahead of print] [PMID: 27625397]
• K. Yale, A.J. Tackett, M. Neuman, E. Bulley, B.T. Chait, E. Wiley. “Phosphorylation-Dependent Targeting of Tetrahymena HP1 to Condensed Chromatin”, mSphere. 2016 Aug 24. 1(4): e00142-16. [PMID: 27579368]
• M. Domanski, P. Upla, W.J. Rice, K.R. Molloy, N.E. Ketaren, D.L. Stokes, T.H. Jensen, M.P. Rout, J. LaCava. “Purification and analysis of endogenous human RNA exosome complexes”, RNA. 2016 Jul 11. [Epub ahead of print] [PMID: 27402899]

• M. Hunziker, J. Barandun, E. Petfalski, D. Tan, C. Delan-Forino, K.R. Molloy, K.H. Kim, H. Dunn-Davies, Y. Shi, M. Chaker-Margot, B.T. Chait, T. Walz, D. Tollervey, S. Klinge.“UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly”, Nat Commun. 2016 Jun 29. [PMID: 27354316]

• Y. Luo, E.Y. Jacobs, T.M. Greco, K.D. Mohammed, T. Tong, S. Keegan, J.M. Binley, I.M. Cristea, D. Fenyö, M.P. Rout, B.T. Chait, M.A. Muesing.“HIV–host interactome revealed directly from infected cells”, Nat Microbiol. 23 May 2016. [Epub ahead of print] [PMID: 27375898]

• S.O. Obado, M.C. Field, B.T. Chait, M.P. Rout. “High-Efficiency Isolation of Nuclear Envelope Protein Complexes from Trypanosomes”, Methods Mol Biol. 1411 (2016) 67-80. [PMID: 27147034]

• B.T. Chait, M. Cadene, P.D. Olinares, M.P. Rout, Y. Shi. “Revealing Higher Order Protein Structure Using Mass Spectrometry”, J Am Soc Mass Spectrom. 2016 Apr 14. [Epub ahead of print] [PMID: 27080007]

• I.O. Rivera-Torres, T.B. Jin, M. Cadene, B.T. Chait, S.F. Poget. “Discovery and characterisation of a novel toxin from Dendroaspis angusticeps, named Tx7335, that activates the potassium channel KcsA”, Sci Rep. 2016 Apr 5. [PMID: 27044983]

• S.O. Obado, M. Brillantes, K. Uryu, W. Zhang, N.E. Ketaren, B.T. Chait, M.C. Field, M.P. Rout. “Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex”, PLoS Biol. 2016 Feb 18. e1002365. [PMID: 26891179]

• M. Lussignol, M. Kopp, K. Molloy, G. Vizcay-Barrena, R.A. Fleck, M. Dorner, K.L. Bell, B.T. Chait, C.M. Rice, M.T. Catanese. "Proteomics of HCV virions reveals an essential role for the nucleoporin Nup98 in virus morphogenesis", Proc Natl Acad Sci U S A. 2016 Feb 16. [Epub ahead of print] [PMID: 26884193]

• N. Kellner, J. Schwarz, M. Sturm, J. Fernandez-Martinez, S. Griesel, W. Zhang, B.T. Chait, M.P. Rout, U. Kück, E. Hurt. “Developing genetic tools to exploit Chaetomium thermophilum for biochemical analyses of eukaryotic macromolecular assemblies”, Sci Rep. 2016 Feb 11. [PMID: 26864114]

• P.D. Olinares, A.D. Dunn, J.C. Padovan, J. Fernandez-Martinez, M.P. Rout, B.T. Chait. “A robust workflow for native mass spectrometric analysis of affinity-isolated endogenous protein assemblies”, Anal Chem. 2016 Feb 5. [Epub ahead of print] [PMID: 26849307]

• M.K. Thompson, P.C. Fridy, S. Keegan, B.T. Chait, D. Fenyö, M.P. Rout. “Optimizing selection of large animals for antibody production by screening immune response to standard vaccines”, J Immunol Methods. 2016 Jan 9. [Epub ahead of print] [PMID: 26775851]

2015

• D.H. Morris, C.K. Yip, Y. Shi, B.T. Chait, Q.J. Wang. “Beclin 1-Vps34 complex architecture: Understanding the nuts and bolts of therapeutic targets”, Front. Biol. 2015. 10 (5) 398-426. [PMID: 26692106]

  J. Sun, Y. Shi, R.E. Georgescu, Z. Yuan, B.T. Chait, H. Li, M.E. O'Donnell. “The architecture of a eukaryotic replisome”, Nat Struct Mol Biol. 2015 Nov 2. [Epub ahead of print] [PMID: 26524492]

• J. LoPiccolo, S.J. Kim, Y. Shi, B. Wu, H. Wu, B.T. Chait, R.H. Singer, A. Sali, M. Brenowitz, A.R. Bresnick, J.M. Backer. “Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer”, J Biol Chem. 2015 Oct 16. [Epub ahead of print] [PMID: 26475863]

• Y. Shi, R. Pellarin, P.C. Fridy, J. Fernandez-Martinez, M.K. Thompson, Y. Li, Q.J. Wang, A. Sali, M.P. Rout, B.T Chait. “A strategy for dissecting the architectures of native macromolecular assemblies”, Nat Methods. 2015 Oct 5. [Epub ahead of print] [PMID: 26436480]

• R.E. Kleiner, P. Verma, K.R. Molloy, B.T. Chait, T.M. Kapoor. “Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response”, Nat Chem Biol. 2015 Sep 7. [Epub ahead of print] [PMID: 26344695]

  E.A. Hubin, A. Tabib-Salazar, L.J. Humphrey, J.E. Flack, P.D. Olinares, S.A. Darst, E.A. Campbell, M.S. Paget. “Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA”, Proc Natl Acad Sci U S A. 2015 Jun 9. 112 (23) 7171-6. [PMCID: PMC4466734.]

• Z. Hakhverdyan, M. Domanski, L.E. Hough, A.A. Oroskar, A.R. Oroskar, S. Keegan, D.J. Dilworth, K.R. Molloy, V. Sherman, J.D. Aitchison, D. Fenyö, B.T. Chait, T.H. Jensen, M.P. Rout, J. LaCava. "Rapid, optimized interactomic screening", Nat Methods. 2015 May 4. [Epub ahead of print] [PMID: 25938370]

• C. Gadelha, W. Zhang, J.W. Chamberlain, B.T. Chait, B. Wickstead, M.C. Field. “Architecture of a host-parasite interface: complex targeting mechanisms revealed through proteomics”, Mol Cell Proteomics. 2015 Apr 30. [Epub ahead of print] [PMID: 25931509]

• J. LaCava, K.R. Molloy, M.S. Taylor, M. Domanski, B.T. Chait, M.P. Rout. "Affinity proteomics to study endogenous protein complexes: Pointers, pitfalls, preferences and perspectives", Biotechniques. 2015 Mar 1. 58 (3) 103-19. [PMID: 25757543]

  A.N. Krutchinsky, J.C. Padovan, H. Cohen, B.T Chait. “Optimizing Electrospray Interfaces Using Slowly Diverging Conical Duct (ConDuct) Electrodes”, J Am Soc Mass Spectrom. 2015 Feb 10. [Epub ahead of print] [PMID: 25667060]

  K. Uematsu, M. Heiman, M. Zelenina, J. Padovan, B.T. Chait, A. Aperia, A. Nishi, P. Greengard. “Protein kinase A directly phosphorylates metabotropic glutamate receptor 5 to modulate its function”, J Neurochem. 2015 Feb 1. [Epub ahead of print] [PMID: 25639954]

  A.N. Krutchinsky, J.C. Padovan, H. Cohen, B.T. Chait. “Maximizing Ion Transmission from Atmospheric Pressure into the Vacuum of Mass Spectrometers with a Novel Electrospray Interface”, J Am Soc Mass Spectrom. 2015 Jan 15. [Epub ahead of print] [PMID: 25588722]

2014

• M.A. Cevher, Y. Shi, D. Li, B.T. Chait, S. Malik, R.G. Roeder. “Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit”, Nat Struct Mol Biol. 2014 Nov 10. [Epub ahead of print] [PMID: 25383669]

  P.C. Fridy, Y. Li, S. Keegan, M.K. Thompson, I. Nudelman, J.F. Scheid, M. Oeffinger, M.C. Nussenzweig, D. Fenyö, B.T. Chait, M.P. Rout. “A robust pipeline for rapid production of versatile nanobody repertoires”, Nature Methods. 2014 Nov 2. [Epub ahead of print] [PMID: 25362362]

  R.I. Subbotin, B.T. Chait. “A Pipeline for Determining Protein-Protein Interactions and Proximities in the Cellular Milieu”, Mol Cell Proteomics. 2014 Aug 29. [Epub ahead of print] [PMID: 25172955]

• Y. Shi, J. Fernandez-Martinez, E. Tjioe, R. Pellarin, S.J. Kim, R. Williams, D. Schneidman, A. Sali, M.P. Rout, B.T. Chait. “Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex”, Mol Cell Proteomics. 2014 Aug 26. [Epub ahead of print] [PMID: 25161197]

• S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, A. Martel, T. Matsui, H. Tsuruta, T.M. Weiss, Y. Shi, A. Markina-Inarrairaegui, J.B. Bonanno, J.M. Sauder, S.K. Burley, B.T. Chait, S.C. Almo, M.P. Rout, A. Sali. “Integrative structure-function mapping of the nucleoporin nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex”, Mol Cell Proteomics. 2014 Aug 19. [Epub ahead of print] [PMID: 25139911]

• Y. Zhong, D.H. Morris, L. Jin, M.S. Patel, S.K. Karunakaran, Y.J. Fu, E.A. Matuszak, H.L. Weiss, B.T. Chait, Q.J. Wang. “Nrbf2 Suppresses Autophagy by Modulating Atg14L-containing Beclin 1-Vps34 Protein Complex Architecture and Reducing Intracellular Phosphatidylinositol-3 Phosphate Levels”, J Biol Chem. 2014 Aug 1. [Epub ahead of print] [PMID: 25086043]

• J.M. Holden, L. Koreny, S. Kelly, B.T. Chait, M.P. Rout, M.C. Field, S.O. Obado. “Touching from a distance: Evolution of interplay between the nuclear pore complex, nuclear basket, and the mitotic spindle”, Nucleus. 2014 Jul 31. [Epub ahead of print] [PMID: 25079062]

  R. Algret, J. Fernandez-Martinez, Y. Shi, S.J. Kim, R. Pellarin, P. Cimermancic, E. Cochet, A. Sali, B.T. Chait, M.P. Rout, S. Dokudovskaya. “Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway”, Mol Cell Proteomics. 2014 Jul 29. [Epub ahead of print] [PMID: 25073740]

• Y. Li, F.R. Cross, B.T. Chait. “Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes,” PNAS. 2014 Jul 21. [Epub ahead of print] [PMID: 25049391]

• T. Jovanovic-Talisman, B.T. Chait, M.P. Rout. “NPC Mimics: Probing the Mechanism of Nucleocytoplasmic Transport”, Methods Cell Biol. 122 (2014) 379-393. [PMID: 24857739]

• P. Anand, A. Grigoryan, M.H. Bhuiyan, B. Ueberheide, V. Russell, J. Quinoñez, P. Moy, B.T. Chait, S.F. Poget, M. Holford. “Sample Limited Characterization of a Novel Disulfide-Rich Venom Peptide Toxin from Terebrid Marine Snail Terebra variegata”, PLoS One. 2014 Apr 8. e94122. [PMID: 24713808]

• Chait B. “Frank H. Field (1922-2013)”, J Am Soc Mass Spectrom. 2014 May. 25 (5) 702-4.  [PMID: 24658810]

• J.M. Holden, L. Koreny, S. Obado, A.V. Ratushny, W.M. Chen, J.H. Chiang, S. Kelly, B.T. Chait, J.D. Aitchison, M.P. Rout, M.C. Field. “Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity”, Mol Biol Cell. 2014 May. 25(9):1421-36. [PMID: 24600046]

2013

• M. Niepel, K.R. Molloy, R. Williams, J.C. Farr, A.C. Meinema, N. Vecchietti, I.M. Cristea, B.T. Chait, M.P. Rout, C. Strambio-De-Castillia. “The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome”, Mol Biol Cell. 2013 Dec 15. 24 (24) 3920-38. [PMID: 24152732]

• T.C. Smith, P.C. Fridy, Y. Li, S. Basil, S. Arjun, R.M. Friesen, J. Leszyk, B.T. Chait, M.P. Rout, E.J. Luna. “Supervillin Binding to Myosin II and Synergism with Anillin Are Required for Cytokinesis”, Mol Biol Cell. 2013 Dec 1. 24 (23) 3603-19. [PMID: 24088567]

• M.S. Taylor, J. LaCava, P. Mita, K.R. Molloy, C.R. Huang, D. Li, E.M. Adney, H. Jiang, K.H. Burns, B.T. Chait, M.P. Rout, J.D. Boeke, L. Dai. “Affinity Proteomics Reveals Human Host Factors Implicated in Discrete Stages of LINE-1 Retrotransposition”, Cell. 2013 Nov 21. 155 (5) 1034-48. [PMID: 24267889]

  J.Z. Xue, E.M. Woo, L. Postow, B.T. Chait, H. Funabiki. “Chromatin-Bound Xenopus Dppa2 Shapes the Nucleus by Locally Inhibiting Microtubule Assembly”, Dev Cell. 2013 Oct 14. 27 (1) 47-59. [PMID: 24075807]

  L.A. Baker, B.M. Ueberheide, S. Dewell, B.T. Chait, D. Zheng, C.D. Allis. “The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress”, Mol Cell Biol. October 2013. 33 (19) 3735-48. [PMID: 23878396]

• Y. Bao, S. Waldemarson, G. Zhang, A. Wahlander, B. Ueberheide, S. Myung, B. Reed, K. Molloy, J.C. Padovan, J. Eriksson, T.A. Neubert, B.T. Chait, D. Fenyö. “Detection and Correction of Interference in SRM Analysis”, Methods. 2013 Jun 15. 61 (3) 299-303. [PMID: 23707623]

• X. Li, E.A. Foley, S.A. Kawashima, K.R. Molloy, Y. Li, B.T. Chait, T.M. Kapoor. "Examining posttranslational modification-mediated protein-protein interactions using a chemical proteomics approach", Protein Sci. March 2013. 22 (3) 287-295. [PMCID: PMC3595459]

• S.E. Peterson, Y. Li, F. Wu-Baer, B.T. Chait, R. Baer, H. Yan, M.E. Gottesman, J. Gautier. "Activation of DSB Processing Requires Phosphorylation of CtIP by ATR", Mol Cell. 2013 Feb 21. 49 (4) 657-667. [PMCID: PMC3582837] 

• Y.S. Oh, P. Gao, K.W. Lee, I. Ceglia, J.S. Seo, X. Zhang, J.H. Ahn, B.T. Chait, D.J. Patel, Y. Kim, P. Greengard. “SMARCA3, a Chromatin-Remodeling Factor, Is Required for p11-Dependent Antidepressant Action”, Cell. 2013 Feb 14. 152 (4) 831-843. [PMCID: PMC3633087]

• M. Di Virgilio, E. Callen, A. Yamane, W. Zhang, M. Jankovic, A.D. Gitlin, N. Feldhahn, W. Resch, T.Y. Oliveira, B.T. Chait, A. Nussenzweig, R. Casellas, D.F. Robbiani, M.C. Nussenzweig. “Rif1 Prevents Resection of DNA Breaks and Promotes Immunoglobulin Class Switching”, Science. 2013 Feb 8. 339 (6120) 711-5. [PMID 23306439]   

2012

• L. Bozzacco, H. Yu, J. Dengjel, C. Trumpfheller, H.A. Zebroski 3rd, N. Zhang, V. Küttner, B.M. Ueberheide, H. Deng, B.T. Chait, R.M. Steinman, S. Mojsov, D. Fenyö. "Strategy for Identifying Dendritic Cell-Processed CD4(+) T Cell Epitopes from the HIV Gag p24 Protein", PLoS One 7 (2012) e41897. [PMCID: PMC3408443]
• E.A. Heller, W. Zhang, F. Selimi, J.C. Earnheart, M.A. Slimak, J. Santos-Torres, I. Ibañez-Tallon, C. Aoki, B.T. Chait, N. Heintz. "The biochemical anatomy of cortical inhibitory synapses", PLoS One 7 (2012) e39572. [PMCID: PMC3387162]      
• S. Bhatia, Y.J. Kil, B. Ueberheide, B.T. Chait, L. Tayo, L. Cruz, B. Lu, J.R. Yates, M. Bern. "Constrained De Novo Sequencing of Conotoxins", J Proteome Res. 2012 Aug 3. 11 (8) 4191-4200. [PMCID: PMC3412931]
• M. Domanski, K. Molloy, H. Jiang, B.T. Chait, M.P. Rout, T.H. Jensen, J. LaCava. "Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels", Biotechniques. May 2012. [PMCID: PMC3605737]
• A.K. Chakravarty, R. Subbotin, B.T. Chait, S. Shuman. "RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates", PNAS. 2012 Apr 17. 109 (16) 6072-60777. [PMCID: PMC3341019]
• J. Fernandez-Martinez, J. Phillips, M.D. Sekedat, R. Diaz-Avalos, J. Velazquez-Muriel, J.D. Franke, R. Williams, D.L. Stokes, B.T. Chait, A. Sali, M.P. Rout. "Structure-function mapping of a heptameric module in the nuclear pore complex", J Cell Biol. 2012 Feb 20. 196 (4) 419-434. [PMCID: PMC3283990]
• M.C. Field, V. Adung'a, S. Obado, B.T. Chait, M.P. Rout. "Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes", Parasitology. 2012 Aug. 139 (9) 1158-1167. [PMID: 22309600]
• M. Jishage, S. Malik, U. Wagner, B. Ueberheide, Y. Ishihama, X. Hu, B.T. Chait, A. Gnatt, B. Ren, R.G. Roeder. "Transcriptional Regulation by Pol II(G) Involving Mediator and Competitive Interactions of Gdown1 and TFIIF with Pol II", Mol Cell. 45 (2012) 51-63. Erratum. [PMCID: PMC3259531]
• X. Li, E.A. Foley, K.R. Molloy, Y. Li, B.T. Chait, T.M. Kapoor. "Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions", J Am Chem Soc. 2012 Feb 1. 134 (4) 1982-1985. [PMCID: PMC3520067]
• L.T. Donlin, C. Andresen, S. Just, E. Rudensky, C.T. Pappas, M. Kruger, E.Y. Jacobs, A. Unger, A. Zieseniss, M.W. Dobenecker, T. Voelkel, B.T. Chait, C.C. Gregorio, W. Rottbauer, A. Tarakhovsky, W.A. Linke. "Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization", Genes Dev. 2012 Jan 15. 26 (2) 114-119. [PMCID: PMC3273835]
• J.M. Manning, A.M. Popowicz, J.C. Padovan, B.T. Chait, L.R. Manning. "Intrinsic regulation of hemoglobin expression by variable subunit interface strengths", FEBS J. 279 (2012) 361-369. [PMCID: PMC3270300]

2011

• C. Wilczek, R. Chitta, E. Woo, J. Shabanowitz, B. Chait, D.F. Hunt, D. Shechter. "Protein arginine methyltransferase PRMT5/MEP50 methylates histones H2A and H4 and the histone chaperone nucleoplasmin in Xenopus laevis eggs", J Biol Chem. 286 (2011) 42221-31. [PMCID: PMC3234966]
• S.E. Peterson, Y. Li, B.T. Chait, M.E. Gottesman, R. Baer, J. Gautier. "Cdk1 uncouples CtIP-dependent resection and Rad51 filament formation during M-phase double-strand break repair", J Cell Biol. 194 (5) 705-720. [PMCID: PMC3171114]
• J.F. Scheid, H. Mouquet, B. Ueberheide, R. Diskin, F. Klein, T.Y.K. Olivera, J. Pietzsch, D. Fenyo, A. Abadir, K. Velinzon, A. Hurley, S. Myung, F. Boulad, P. Poignard, D. Burton, F. Pereyra, D.D. Ho, B.D. Walker, M.S. Seaman, P.J. Bjorkman, B.T. Chait, M.C. Nussenzweig. "Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding", Science 6049 (2011): 1633-7. [PMCID: PMC3351836]
• B.T. Chait. "Mass spectrometry in the postgenomic era", Annu Rev Biochem. 80 (2011) 239-46.
• I.M. Cristea, B.T. Chait. "Conjugation of magnetic beads for immunopurification of protein complexes", Cold Spring Harb Protoc. 2011 May 1.
• I.M. Cristea, B.T. Chait. "Affinity purification of protein complexes", Cold Spring Harb Protoc. 2011 May 1.
• S. Myung, H. Cohen, D. Fenyö, J.C. Padovan, A.N. Krutchinsky, B.T. Chait. "High-capacity ion trap coupled to a time-of-flight mass spectrometer for comprehensive linked scans with no scanning losses", International Journal of Mass Spectrometry 301 (2011) 211-219.[PMCID: PMC3079222]
• J. Eriksson, D. Fenyö. "Modeling mass spectrometry-based protein analysis", Methods Mol Biol. 694 (2011) 109-17. [PMCID: PMC3757507S.]
• Dokudovskaya, F. Waharte, A. Schlessinger, U. Pieper, D.P. Devos, I.M. Cristea, R. Williams, J. Salamero, B.T. Chait, A. Sali, M.C. Field, M.P. Rout, C. Dargemont. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae", Mol Cell Proteomics. 10 (2011) M110.006478. [PMCID: PMC3108837X]
• Li, Q.J. Wang, N. Pan, S. Lee, Y. Zhao, B.T. Chait, and Z. Yue. "Phosphorylation-Dependent 14-3-3 Binding to LRRK2 Is Impaired by Common Mutations of Familial Parkinson's Disease." PLoS ONE 6 (2011) e17153. [PMCID: PMC3046972]
• A. Gazumyan, K. Timachova, G. Yuen, E. Siden, M. Di Virgilio, E.M. Woo, B.T. Chait, B.R. San-Martin, M.C. Nussenzweig, K.M. McBride. "Amino Terminal Phosphorylation of Activation-Induced Cytidine Deaminase Suppresses c-myc-IgH Translocation", Mol Cell Biol. 31 (2011) 442-449. [PMCID: PMC3028632]

2010

• J. Bloom, I.M. Cristea, A.L. Procko, V. Lubkov, B.T. Chait, M. Snyder, F.R. Cross. "Global analysis of CDC14 phosphatase reveals diverse roles in mitotic processes", J Biol Chem. 286 (2010) 5434-5445. [PMCID: PMC3037656]
• Z. Berdygulova, L.F. Westblade, L. Florens, E.V. Koonin, B.T. Chait, E. Ramanculov, M.P. Washburn, S.A. Darst, K. Severinov, L. Minakhin. "Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45", Journal of Molecular Biology 2010. [PMCID: PMC3018760]
• Y. Li, N.K. Stewart, A.J. Berger, S. Vos, A.J. Schoeffler, J.M. Berger, B.T. Chait, M.G. Oakley. "Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction", Proc Natl Acad Sci U S A 2010 Oct 4. [PMCID: PMC2973889]
• J. Eriksson, D. Fenyö, "Modeling experimental design for proteomics", Methods Mol Biol 673 (2010) 223-30. [PMCID: PMC3745767]
• G. Zhang, B.M. Ueberheide, S. Waldemarson, S. Myung, K. Molloy, J. Eriksson, B.T. Chait, T.A. Neubert, D. Fenyö, "Protein quantitation using mass spectrometry", Methods Mol Biol 673 (2010) 211-22. [PMCID: PMC3758905]
• D. Fenyö, J. Eriksson, R. Beavis, "Mass spectrometric protein identification using the global proteome machine", Methods Mol Biol 673 (2010) 189-202. [PMCID: PMC3757509]
• S.S. Terhune, N.J. Moorman, I.M. Cristea, J.P. Savaryn, C. Cuevas-Bennett, M.P. Rout, B.T. Chait, T. Shenk, "Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA", PLoS Pathog. 6 (2010) e1000965.[PMCID: PMC2891856]
• L.R. Manning, A.M. Popowicz, J. Padovan, B.T. Chait, J.E. Russell, J.M. Manning, "Developmental expression of human hemoglobins mediated by maturation of their subunit interfaces", Protein Sci. 2010 Jun 23. [PMCID: PMC2923512]
• A. Zilman, S. Di Talia, T. Jovanovic-Talisman, B.T. Chait, M.P. Rout, M.O. Magnasco, "Enhancement of transport selectivity through nano-channels by non-specific competition", PLoS Comput Biol. 6 (2010) e1000804. [PMCID: PMC2883555]
• L. Peng, E.A. Kapp, D. Fenyö, M.S. Kwon, P. Jiang, S. Wu, Y. Jiang, M.I. Aguilar, N. Ahmed, M.S. Baker, Z. Cai, Y.J. Chen, P. Van Chi, M.C. Chung, F. He, A.C. Len, P.C. Liao, K. Nakamura, S.M. Ngai, Y.K. Paik, T.L. Pan, T.C. Poon, G. Hosseini Salekdeh, R.J. Simpson, R. Sirdeshmukh, C. Srisomsap, J. Svasti, Y.C. Tyan, F.S. Dreyer, D. McLauchlan, P. Rawson, T.W. Jordan, "The asia oceania human proteome organisation membrane proteomics initiative. preparation and characterization of the carbonate-washed membrane standard", Proteomics 2010 May 18.
• A.G. Paulovich, D. Billheimer, A.J. Ham, L. Vega-Montoto, P.A. Rudnick, D.L. Tabb, P. Wang, R.K. Blackman, D.M. Bunk, H.L. Cardasis, K.R. Clauser, C.R. Kinsinger, B. Schilling, T.J. Tegeler, A.M. Variyath, M. Wang, J.R. Whiteaker, L.J. Zimmerman, D. Fenyo, S.A. Carr, S.J. Fisher, B.W. Gibson, M. Mesri, T.A. Neubert, F.E. Regnier, H. Rodriguez, C. Spiegelman, S.E. Stein, P. Tempst, D.C. Liebler, "Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance", Mol Cell Proteomics, 9 (2010) 242-254. [PMCID: PMC2830837]
• I.M. Cristea, Nathaniel J. Moorman, S.S. Terhune, C.D. Cuevas , E.S. O'Keefe, M.P. Rout3, B.T. Chait, T. Shenk, "Human Cytomegalovirus pUL83 Stimulates Activity of the Viral Immediate-Early Promoter through its Interaction with the Cellular IFI16 Protein", J. Virology 2010 May 26. [PMCID: PMC2897612]
• I.M. Cristea, H. Rozjabek, K.R. Molloy, S. Karki, L.L. White, C.M. Rice, M.P. Rout, B.T. Chait, M.R. Macdonald, "Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: a role for G3BP1 and G3BP2 in virus replication", J. Virol. 2010 Apr 14 [PMCID: PMC2903289]
• M.D. Sekedat, D. Fenyö, R.S. Rogers, A.J. Tackett, J.D. Aitchison, B.T. Chait, "GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome", Mol Syst Biol. 6 (2010) 353. [PMCID: PMC2858444]
• D. Nešić, M.C. Miller, Z.T. Quinkert, M. Stein, B.T. Chait, C. E. Stebbins, "Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates", Nature Structural Biology 17 (2010) 130-132. [PMCID: PMC3006182]

2009

• M.R. Pratt, M.D. Sekedat, K.P. Chiang, T.W. Muir. "Direct measurement of cathepsin B activity in the cytosol of apoptotic cells by an activity-based probe", Chem Biol. 16 (2009) 1001-12. [PMCID: PMC3115634]
• M. Samuels, G. Gulati, J.H. Shin, R. Opara, E. McSweeney, M. Sekedat, S. Long, Z. Kelman, D. Jeruzalmi. "A biochemically active MCM-like helicase in Bacillus cereus", Nucleic Acids Res. 37 (2009) 4441-52. [PMCID: PMC2715239]
• A. Basu, K.L. Rose, J. Zhang, R.C. Beavis, B. Ueberheide, B.A. Garcia, B. Chait, Y. Zhao, D.F. Hunt, E. Segal, C.D. Allis, S.B. Hake, "Proteome-wide prediction of acetylation substrates", Proc Natl Acad Sci U S A. 106 (2009) 13785-13790. [PMCID: PMC2728972]
• M. Oeffinger, D. Zenklusen, A. Ferguson, K.E. Wei, A. El Hage, D. Tollervey, B.T. Chait, R.H. Singer and M.P. Rout, "Rrp17p Is a Eukaryotic Exonuclease Required for 5′ End Processing of Pre-60S Ribosomal RNA", Mol Cell 36 (2009) 768-781. [PMCID: PMC2806520]
• L. Postow, E.M. Woo, B.T. Chait, H. Funabiki, "Identification of SMARCAL1 as a component of the DNA damage response", J Biol Chem. 284 (2009) 35951-35961. [PMCID: PMC2791023]
• J.A. DeGrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, and B.T. Chait, "Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor", Mol Cell Proteomics. 8 (2009) 2119-2130. [PMCID: PMC2742445]
• B. Reed, J. Varon, B.T. Chait, M.J. Kreek, "Carbon dioxide-induced anesthesia results in a rapid increase in plasma levels of vasopressin", Endocrinology. 150 (2009) 2934-2939. [PMCID: PMC2689799]
• B.M. Ueberheide, D. Fenyo, P.F. Alewood, B.T. Chait, "Rapid sensitive analysis of cysteine rich peptide venom components", Proc Natl Acad Sci 106 (2009) 6910-6915. [PMCID: PMC2678425]
• T.N. Siegel, D.R. Hekstra, L.E. Kemp, L.M. Figueiredo, J.E. Lowell, D. Fenyo, X. Wang, S. Dewell, G.A. Cross, "Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei", Genes Dev. 23 (2009) 1063-1076. [PMCID: PMC2682952]
• F. Selimi, I.M. Cristea, E. Heller, B.T. Chait, N. Heintz, "Proteomic Studies of a Single CNS Synapse Type: The Parallel Fiber/Purkinje Cell Synapse", PLoS Biology 7 (2009) e83. [PMCID:PMC2672601]
• Y. Zhong, Q.J. Wang, X. Li, Y. Yan, J.M. Backer, B.T. Chait, N. Heintz, Z. Yue, "Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex", Nat Cell Biol. 11 (2009) 468-476. [PMCID: PMC2664389]
• Z. Yue, G.R. Holstein, B. T. Chait, Q.J. Wang, "Using genetic mouse models to study the biology and pathology of autophagy in the central nervous system", Methods Enzymol. 453 (2009) 159-80.
• T. Jovanovic-Talisman, J. Tetenbaum-Novatt, A.S. McKenney, A. Zilman, R. Peters, M.P. Rout, B.T. Chait, "Artificial nanopores that mimic the transport selectivity of the nuclear pore complex", Nature 457 (2009) 1023-1027. [PMCID: PMC2764719]
• G. Zhang, D. Fenyö, T.A. Neubert, "Evaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope Labeling by Amino Acids in Cell Culture", J Proteome Res 8 (2009) 1285-1292. [PMCID: PMC2693445]

2008

• J.A. DeGrasse, B.T. Chait, M.C. Field, M.P. Rout. "High-yield isolation and subcellular proteomic characterization of nuclear and subnuclear structures from trypanosomes", Methods Mol Biol. 463 (2008) 77-92.
• J. Eriksson and D. Fenyö, "Optimizing Sensitivity and Specificity in Mass Spectrometric Proteome Analysis", pp. 211-222 in: Mass Spectrometry: Instrumentation, Interpretation, and Applications, Eds. R. Ekman, J. Silberring, A.M. Brinkmalm, D.M. Desiderio, N.M. Nibbering, Wiley 2008.
• G. Zhang, D. Fenyö, T.A. Neubert, "Use of DNA Ladders for Reproducible Protein Fractionation by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) for Quantitative Proteomics", J Proteome Res 7 (2008) 678-686.[PMCID: PMC2667379]
• G. Zhang, D. Fenyö, T.A. Neubert, "Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer", J Proteome Res 7 (2008) 4715-4726. [PMCID: PMC2673988]
• K.M. McBride, A. Gazumyan, E.M. Woo, T.A. Schwickert, B.T. Chait, M.C. Nussenzweig, "Regulation of class switch recombination and somatic mutation by AID phosphorylation", J Exp Med. 205 (2008) 2585-2594. [PMCID: PMC2571933]
• C. Seibert, C.T. Veldkamp, F.C. Peterson, B.T. Chait, B.F. Volkman, T.P. Sakmar, "Sequential Tyrosine Sulfation of CXCR4 by Tyrosylprotein Sulfotransferases", Biochemistry 47 (2008) 11251-11262. [PMCID: PMC2662774]
• F. Alber, B.T. Chait, M.P. Rout, A. Sali, "Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints", in Protein-protein Interactions and Networks, A. Panchenko, T. Przytycka (eds.), Springer-Verlag London 2008.
• L. Postow, C. Ghenoiu, E.M. Woo, A.N. Krutchinsky, B.T. Chait, H. Funabiki, "Ku80 removal from DNA through double strand break-induced ubiquitylation", J Cell Biol. 182 (2008) 467-479. [PMCID: PMC2500133]
• M. Falth, M. Svensson, A. Nilsson, K. Skold, D. Fenyö, P.E. Andren, "Validation of Endogenous Peptide Identifications Using a Database of Tandem Mass Spectra", J Proteome Res 7 (2008) 3049-3053.
• N.J. Moorman, I.M. Cristea, S.S. Terhune, M.P. Rout, B.T. Chait, T. Shenk, "Human Cytomegalovirus Protein UL38 Inhibits Host Cell Stress Responses by Antagonizing the Tuberous Sclerosis Protein Complex", Cell Host Microbe 3 (2008) 253-62. [PMCID: PMC2759192]
  B. Reed, J.M. Bidlack, B.T. Chait, M.J. Kreek,"Extracellular Biotransformation of beta-Endorphin in Rat Striatum and Cerebrospinal Fluid" J Neuroendocrinol. 20 (2008) 606-616. [PMCID: PMC2682726]
• E.R. Butelman, B. Reed, B.T. Chait, M. Mandau, V. Yuferov, M.J. Kreek, "Limited effects of beta-endorphin compared to loperamide or fentanyl in a neuroendocrine biomarker assay in non-human primates", Psychoneuroendocrinology 33 (2008) 292-304. [PMCID: PMC2275163]
• E.M. Woo, D. Fenyö, B.H. Kwok, H. Funabiki, B.T. Chait BT, "Efficient Identification of Phosphorylation by Mass Spectrometric Phosphopeptide Fingerprinting", Anal Chem 80 (2008) 2419-2425.
• D. Savalia, L.F. Westblade, M. Goel, L. Florens, P. Kemp, N. Akulenko, O. Pavlova, J.C. Padovan, B.T. Chait, M.P. Washburn, H.-W. Ackermann, A. Mushegian, T. Gabisonia, I. Molineux, K. Severinov, "Genomic and Proteomic Analysis of phiEco32, a Novel Escherichia coli Phage", J. Mol. Biol. 377 (2008) 774-789.[PMCID: PMC2587145]
• L.F. Westblade, L. Minakhin, K. Kuznedelov, A.J. Tackett, E.J. Chang, R.A. Mooney, I. Vvedenskaya, Q.J. Wang, D. Fenyö, M.P. Rout, R. Landick, B.T. Chait, K. Severinov, S.A. Darst, "Rapid Isolation and Identification of Bacteriophage T4-Encoded Modifications of Escherichia coli RNA Polymerase: A Generic Method to Study Bacteriophage/Host Interactions.", J Proteome Res 7 (2008) 1244-1250. [PMCID: PMC2612130]
• D. Fenyö, R.C. Beavis, "Informatics development: Challenges and solutions for MALDI mass spectrometry", Mass Spectrom Rev 27 (2008) 1-19.
• Z. Yue, Q.J. Wang, M. Komatsu, "Neuronal autophagy: Going the distance to the axon", Autophagy 4 (2008) 94-96. [PMCID: PMC2675167]
• D.J. Lee, S.J.W. Busby, L.F. Westblade, B.T. Chait, "Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex", J Bacteriol 190 (2008) 1284-1289. [PMCID: PMC2238195]

2007

• A.N. Krutchinsky, H. Cohen, B.T. Chait, "A novel high-capacity ion trap-quadrupole tandem mass spectrometer", Int J Mass Spectrom 268 (2007) 93-105.
• F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, A. Sali, M.P. Rout, "The molecular architecture of the nuclear pore complex", Nature 450 (2007) 695-701.
• F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, M.P. Rout, A. Sali, "Determining the architectures of macromolecular assemblies", Nature 450 (2007) 683-694.
• J. Brandenburg, B. Schimanski, E. Nogoceke, T.N. Nguyen, J.C. Padovan, B.T. Chait, G.A. Cross, A. Günzl, "Multifunctional class I transcription in Trypanosoma brucei depends on a novel protein complex", EMBO J. 26 (2007) 4856-4866.
• M. Oeffinger, K.E. Wei, R. Rogers, J.A. DeGrasse, B.T. Chait, J.D. Aitchison & M.P. Rout, "Comprehensive analysis of diverse ribonucleoprotein complexes". Nature Methods, 4 (2007) 951-956.
• M. Komatsu, Q.J. Wang, G.R. Holstein, V.L. Friedrich, Jr., J. Iwata, E. Kominami, B.T. Chait, K. Tanaka, Z. Yue, "Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration". Proc Natl Acad Sci, 104 (2007) 14489-14494.
• S.C. Sampath, I. Marazzi, K.L. Yap, S.C. Sampath, A.N. Krutchinsky, I Mecklenbrauker, A. Viale, E. Rudensky, M.M. Zhou, B.T. Chait, A. Tarakhovsky, "Methylation of a Histone Mimic within the Histone Methyltransferase G9a Regulates Protein Complex Assembly". Mol Cell. 27 (2007) 596-608.
• M. Nishida, M. Cadene, B.T. Chait, R. Mackinnon, "Crystal structure of a Kir3.1-prokaryotic Kir channel chimera". EMBO J. 26 (2007) 4005-4015.
• E.J. Chang, R. Begum, B.T. Chait, T. Gaasterland, "Prediction of cyclin-dependent kinase phosphorylation substrates". PLoS ONE 2 (2007) e656.
• L.R. Manning, J.E. Russell, J.C. Padovan, B.T. Chait, A. Popowicz, R.S. Manning, J.M. Manning, "Human embryonic, fetal, and adult hemoglobins have different subunit interface strengths. Correlation with lifespan in the red cell". Protein Science 16 (2007) 1641-1658.
• A. Zilman, S. Di Talia, B.T. Chait, M.P. Rout, M.O. Magnasco, "Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport". PLoS Comput Biol. 3. (2007) e125
• J. Eriksson, D. Fenyö, "Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs". Nature Biotechnology 25 (2007) 651-655.
• D. Fenyö, Q.J. Wang, J.A. DeGrasse, J.C. Padovan, M. Cadene, B.T. Chait, "MALDI sample preparation: the ultra thin layer method". Journal of Visualized Experiments Issue 3 (2007)
• D. Fenyö, B.S.Phinney, R.C. Beavis, "Determining the Overall Merit of Protein Identification Data Sets: rho-Diagrams and rho-Scores". J Proteome Res 6 (2007) 1997-2004
• M. Falth, K. Skold, M. Svensson, A. Nilsson, D. Fenyö, P.E. Andren, "Neuropeptidomics: Strategies for specific and sensitive identification of endogenous peptides". Mol Cell Proteomics 6 (2007) 1188-1197
• J.S. Glavy, A.N. Krutchinsky, I.M. Cristea, I.C. Berke, T. Boehmer, G. Blobel, B.T. Chait, "Cell-cycle-dependent phosphorylation of the nuclear pore Nup107-160 subcomplex". Proc Natl Acad Sci, 104 (2007) 3811-3816.
• S.D Taverna, B.M. Ueberheide, Y. Liu, A.J. Tackett, R.L. Diaz, J. Shabanowitz, B.T. Chait, D.F. Hunt, C.D. Allis, "Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini". Proc Natl Acad Sci, 104 (2007) 2086-2091.
• A.E. Kelly, S.C. Sampath, T.A. Maniar, E.M. Woo, B.T. Chait, H. Funabiki, "Chromosomal enrichment and activation of the aurora B pathway are coupled to spatially regulate spindle assembly", Dev Cell. 12 (2007) 31-43.

2006

• M.Y. Kim , E.M. Woo, Y.T. Chong, D.R. Homenko , W.L. Kraus, "Acetylation of estrogen receptor alpha by p300 at lysines 266 & 268 enhances the deoxyribonucleic acid binding & transactivation activities of the receptor", Mol Endocrinol. 20 (2006) 1479-1493.
• S.D. Taverna, S. Ilin, R.S. Rogers, J.C. Tanny, H. Lavender, H. Li, L. Baker, J. Boyle, L.P. Blair, B.T. Chait, D.J. Patel, J.D. Aitchison, A.J. Tackett, C.D. Allis "Yng1 PHD Finger Binding to H3 Trimethylated at K4 Promotes NuA3 HAT Activity at K14 of H3 and Transcription at a Subset of Targeted ORFs", Mol Cell. 24 (2006) 785-796.
• B.T. Chait, "Mass spectrometry: bottom-up or top-down?" Science, 314 (2006) 65-66.
• B.L. Timney, T. Tetenbaum-Novatt, D.S. Agate, R. Williams, W. Zhang, B.T. Chait, M.P. Rout, "Simple kinetic relationships and nonspecific competition govern nuclear import rates in vivo" J. Cell Biol. 175 (2006) 579-593.
• Q.J. Wang, Y. Ding, S. Kohtz, N. Mizushima, I.M. Cristea, M.P. Rout, B.T. Chait, Y. Zhong, N. Heintz, Z. Yue "Induction of autophagy in axonal dystrophy and degeneration" J Neurosci, 26 (2006) 8057-68.
• I.M. Cristea, J.W. Carroll, M.P. Rout, C.M. Rice, B.T. Chait, M.R. Macdonald "Tracking and elucidating alphavirus-host protein interactions"J Biol Chem, 281 (2006) 30269-30278.
• M. Guermah, V.B. Palhan, A.J. Tackett, B.T. Chait, R.G. Roeder "Synergistic functions of SII and p300 in effecting productive activator-dependent transcription of chromatin templates" Cell, 125 (2006) 275-86.
• J. Wysocka, T. Swigut, H. Xiao, J. Landry, M. Kauer, A.J. Tackett, B.T. Chait, C. Wu, C.D. Allis "A PHD finger of the largest NURF subunit couples histone H3 K4 trimethylation with chromatin remodeling" Nature, 442 (2006) 86-90.
• K.M. McBride, A. Gazumyan, E.M. Woo, V.M. Barreto, D. F. Robbiani, B.T. Chait, M.C. Nussenzweig "Regulation of hypermutation by AID phosphorylation" Proc Natl Acad Sci, 103 (2006) 8798-803.
• S. Dokudovskaya, R. Williams, D. Devos, A. Sali, B.T. Chait, M.P. Rout "Protease Accessibility Laddering: A Proteomic Tool for Probing Protein Structure Structure" Structure, 14 (2006) 653-60.
• W.Y. Kao, J. Qin, K. Fushitani, S.S. Smith, T.A. Gorr, C.K. Riggs, J.E. Knapp, B.T. Chait, A.F. Riggs "Linker chains of the gigantic hemoglobin of the earthworm Lumbricus terrestris: primary structures of linkers L2, L3, and L4 and analysis of the connectivity of the disulfide bonds in linker L1" Proteins, 63 (2006) 174-87.
• D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali "Simple fold composition and modular architecture of the nuclear pore complex" Proc Natl Acad Sci, 103 (2006) 2172-2177.
• R. Craig, J.C. Cortens, D. Fenyö, R.C. Beavis, "Using Annotated Peptide Mass Spectrum Libraries for Protein Identification" Journal of Proteome Research, 5 (2006) 1843-1849.
• M. Fälth, K. Sköld, M. Norrman, M. Svensson, D. Fenyö, P.E. Andren, "SwePep – A Database Designed for Endogenous Peptides and Mass Spectrometry" Molecular and Cellular Proteomics 5 (2006) 998-1005.
• E. Ossipova, D. Fenyö, J. Eriksson, "Optimizing Search Conditions for the Mass-Fingerprint-Based Identification of Proteins" Proteomics 6 (2006) 2079-85.

2005

• D.J. Dilworth, A.J. Tackett, R.S. Rogers, E.C. Yi, R.H. Christmas, J.J. Smith, A.F. Siegel, B.T. Chait, R.W. Wozniak, J.D. Aitchison "The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control" J Cell Biol 171 (2005) 955-65.
• C. Strambio-de-Castillia, J. Tetenbaum-Novatt, B.S. Imai, B.T. Chait, M.P. Rout "A method for the rapid and efficient elution of native affinity-purified Protein A tagged complexes" Journal of Proteome Research (2005), 4, 2250-2256.
• M. Jin, H. Bateup, J.C. Padovan, P. Greengard, A.C. Nairn, B.T. Chait "Quantitative analysis of protein phosphorylation in mouse brain by hypothesis-driven multi-stage mass spectrometry" Anal Chem (2005), 77, 7845-7851.
• A.J. Tackett, J.A. DeGrasse, M.D. Sekedat, M. Oeffinger, M.P. Rout, B.T. Chait "I-DIRT, A General Method for Distinguishing between Specific and Nonspecific Protein Interactions" Journal of Proteome Research (2005), 4, 1752-6.
• I.M. Cristea, R. Williams, B.T. Chait, M.P. Rout "Fluorescent proteins as proteomic probes" Mol Cell Proteomics (2005) 4, 1933-1941.
• P. Hook, A. Mikami, B. Shafer, B.T. Chait, S.S. Rosenfeld, R.B. Vallee "Long-range allosteric control of cytoplasmic dynein ATPase activity by the stalk and C-terminal domains" J Biol Chem (2005), 280, 33045-54.
• M. Niepel, C. Strambio-de-Castillia, J. Fasolo, B.T. Chait, M.P. Rout. "The nuclear pore complex-associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly" J Cell Biol 170 (2005) 225-35.
• X. Zhang, A. Krutchinsky, A. Fukuda, W. Chen, S. Yamamura, B.T. Chait, R.G. Roeder "MED1/TRAP220 exists predominantly in a TRAP/ Mediator subpopulation enriched in RNA polymerase II and is required for ER-mediated transcription" Mol Cell 19 (2005) 89-100.
• V.B. Palhan, S. Chen, G. Peng, A. Tjernberg, A.M. Gamper, Y. Fan, B.T. Chait, A.R. La Spada, R.G. Roeder "Polyglutamine-expanded ataxin-7 inhibits STAG histone acetylltransferase activity to produce retinal degeneration" Proc Natl Acad Sci 102 (2005) 8472-8477.
• Y. Dou, T. A. Milne, A.J. Tackett , E.R. Smith, A. Fukuda, J. Wysocka , C.D. Allis, B.T. Chait, J.L. Hess, R.G. Roeder "Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF" Cell 121 (2005) 873-885.
• M. Matsushita, J. Ashot Kozak, Y. Shimizu, D.T. McLachlin, H. Yamaguchi, F.-Y. Wei, K. Tomizawa, H. Matsui, B.T. Chait, M.D. Cahalan, A.C. Nairn "Channel function is dissociated from the intrinsic kinase activity and autophosphorylation of TRPM7/CHAK1" J Biol Chem 280 (2005) 20793-20803.
• A.J. Tackett, D.J. Dilworth, M.J. Davey, M. O’Donnell, J.D. Aitchison, M.P. Rout, B.T. Chait "Proteomic and Genomic Characterization of Chromatin Complexes at a Boundary" J Cell Biol 169 (2005) 35-47.
• M. Ashiuchi, T. Yagami, R.J. Willey, J.C. Padovan, B.T. Chait, A.Popowicz, L.R. Manning, J.M. Manning "N-terminal Acetylation and protonation of individual hemoglobin subunits" Protein Science 14 (2005) 1458-1467.
• L. Csanády, D. Seto-Young, K.W. Chan, C. Cenciarelli, B.B. Angel, J. Qin, D.T. McLachlin, A.N. Krutchinsky, B.T. Chait, A.C. Nairn, D.C. Gadsby "Preferential Phosphorylation of R-Domain Serine 768 Dampens Activation of CFTR Channels by PKA" J Gen Physiol 125 (2005) 171-86.
• J. Eriksson, D. Fenyö "Protein Identification in Complex Mixtures" J Proteome Research 4 (2005) 387-93.

2004

• D. Devos, S. Dokudovskaya, F. Alber, R. Williams, B.T. Chait, A. Sali, M.P. Rout "Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular architecture" PLoS Biology 2 (2004) e380.
• J. Zheng-Sheng Ye, J. Donigian, M. van Overbeek, D. Loayza, Y. Luo, A.N. Krutchinsky, B.T. Chait, T. de Lange "TIN2 binds TRF1 and TRF2 simultaneously and stabilizes the TRF2 complex on telomeres" J Biol Chem 279 (2004) 47264-71.
• V. Muralidharan, J. Cho, M. Trester-Zedlitz, L. Kowalik, B.T. Chait, D.P. Raleigh, T.W. Muir "Domain-specific incorporation of noninvasive optical probes into recombinant proteins" J Am Chem Soc 126 (2004) 14004-14012.
• M.M. Coman, M. Jin, R. Ceapa, J. Finkelstein, B.T. Chait, M. O’Donnell, M. Hingorani "Dual functions--clamp opening and primer-template recognition--define a key clamp loader subunit" J Mol Biol 342 (2004) 1457-1469.
• J. Zhang, M. Kalkum, S. Yamamura, B.T. Chait, R.G. Roeder "E protein silencing by the leukemogenic AML1-ETO fusion protein" Science 305 (2004) 1286-1289.
• D.M. Leslie, M.P. Rout, W. Zhang, B.L. Timney, B.T. Chait, R. W. Wozniak, J. D. Aitchison "Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import" Mol Cell Biol 24 (2004) 8487-8503.
• V. Archambault, E.J. Chang, B.J. Drapkin, F.R. Cross, B.T. Chait, M.P. Rout "Targeted proteomic study of the Cyclin-Cdk module" Molecular Cell 14 (2004) 699-711.
• J. Zheng-Sheng Ye, D. Hockemeyer, A.N. Krutchinsky, D. Loayza, S.M. Hooper, B.T. Chait, T. de Lange "POT1 Interacting Protein PIP1: a telomere length regulator that recruits POT1 to the TIN2/TRF1 complex" Genes and Development 18 (2004) 1649-54.
• E.J. Chang, V. Archambault, D.T. McLachlin, A.N. Krutchinsky, B.T. Chait "Analysis of Protein Phosphorylation by Hypothesis-driven Multiple Stage Mass Spectrometry" Anal Chem 76 (2004) 4472-83.
• J. Eriksson, D. Fenyö "The Statistical Significance of Protein Identification Results as a Function of the Number of Protein Sequences Searched", J. Proteome Research 3 (2004) 979-82.
• J. Eriksson, D. Fenyö "Probity: A Protein Identification Algorithm with Accurate Assignment of the Significance of the Results", J Proteome Research 3 (2004) 32-36.

2003

• D. Fenyö, R.C. Beavis "A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes", Analytical Chemistry 75 (2003) 768-74.
• D.T. McLachlin, B.T. Chait "Improved β-elimination-based affinity purification strategy for enrichment of phosphopeptides" Anal Chem 75 (2003) 6826-6836.
• V. Archambault, C.X. Li, A.J. Tackett, R. Wasch, B.T. Chait, M.P. Rout, F.R. Cross "Genetic and biochemical evaluation of the importance of Cdc6 in regulating mitotic exit" Mol Biol Cell 14 (2003) 4592-4604.
• M.P. Rout, J.D. Aitchison, M.O. Magnasco, B.T. Chait "Virtual Gating and Nuclear Transport: The Hole Picture" Trends in Cell Biology 13 (2003) 622-628.
• K. Moffat, B.T. Chait "Biophysical methods: doing more with less" Current Opinion in Structural Biology, 13 (2003) 535-7.
• K-A. Wilson, M. Kalkum, J. Ottesen, J. Yuzenkova, B.T. Chait, R. Landick, T. Muir, K. Severinov, S. A. Darst "Structure of Microcin J25, a Peptide Inhibitor of Bacterial RNA Polymerase, is a Lassoed Tail" J Am Chem Soc 125 (2003) 12475-12483.
• Sehayek, R. Wang, J.G. Ono, V.S. Zinchuk, E.M. Duncan, S. Shefer, D.E. Vance, M. Ananthanarayanan, B.T. Chait, J.L. Breslow "Localization of the phosphatidylethanolamine methylation pathway and scavenger receptor class B type I to the canalicular membrane: Evidence for apical phosphatidylcholine biosynthesis that may promote biliary excretion of phospholipid and cholesterol" J Lipid Res 44 (2003) 1605-1613.
• Y. Jiang, A. Lee, J. Chen, V. Ruta, M. Cadene, B.T. Chait, R. Mackinnon "X-ray structure of a voltage-dependent K⁺ channel" Nature 423 (2003) 33-41.
• B. Reed, Y. Zhang, B.T. Chait, M.J. Kreek "Dynorphin A(1-17) Biotransformation in Striatum of Freely Moving Rats using Microdialysis and Matrix-assisted Laser Desorption/Ionization Mass Spectrometry" J Neurochem 86 (2003) 815-23.
• W. Zhang, A.N. Krutchinsky, B.T. Chait "De Novo Peptide Sequencing by MALDI-Quadrupole-Ion Trap Mass Spectrometry: A Preliminary Study" J Am Soc Mass Spectrom 14 (2003) 1012-1021.
• M. Trester-Zedlitz, K. Kamada, S.K. Burley, D. Fenyö, B.T. Chait, T.W. Muir "A Modular Cross-Linking Approach for Exploring Protein Interactions" J Am Chem Soc 125 (2003) 2416-2425.
• S. Jin, M. Kalkum, M. Overholtzer, A.Stoffel, B.T. Chait, A.J. Levine "CIAP1 and the serine protease HTRA2 are involved in a novel p53-dependent apoptosis pathway in mammals" Genes Dev. 17 (2003) 359-367.
• M. Kalkum, G.J. Lyon and B.T. Chait "Detection of Secreted Peptides using Hypothesis-driven Multistage Mass Spectrometry" Proc Natl Acad Sci USA 100 (2003) 2795-2800.
• I.H. Su, A. Basavaraj, A.N. Krutchinsky, O. Hobert, A. Ullrich, B.T. Chait, A. Tarakhovsky "Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement" Nat Immunol 4 (2003) 124-31.

2002

• L. Lopez-Molina, S. Mongrand, D.T. McLachlin, B.T. Chait, N.H. Chua "ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination" Plant J 32 (2002) 317-328.
• C. Seibert, M. Cadene, A. Sanfiz, B.T. Chait and T.P. Sakmar "Tyrosine Sulfation of CCR5 N-Terminal Peptide by Tyrosylprotein Sulfotransferases 1 & 2 Follows a Discrete Pattern & Temporal Sequence" Proc Natl Acad Sci USA 99 (2002) 11031-6.
• J.M. Cronshaw, A.N. Krutchinsky, W. Zhang, B.T. Chait, M.J. Matunis "Proteomic Analysis of the Mammalian Nuclear Pore Complex" J Cell Biology 158 (2002) 915-27.
• Y. Jiang, A. Lee, J. Chen, M. Cadene, B. T. Chait, R. MacKinnon "The open pore conformation of potassium channels" Nature 417 (2002) 523-526.
• Y. Jiang, A. Lee, J. Chen, M. Cadene, B. T. Chait, R. MacKinnon "Crystal structure and mechanism of a calcium-gated potassium channel" Nature 417 (2002) 515-522.
• J.S. Nair, C.J. DaFonseca, A. Tjernberg, W. Sun, J.E. Darnell Jr, B.T. Chait, J.J. Zhang "Requirement of Ca2+ and CaMKII for Stat1 Ser-727 phosphorylation in response to IFN-gamma" Proc Natl Acad Sci USA 99 (2002) 5971-6.
• R. Wang, B.T. Chait "Protein ladder sequencing" Editor(s): Walker, John M. Protein Protocols Handbook (2nd Edition) (2002).
• J. Zhang, M. Kalkum, B.T. Chait, R.G. Roeder "The N-CoR-HDAC3 Nuclear Receptor Corepressor Complex Inhibits the JNK Pathway through the Integral Subunit GPS2" Molecular Cell 9 (2002) 611-623.
• C.A. Bradley, J.C. Padovan, T.L. Thompson, C.A. Benoit, B.T. Chait, R.E. Rhoads "Mass spectrometric analysis of the N-terminus of translational initiation factor eIF4G-1 reveals novel isoforms" J. Biol. Chem. 277 (2002) 12559-12571.
• R. Dutzler, E.R. Campbell, M. Cadene, B.T. Chait, R. MacKinnon "X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity" Nature 415 (2002) 287-94.
• T. Yagami, B.T. Ballard, J.C. Padovan, B.T. Chait, A.M. Popowicz, J.M. Manning "N-terminal contributions of the gamma-subunit of fetal hemoglobin to its tetramer strength: Remote effects at subunit contacts" Protein Sci 11 (2002) 27-35.
• H. Kato, A. Tjernberg, W. Zhang, A.N. Krutchinsky, W. An, T. Takeuchi, Y. Ohtsuki, S. Sugano, B.T. Chait, R.G. Roeder "SYT associates with human SNF/SWI complexes and C-terminal region of its fusion partner SSX1 targets histones" J Biol Chem 277 (2002) 5498-5505.
• A.N. Krutchinsky, B.T. Chait "On the Nature of the Chemical Noise in MALDI mass spectra" J Am Soc Mass Spectrom 13 (2002) 129-134.
• D. Fenyö, R.C. Beavis "Informatics and data management in proteomics" Trends Biotechnol 20 (2002) S35-8.
• J. Eriksson, D. Fenyö "A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis" Proteomics. 2 (2002) 262-70. Erratum in: Proteomics 2 (2002) 603.
• H.I. Field, D. Fenyö, R.C. Beavis "RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database" Proteomics 2 (2002) 36-47.
• R.R. Flavell, M. Huse, M. Goger, M. Trester-Zedlitz, J. Kuriyan, T.W. Muir, "Efficient semisynthesis of a tetraphosphorylated analogue of the Type I TGFbeta receptor" Org Lett 4 (2002) 165-8.

2001

• A.N. Krutchinsky, M. Kalkum, B.T. Chait "Automatic Identification of Proteins Using a MALDI-Quadrupole Ion trap Mass Spectrometer" Anal Chem 73 (2001) 5066-5077.
• D.T. McLachlin, B.T. Chait "Analysis of phosphorylated proteins and peptides by mass spectrometry" Current Opinions in Chemical Biology 5 (2001) 591-602.
• C-Y. Yang, J. Wang, A.N. Krutchinsky, B.T. Chait, J.D. Morrisett, V.V. Smith "Selective oxidation in vitro by myeloperoxidase of the N-terminal amine in apoliporpotein B-100" J. Lipid Research 42 (2001) 1891-1896.
• E. Martinez, V. Palhan, A. Tjerberg, E. Lymar, A. Gamper, T. Kundu, B.T. Chait, R.G. Roeder "Human STAGA complex links GCN5 acetyltransferase to transcriptional activation, splicing regulation and UV-damaged DNA recognition" Molecular and Cellular Biology 21 (2001) 6782-95.
• D.J. Dilworth, A. Suprapto, J.C. Padovan, B.T. Chait, R.W. Wozniak, M.P. Rout, J.D. Aitchison "Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex" J Cell Biol 153 (2001) 1465-1478.
• S.L. Cohen, B.T. Chait "Mass Spectrometry as a tool for Studying Protein Structure" Ann Reviews of Biophysics and Biomolecular Structure 30 (2001) 67-85.
• Y. Oda, T. Nagasu, B.T. Chait "Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome" Nature Biotechnology 19 (2001) 379-382.
• N.A. Linderoth, M.N. Simon, N.A. Rodionova, M. Cadene, W.R. Laws, B.T. Chait, S. Sastry "Biophysical Analysis of the Endoplasmic Reticulum-Resident Chaperone/Heat Shock Protein gp96/GRP94 and Its Complex with Peptide Antigen." Biochemistry 40 (2001) 1483-1495.
• Y. Jiang, A. Pico, M. Cadene, B.T. Chait, R.D. MacKinnon "X-ray Structure of the RCK Domain from the E. coli Potassium channel and Demonstration of its presence in Large–Conductance Ca²⁺–activated Potassium Channels" Neuron 29 (2001) 593-601.

2000

• K. Inagaki, J. Inagaki, A. Dumoulin, J.C. Padovan, B.T. Chait, A. Popowicz, l.R. Manning, J.M. Manning "Expression and properties of recombinant HbA2(α2δ2) and hybrids containing δ-β sequences" J Prot Chem19(2000) 649-662.
• C. Griesinger, B.T. Chait "Analytical Techniques: From Proteome Analysis to Mechanical Phenotypes of Multiprotein Assemblies" Current Opinion in Chemical Biology 5 (2000) 487-488.
• M. Cadene, B.T. Chait "A Robust Detergent-Friendly for Mass Spectrometric Analysis of Integral Membrane Proteins" Anal Chem 72 (2000) 5655-5658.
• B.R. Ali, A. Tjernberg, B.T. Chait, M.C. Field "A putative microsomal GTPase is required for glycopeptide export from mammalian endoplasmic reticulum" J Biol Chem 275 (2000) 33222-30.
• S. Sechi, B.T. Chait "A method to define the carboxyl terminal of proteins" Anal Chem 72 (2000) 3374-3378.
• A.N. Krutchinsky, W. Zhang, B.T. Chait "Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification" J Am Soc Mass Spectrom 11 (2000) 493-504.
• W. Zhang, B.T. Chait "ProFound – An expert system for protein identification using mass spectrometry peptide mapping information" Anal Chem 72 (2000) 2482-2489.
• W. Chen, A. Dumoulin, X. Li, J.C. Padovan, B.T. Chait, R. Buonopane, O.S. Platt, L.R. Manning, J.M. Manning "Transposing sequences between fetal and adult hemoglobins indicates which subunit and regulatory molecule interfaces are functionally related" Biochem 39 (2000) 3774-3781.
• M.P. Rout, J.D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, B.T. Chait "The yeast nuclear pore complex: composition, architecture and transport mechanism" J Cell Biol 148 (2000) 635-652.
• J. Eriksson, B.T. Chait, D. Fenyö "A statistical basis for testing the significance of mass spectrometric protein identification results" Anal Chem 72 (2000) 999-1005.
• S.L. Cohen, J.C. Padovan, B.T. Chait "Mass spectrometric analysis of mass spectrometric analysis of mercury incorporation into proteins for X-ray diffraction phase determination" Anal Chem 72 (2000) 574-579.
• S.N. Uljon, L. Mazzarelli, B.T. Chait, R. Wang "Analysis of proteins and peptides directly from biological fluids by immunoprecipitation/mass spectrometry" Proteins and Peptide Analysis: New Mass Spectrometric Applications, J. Chapman Ed. In the series Methods in Molecular Biology 146 (2000) 439-52, Humana Press Inc.
• D. Fenyö "Identifying the proteome: software tools" Current Opinion in Biotechnology, 11 (2000) 391-395.

1999

• M. Teichmann, Z. Wang, E. Martinez, A. Tjernberg, D. Zhang, F. Vollmer, B.T. Chait, R.G. Roeder "Human TBP-related Factor 2 (hTRF2) stably associates with hTFIIA in HeLa cells" Proc. Natl. Acad. Sci. USA, 96 (1999) 13720-13725.
• R. Wang, B.T. Chait, I. Wolf, R.H. Kohanski, C. Cardova "Lysozyme degradation by the bovine multicatalytic proteinase complex (proteasome): evidence for a non-processive mode of degradation" Biochemistry, 38 (1999) 14573-14581.
• E. Maréchal, K. Hiratsuka, J. Delgado, A. Nairn, J. Qin, B.T. Chait, N.H. Chua "Modulation of GT-1 DNA-binding activity by calcium-dependent phosphorylation E." Plant Mol.Biol. (1999) 40373-40386.
• N. Srinivasan, C.A. Haney, J.S. Lindsey, W. Zhang, B.T. Chait "Investigation of MALDI-TOF Mass Spectrometry of Diverse Synthetic Metalloporphyrins, Phthalocyanines, and Multiporphyrin Arrays" J Porphyrin and Phthalocyanines 3 (1999) 283-291.
• Y. Oda, K. Huang, F.R. Cross, D. Cowburn, B.T. Chait "Accurate Quantitation of Protein Expression and Site-Specific Phosphorylation" Proc. Natl. Acad. Sci. USA, 96 (1999) 6591-6596.
• J. Qin, B.T. Chait "Collision-Induced Dissociation of Singly Charged Peptide Ions in a MALDI-Ion Trap Mass Spectrometer" Int. J Mass Spectrom Ion Processes 191 (1999) 313-320.
• T. Nagata, V. Gupta, W-Y. Kim, A. Sali, B.T. Chait, K. Shigesada, Y. Ito, M.H. Werner "Immunoglobulin Motif DNA Recognition and Heterodimerization for the PEBP2/CBF Runt-domain" Nature Structural Biology 6 (1999) 615-619.
• J.M. Manning, A. Dumoulin, L.R. Manning, W. Chen, J.C. Padovan, B.T. Chait, A. Popowicz "Remote Contributions to Protein subunit Interactions: Lessons from Adult and Fetal Hemoglobins" Trends Biochem Sci 24 (1999) 211-212.
• X. Li, J-P. Himanen, J.J. Martin de Llano, J.C. Padovan, B.T. Chait, J.M. Manning "Mutational Analysis of Sickle Hemoglobin Gelation" Biotechnol App Biochem 29 (Pt 2) (1999) 165-184.
• D. Fenyö "The Biopolymer Markup Language" Bioinformatics 15 (1999) 339-340.

1998

• D. Fenyö and R.C. Beavis, "Network-Based Bioinformatics in Protein Mass Spectrometry", in Mass spectrometry of Biological Materials, Eds. B. Larsen & C. McEwen, Marcel Dekker, 1998.
• A. Dumoulin, J.C. Padovan, L.R. Manning, A. Popowicz, R.M. Winslow, B.T. Chait, J.M. Manning "The N-terminal Sequence Affects Distant Helix Interactions in Hemoglobin. Implications for mutant proteins from studies on recombinant hemoglobin felix" J Biol Chem 273 (1998) 35032-35038.
• J.J. Zhang, Y. Zhao, B.T. Chait, W.W Lathem, M. Ritzi, R. Knippers, J.E. Darnell "Sta1α recruits the DNA replication factor MCM5 in IFN–ϒ–induced transcriptional activation" EMBO J 17 (1998) 6963-6971.
• S. Sechi, B.T. Chait "Cysteine alkylation– a tool in peptide mapping and protein identification" Anal Chem 70 (1998) 5150-5158.
• J.H. Morais Cabral, A. Lee, S. Cohen, B.T. Chait, M. Li, R. Mackinnnon "Structure of the HERG potassium channel amino-terminal domain: definition of a structural family of PAS domains" Cell 95 (1998) 649-55.
• C.L. Peterson, Y. Zhao, B.T. Chait "Subunits of the yeast SWI/SNF Complex are Members of the Actin Related Protein (ARP) Family" J Biol Chem 273 (1998) 23641-4.
• R. MacKinnon, S. L. Cohen, A. Kuo, A. Lee, B. T. Chait "Structural Conservation in Prokaryotic and Eukaryotic Potassium Channels" Science 280 (1998) 106-109.
• D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon "The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity" Science 280 (1998) 69-77.
• W. Zhang, S. Niu, B.T. Chait "Exploring Infrared Wavelength Matrix-Assisted Laser Desorption/Ionization of Proteins with Delayed-Extraction Time-of-Flight Mass Spectrometry" J Am Soc Mass Spectrom 9 (1998) 879-884.
• D. Fenyö, J. Qin, B.T. Chait "Protein Identification using Mass Spectrometric Information" Electrophoresis 19 (1998) 998-1005.
• H. Xu, G.K. Gouras, J. Greenfield, B. Vincent, J. Nas lund, L. Mazzarelli, G. Fried, J.N. Jovanovic, M. Seeger, N.R. Relkin, F. Liao, F. Checler, J.D. Buxbaum, B.T. Chait, G. Thinakaran, S.S. Sisodia, R.Wang, P. Greengard, S. Gandy "Estrogen Reduces Neuronal Generation of Alzheimer β-Amyloid Protein" Nature Medicine 4 (1998) 447-451.
• K.A. Hajjar, L. Mauri, A. Jacovina, F. Zhong, U.A. Mirza, J.C. Padovan, B.T. Chait "Tissue Plasminogen Activator Binding to the Annexin II Tail Domain: Direct Modulation by Homocystine" J Biol Chem 273 (1998) 9987-9993.
• P.W. van Ophem, S.D. Erickson, A.M. del Pozo, I. Haller, B.T. Chait, T. Yoshimuta, K. Soda, D. Ringe, G. Petsko, J.M. Manning "Substrate Inhibition of D-Amino acid Transaminase and Protection by Salts and by NADH. Isolation and Initial Characterization of a Pyridoxo-Intermediate related to Inactivation" Biochem 37 (1998) 2879-2888.
• S. Niu, W. Zhang and B.T. Chait "Direct Comparison of Infrared and Ultraviolet Wavelength Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry of Proteins" J Am Soc Mass Spectrom 9 (1998) 1-7.

1997

• Y. Wang, K. Severinov, N. Loizos, D. Fenyö, E. Heyduk, T. Heyduk, B. T. Chait, S.A. Darst "Determinants for Escherichia coli RNA Polymerase Assembly within the β Subunit" J Mol Biol (1997) 648-662.
• R.K. Upmacis, D.P. Hajjar, B.T. Chait, U.A. Mirza "Direct Observation of Nitrosylated Heme in Myoglobin and Hemoglobin by Electrospray Ionization-Mass Spectrometry" J Am Chem Soc 119 (1997) 10424-10429.
• X. Li, U.A. Mirza, B.T. Chait, J.M. Manning "Systematic enhancement of Polymerization of Recombinant Sickle Hemoglobin Mutants: implications for Transgenic Mouse Model for Sickle Cell Anemia" Blood 90 (1997) 4620-4627.
• J. Qin, B. T. Chait "Rapid, Accurate Identification and Characterization of Posttranslational Modifications of Proteins by MALDI Ion Trap Mass Spectrometry" Anal Chem 69 (1997) 4002-4009.
• J. Qin, D. Fenyö, Y. Zhao, W.W. Hall, D.M. Chao, C.J. Wilson, R.A. Young and B.T. Chait "A Strategy for Rapid, High Confidence Protein Identification" Anal Chem 69 (1997) 3995-4001.
• J. Yu, E.R. Butelman, J.H. Woods, B.T. Chait, M.J. Kreek "Dynorphin A (1-8) analog, E-2078, crosses the blood-brain barrier in rhesus monkeys" J Pharmacol Exp Ther 282 (1997) 633-638.
• J. Yu, E.R. Butelman, J.H. Woods, B.T. Chait, M.J. Kreek "Dynorphin A(1-8) Analog, E-2078, is stable in Human and Rhesus Monkey Blood" J. Pharm. Experimental Therapeutics 280 (1997) 1147-1151.
• P.L. Stewart, C.Y. Chiu, S. Huang, T. Muir, Y. Zhao, B. Chait, P. Mathias and G.R. Nemerow "Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization" EMBO J 16 (1997) 1189-1198.
• S.L. Cohen, B.T. Chait "Mass Spectrometry of Whole Proteins Eluted from SDS-PAGE Gels" Anal Biochem 247 (1997) 257-267.
• Y. Zhao, S.B.H. Kent, B.T. Chait "Rapid, Sensitive Analysis of Oligosaccharides" Proc Natl Academy Sci USA 94 (1997) 1629-1633.
• W. Zhang, B.T. Chait "Radial Velocity Distributions of Molecule Ions Produced by Matrix-Assisted Laser Desorption/Ionization" Int J Mass Spectrom Ion Processes 160 (1997) 259-267.
• U.A. Mirza, B.T. Chait, "Do Proteins Denature During Droplet Evolution in Electrospray Ionization ?" Int J Mass Spectrom Ion Processes 162 (1997) 173-181.
• D. Fenyö, B.T. Chait, T.E. Johnson, J.S. Lindsey "Laser desorption Mass Spectrometry of Large Synthetic Porphyrin Arrays" J Por and Phthalocy 1 (1997) 93-99.
• H.M. Lander, D.P. Hajjar, B.L. Hemstead, G.D. Schwartz, U.A. Mirza, B.T. Chait, S. Campbell Burk, and L.A. Quillium "A Molecular Redox Switch on p21ras: Structural Basis for Nitric Oxide-p21ras Interaction" J Biol Chem 272 (1997) 4323-4326.
• Q. Xie, R.A. Donahue, Jr., K. Schneider, U.A. Mirza, I. Haller, B.T. Chait, A.F. Riggs "Structure of chain d of the gigantic hemoglobin of the earthworm" BBA 1337 (1997) 241-247.
• D. Fenyö "A Software Tool for Analysis of Mass Spectrometric Disulfide Mapping Experiments" Computer Applications in the Biosciences (CABIOS) 13 (1997) 617-8.

1996

• J. Z. Chou, B.T. Chait, R. Wang, M.J. Kreek "Differential Biotransformation of Dynorphin A (1-17) and Dynorphin A (1-13) Peptides in Human Blood, ex vivo" Peptides. (Tarrytown, NY) 17 (1996) 983-990.
• B.T. Chait "Trawling for Proteins in the Post-genome Era" Nature Biotechnology 14 (1996) 1544.
• E. Severinova, K. Severinov, D. Fenyö, M. Marr, E.N. Brody, J.W. Roberts, B.T. Chait, S.A. Darst "Organization of the Escherichia coli RNA polymerase σ⁷⁰ subunit" J Mol Biol, 263 (1996) 637-647.
• D. Fenyö, W. Zhang, B.T. Chait, R.C. Beavis "Internet-based Analytical Chemistry Resources. A Model Project" Anal Chem 68 (1996) 721A-726A.
• J. Godinho da Silva, Jr., O.L.T. Machado, C. Izumi, J.C. Padovan, B.T. Chait, U.A. Mirza, L.J. Greene "Amino acid sequence of a new allergenic 2S albumin storage protein from Ricinus communis which is part of a 30 kDa precursor protein" Archives of Biochem & Biophys 336 (1996) 10-18.
• U. Vinkemeier, S.L. Cohen. I. Moarefi, B.T. Chait, J. Kuriyan, J.E. Darnell "DNA binding of in vitro activated Stat1α, Stat1β and truncated Stat1: interaction between NH2-terminal domains stabilizes binding of two dimers to tandem DNA sites" EMBO J 15 (1996) 5616-5626.
• J. Yu, E.R. Butelman, J.H Woods, B.T. Chait, M.J. Kreek "In vitro Biotransformation of Dynorphin A (1-17) is Similar in Human and Rhesus Monkey Blood as studied by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry" J Pharmacology and Experimental Therapeutics, 279 (1996) 507-514.
• J.-P. Himanen, U.A. Mirza, B.T. Chait, R. M. Bookchin, J. M. Manning "A Recombinant Sickle Hemohlobin Triple Mutant with independent Inhibitory effects on Polymerization" J Biol Chem 271 (1996) 25152-25156.
• S.L. Cohen, J.F. Halaas, J.M. Friedman, B.T. Chait, L. Bennett, D. Chang, R. Hecht, F. Collins "Characterization of Endogenous Human Leptin" Nature 382 (1996) 589.
• A.A. Stewart, J.D. Haley, G.-Y. Qu, K. Stam, D. Fenyö, B.T. Chait, D.R. Marshak, A.Y.-K. Ng, G. Marley, K.K. Iwata "Unbilical Cord Transforming Growth Factor-β3. Isolation, Comparison with Recombinant TGF-β3 and Cellular Localization" Growth Factors, 13 (1996) 87-98.
• J.W. Lustbader, S. Birken, S. Pollak, R.E. Cansfield, B.T. Chait, U.A. Mirza, S. Ramnarain, J.M. Brown "Expression of hCG Uniformly Labeled with NMR-Isotopes in Chinese Hamster Ovary Cells: An Advance Towards Rapid Determination of the Structures of Glycoproteins" J Biom NMR 7 (1996)295-304.
• C.-H. Lee, K. Saksela, U.M. Mirza, B.T. Chait, J. Kuriyan "Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain" Cell 85 (1996) 931-942.
• H.M. Lander, A.J. Milbank, J.M Taurus, D.P. Hajjar, B.L. Hempstaed, G.D. Schwartz, R.T. Kraemer, U.A. Mirza, B.T. Chait "Redox Regulation of Cell Signalling" Nature 381 (1996) 380-381.
• Y. Zhao, B.T. Chait "Probing Antibody-Antigen Interactions by Mass Spectrometry" Methods in Molecular Medicine, Vol. 66: Epitope Mapping Protocols. Ed. G.E. Morris, Humana Press Inc., Totowa NJ 1996, Chapter 13, pp 129 - 136.
• R.C. Beavis, B.T. Chait "Matrix-Assisted Laser Desorption Mass Spectrometry of Proteins" Methods in Enzymology. Vol. 270 (1996) Chap. 22, p. 519-551.
• J. Qin, B.T. Chait "Matrix-assisted laser desorption ion trap mass spectrometry: Efficient isolation and effective fragmentation of peptide ions" Anal. Chem. 68 (1996) 2108 - 2112.
• J. Qin, B.T. Chait "Matrix-assisted laser desorption ion trap mass spectrometry: efficient trapping and ejection of ions" Anal. Chem. 68 (1996) 2102 - 2107.
• J. Qin, J.M. Steenvoorden, B.T. Chait "A practical ion trap mass spectrometer for the analysis of peptides by matrix-assisted laser desorption/ionization" Anal. Chem. 68 (1996) 1784 - 1791.
• R.Wang, B.T. Chait "N-terminal ladder sequencing" in Methods in Molecular Biology, Vol. 64: Protein Sequencing Protocols. Chapter 18. Humana Press Inc., Totowa, NJ, 1996.
• R. Wang, B.T. Chait "Posttranslational modifications analyzed by automated protein ladder sequencing" in Methods in Molecular Biology, Vol. 61: Protein and Peptide Analysis by Mass Spectrometry. Ed. J.R. Chapman, Humana Press Inc., Totowa, NJ. 1996. Chapter 12, p.161 - 170.
• X. Xie, T. Kokubo, S,L. Cohen, U.A. Mirza, A. Hoffmann, B.T. Chait, R.G. Roeder, Y. Nakatani, & S. K. Burley "Structural Similarity between TAFS & the heterotetrameric core of the histone octamer" Nature 380 (1996) 316 - 322.
• Haller, U.A. Mirza, B.T. Chait "Collision Induced Decomposition of Peptides. Choice of Collision Parameters" J. Am. Soc. Mass spectrom. 7 (1996) 677 - 681.
• J. Yu, B.T. Chait, L. Toll, M.J. Kreek "Noniceptin in vitro Biotransformation in Human Blood" Peptides 17 (1996) 873-876.
• Y. Zhao, T.W. Muir, S.B.H. Kent, E. Tischer, J.M. Scardina, B.T. Chait "Mapping Protein-Protein Interactions by Affinity-Directed Mass Spectrometry" Proc Natl Academy Sci USA. 93 (1996) 4020 - 2024.
• S.L. Cohen, B.T. Chait "Influence of Matrix Solution Conditions on the MALDI-MS Analysis of Peptides and Proteins" Anal Chem 68 (1996) 31.

1995

• U.A. Mirza, B.T. Chait, H.M. Lander "Monitoring Reactions of Nitric Oxide with Peptides and Proteins by Electrospray Ionization Mass Spectrometry" J Biol Chem 270 (1995) 17185-17188.
• A.B. Smith III, H. Tokuyama, R.M. Strongin, G.T. Furst, W.J. Romanow, B.T. Chait, U.A. Mirza, I. Haller, "Synthesis of Oxo- and Methylene-Bridged C60 Dimers, the First Well-Characterized Species Containing Fullerene-Fullerene Bonds" J Am Chem Soc 117 (1995) 9359-9360.
• J.L. Halaas, K.S. Gajiwala, M. Maffei, S.L. Cohen, B.T. Chait, D. Rabinowitz, R.L. Lallone, S.K. Burley, J.M. Friedman "Weight Reducing Effects of the Plasma Protein Encoded by the obese Gene" Science (1995) 269, 543-546.
• S.L. Cohen, A.R. Ferre-D’Amare, S.K. Burley, B.T. Chait "Probing the Solution Structure of the DNA-binding Protein Max by a Combination of Proteolysis and Mass Spectrometry" Protein Science 4 (1995) 1088.
• S. Kazanis, T.C. Pochapsky, T.M. Bernhart, J.E. Penner-Hahn, U.A. Mirza, B.T. Chait "Conversion of a Fe₂S₂ Ferredoxin into a Ge³⁺ Rubredoxin" J Am Chem Soc 117 (1995) 6625-6626.
• J-P. Himanen, K. Schneider, B.T. Chait, J.M. Manning "Participation and Strength of Interaction of Lysine 95(b) in the Polymerization of Hemoglobin S as Determined by Its Site-directed Substitution by Isoleucine" J Biol Chem 270 (1995) 13885-13891.
• K. Schneider, B.T. Chait "Increased Stability of Nucleic Acids Containing 7-Deaza-Guanosine and 7-Deaza-Adenosine may Enable Rapid DNA Sequencing by Matrix-assisted Laser Desorption Mass Spectrometry" Nucleic Acids Res 23 (1995) 1570-1575.
• S.K. Chowdhury, K.J. Vavra, P.G. Brake, T. Banks, J. Falvo, R. Wahl, J. Eshraghi, G. Gonyea, B.T. Chait, C.H. Vestal "Examination of Recombinant Truncated Mature Human Fibroblast Collagenase by Mass Spectrometry: Identification of Differences with the Published Sequence and Determination of Stable Isotope Incorporation" Rapid Commun Mass Spectrom 9 (1995) 563-569.
• J. Qin, B.T. Chait "Preferential Fragmentation of Protonated Gas-Phase Peptide Ions Adjacent to Acidic Amino Acid Residues" J Am Chem Soc 117 (1995) 5411-5412.
• Y. Yang, W.V. Sweeney, S. Thornqvist, K. Schneider, B.T. Chait, J.P. Tam "Characterization of a Side Reaction Using Stepwise Detection in Peptide Synthesis with Fmoc Chemistry" Techniques in Protein Chemistry VI (1995) 555-562.
• A. Shartava, C.A. Monteiro, F. Aladar Bencsath, K. Schneider, B.T. Chait, R. Gussio, L.A. Casoria-Scott, A.K. Shah, C.A. Heuerman, S.R. Goodman "A Posttranslational Modification of b-Actin Contributes to the Slow Dissociation of the Spectrin-Protein 4.1-Actin Complex of Irreversibly Sickled Cells" J Cell Biol 128 (1995) 805.
• J. Chauvet, G. Michel, V. Ouedraogo, J. Chou, B.T. Chait, R. Acher "A New Neurohypophysial Peptide, Seritocin ([Ser⁵, IIe⁸]-oxytocin), Identified in a Dryness- Resistant African Toad, Bufo Regularis" Int J Peptide Protein Res 0 (1995) 1-6.
• K. Stam, A.A. Stewart, G.Y. Qu, K.K. Iwata, D. Fenyö, B.T. Chait, D.R. Marshak, J.D. Haley "Physical and Biologial Characterization of a Growth-Inhibitors Activity Purified from the Neuroepithelioma cell-line A673" Biochem J 305 (1995) 87.

1994

• K. Severinov, D. Fenyö, E. Severinov, B.T. Chait, A. Goldfarb, S. Darst, "The σ-Subunit Conserved Region 3 is Part of the "5’-Face" of the active Center of E. coli RNA Polymerase" J Biol Chem 269 (1994) 20826-8.
• H. Tang, K. Severinov, A. Goldfarb, D. Fenyö, B.T. Chait, R. Ebright "Location, Structure, and Function of the Target of a Transcription Activator Protein" Gene Dev 8 (1994) 3058-67.
• Y. Yang, W.V. Sweeney, K. Schneider, S. Thornqvist, B.T. Chait, J.P. Tam "Aspartimide formation in base-driven 9-fluorenylmethoxycarbonyl chemistry" Tetrahedron Letters 35 (1994) 9689-9692.
• H. Ge, Y. Zhao, B.T. Chait, R.G. Roeder "Phosphorylation Negatively Regulates the Function of Coactivator PC4" Proc Natl Acad Sci USA 91 (1994) pp.12691-12695.
• H. Yanase, S. Cahill, J.J.M. de Llano, L.R. Manning, K. Schneider, B.T. Chait, K.D. Vandegriff, R.M. Winslow, J.M. Manning "Properties of a Recombinant Human Hemoglobin with Aspartic Acid 99(b), an important intersubunit Conyact Side, Substituted by Lysine" Protein Sci 3 (1994) 1213-1223.
• Y. Zhao, B.T. Chait, "Protein Epitope Mapping by Mass Spectrometry" Anal Chem 66 (1994) 3723-3726.
• P. Sinnis, P. Clavijo, D. Fenyö, B.T. Chait, C. Cerami, V. Nussenzweig, "Structural and Functional Properties of Region II-Plus of the Malaria Circumsporozoite Protein" J Exp Med 180 (1994) 297-306.
• T.S.R. Krishna, D. Fenyö, X–P. Kong, S. Gary, B.T. Chait, P. Burgers, J. Kuriyan "Crystallization of Proliferating Cell Nuclear Antigen (PCNA) from Saccharomyces cerevisiae" J Mol Biol 241 (1994) 265-268.
• U.A. Mirza, B.T. Chait, "Effects of Anions on the Positive Ion Electrospray Ionization Mass Spectra of Peptides and Proteins" Anal Chem 66 (1994) 2898-2904.
• Y. Yang, W.V. Sweeney, K. Schneider, B.T. Chait, J.P. Tam "Two-step selective formation of three disulfide bridges in the synthesis of the C-terminal epidermal growth factor-like domain in human blood coagulation factor IX" Protein Science 3 (1994) 1267-1275.
• M. J. Rao, K. Schneider, B. T. Chait, T. L. Chao, H. Keller, S. Anderson, B. N. Manjula, R. Kumar, A.S. Acharya "Recombinant hemoglobin A produced in transgenic swine: structural equivalence with human hemoglobin A" Artificial Cells, Blood Substitutes, & Immobilization Biotechnology 22 (1994) 695-700.
• B.T. Chait "Mass Spectrometry- A Useful Tool for the Protein X-Ray Crystallographer and NMR Spectroscopist" Structure 2 (1994) 465-467.
• W. Zhang, A.J. Czernik, T. Yungwirth, R. Aebersold and B.T. Chait "Matrix-Assisted Laser Desorption Mass Spectrometric Peptide Mapping of Proteins Separated by Two-Dimensional Gel Electrophoresis: Determination of Phosphorylation in Synapsin I" Protein Science 3 (1994) 677-686.
• G. Carmel, B. Leichus, X. Cheng, S.D. Patterson, U. Mirza, B.T. Chait, J. Kuret "Expression, Purification, Crystallization, & Preliminary X-ray Analysis of Casein Kinase-1 from Schizosaccharomyces pombe" J Biol Chem 269 (1994) 1-6.
• R. Wang and B.T. Chait "High-accuracy Mass Measurement as a Tool for Studying Proteins" Current Opinion in Biotechnology 5 (1994) 77-84.
• R. Wang, B.T. Chait, S.B.H. Kent, "Protein Ladder Sequencing: Towards Automation" Techniques in Protein Chemistry V (1994) 19-26.
• J.Z. Chou, M.J. Kreek and B.T. Chait"Matrix-Assisted Laser Desorption Mass Spectrometry of Biotransformation Products of Dynorphin A in Vitro" J Am Soc Mass Spectrom 5 (1994) 10-16.

1993

• B.T. Chait, R. Wang, R.C. Beavis, S.B.H. Kent "Protein Ladder Sequencing" Science 262 (1993) 89-92.
• J.J. Martin de Llano, W. Jones, K. Schneider, B.T. Chait, J.M. Manning, G. Rodgers, L.J. Benjamin, B. Weksler "Biochemical and Functional Properties of Recombinant Human Sickle Hemoglobin Expressed in Yeast" J Biol Chem 268 (1993) 27005-27011.
• K. Schneider, B.T. Chait "Matrix-assisted Laser Desorption Mass Spectrometry of Homopolymer Oligodeoxyribonucleotides. Influence of Base Composition on the Mass Spectrometric Response" Organic Mass Spectrometry 28 (1993) 1353-1361.
• M.A. Baldwin, R. Wang, K-M Pan, R. Hecker, N. Stahl, B.T. Chait, S.B. Prusiner "Matrix-assisted Laser Desorption/Ionization Mass Spectrometry of Membrane Proteins: The Scrapie Prion Protein" Techniques in Protein Chem. IV (1993) 41-45.
• V. Katta, B.T. Chait "Hydrogen/Deuterium Exchange Electrospray Ionization Mass Spectrometry: A Method for Probing Protein Conformational Changes in Solution" J Am Chem Soc 115 (1993) 6317-6321.
• O. Vancura, A. O’Connor, S.D. Patterson, U. Mirza, B.T. Chait, J. Kuret "Isolation and Properties of YCK2, a Saccharomyces cerevisiae Homolog of Casein Kinase-1" Archives of Biochem & Biophys 305 (1993) 1-7.
• D.W. Ownby, H. Zhu, K. Schneider, R.C. Beavis, B.T. Chait, A.F. Riggs "The Extracellular Hemoglobin of the Earthworm Lumbricus-Terristris. Determination of Subunit Stochiometry" J Biol Chem 268 (1993) 13539-13547.
• R. Wang, B.T. Chait, S.B.H. Kent "Protein Ladder Sequencing: A Conceptually Novel Approach to Protein Sequencing Using Cycling Chemical Degradation and One-Step Readout by Matrix-Assisted Laser Desorption Mass Spectrometry" Techniques in Protein Chemistry IV Mass Spectrometry of Proteins and Peptides, Section I (1993) pp 471.
• D.A. Harris, M.T. Huber, P. van Dijken, S.-L. Shyng, B.T. Chait, R. Wang "Processing of a Cellular Prion Protein: Identification of N- and C-Terminal Cleavage Sites" Biochemistry 32 (1993) 1009-1016.
• U.A. Mirza, S.L. Cohen and B.T. Chait, "Heat Induced Conformational Changes in Proteins Studied by Electrospray Ionization Mass Spectrometry" Analytical Chem. 65 (1993) 1-6.

1992

• J.S. Lindsey, T. Chaudhary, B.T. Chait "²⁵²Cf Plasma Desorption Mass Spectrometry in the Synthesis of Porphyrin Model Systems" Anal Chem 64 (1992) 2804-2814.
• D. Santos, J.S. Imperial, T. Chaudhary, R.C. Beavis, B.T. Chait, J.P. Hunsperger, B.M. Olivera, M.E. Adams, D.R. Hillyard "Heterodimeric structure of the spider toxin omega-agatoxin IA revealed by precursor analysis and mass spectrometry" Journal of Biological Chemistry 267 (1992) 20701-5.
• A.E. Stewart, S. Raffioni, T. Chaudhary, B.T. Chait, P. Luporini, R.A. Bradshaw, "The disulfide bond pairing of the pheromones Er-1 and Er-2 of the ciliated protozoan Euplotes raikovi" Protein Science 1 (1992) 777-785.
• R.C. Beavis, B.T. Chait, H.S. Creel, M.J. Fournier, T.L. Mason, D.A. Tirrel "Analysis of Artificial Proteins by Matrix-Assisted Laser Desorption of Mass Spectrometry" J Am Chem Soc 114 (1992) 7584-7585.
• B.T. Chait, S.B.H. Kent "Weighing Naked Proteins: Practical, High-Accuracy Mass Measurement of Peptides & Proteins" Science 25 (1992) 1885-1894.
• N. Stahl, M.A. Baldwin, D. Teplow, L.E. Hood, R. Beavis, B. Chait, B. Gibson, A.L. Burlingame and S.B. Prusiner, in Prion Diseases in Humans and Animals, S.B. Prusiner, et al. Editor, (1992), Ellis Horwood: London.
• S. Raffioni, C. Miceli, A. Vallesi, S.K. Chowdhury, B.T. Chait, P. Luporini, R.A. Bradshaw "Primary Structure of Euplotes raikovi Pheromones: Comparison of Five Sequences of Pheromones from Cells with Variable Mating Interactions" Proc Natl Acad Sci 89 (1992) 2071-2075.
• R.C. Beavis, T. Chaudhary, B.T. Chait "a-Cyano-4-hydroxycinnamic Acid as a Matrix for Matrix-assisted Laser Desorption Mass Spectrometry" Organic Mass Spectrom 27 (1992) 156-158.

1991

• A. Seetharama Acharya, L. Khandke, B.T. Chait, M.J. Rao "Polymerization of Hemoglobin S Amidated at the Contact Residue Glu 43(b)" Molecular Conformation and Biological Interactions (1991) pp 269-280.
• B.T. Chait, R.C. Beavis "Matrix-assisted laser desorption and ionization of biomolecules" in Lecture Notes in Physics (1991) 389 (Laser Ablation: Mechanisms and Applications) edited by J.C. Miller and R.F. Haglund, Jr., Oak Ridge.
• F. Hillenkamp, M. Karas, R.C. Beavis, B.T. Chait "Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry of Biopolymers" Anal Chem 63 (1991) 1193A-1203A.
• V. Katta, B.T. Chait "Observation of the Heme-Globin Complex in Native Myoglobin by Electrospray Ionization Mass Spectrometry" J Am Chem Soc 113 (1991) 8534-8535.
• P. Low, G. Dallner, S. Mayor, S.L. Cohen, B.T. Chait, A.K. Menon "The Mevalonate Pathway in the Bloodstream Form of Trypanosoma brucei (Identification of Dolichols Containing 11 and 12 Isoprene Residues)" J Biol Chem 266 (1991) 19250-19257.
• R.C. Beavis, B.T. Chait "Velocity Distributions of Intact High Mass Polypeptide Molecule Ions Produced by Matrix Assisted Laser Desorption" Chem Phys Lett 181 (1991) 479-484.
• L.R. Manning, S. Morgan, R.C. Beavis, B.T. Chait, J.M. Manning, J.R. Hess, M. Cross, D.L. Currell, M.A. Marini, R.M. Winslow "Preparation, Properties, and Plasma Retention of Human Hemoglobin Drivatives: Comparison of Uncrosslinked Carboxymethylated Hemoglobin with Crosslinked Tetrameric Hemoglobin" Proc Natl Acad Sci USA 88 (1991) 3329-3333.
• V. Katta, B.T. Chait "Conformational Changes in Proteins Probed by Hydrogen-exchange Electrospray Ionization Mass Spectrometry" Rapid Commun Mass Spectrom 5 (1991) 214-217.
• D.E. Goldberg, A.F.G. Slater, R. Beavis, B.T. Chait, A. Cerami, G.B. Henderson "Hemoglobin Degradation in the Human Malaria Pathogen Plasmodium falciparum: A Catabolic Pathway initiated by a Specific Aspartic Protease" J Exp Med 173 (1991) 961-969.
• S.K. Chowdhury, V. Katta, B.T. Chait "Electrospray ionization mass spectrometric analysis of proteins" in Methods and Mechanisms for Producing Ions from Large Molecules, NATO ASI Series, K.G. Standing and W. Ens (eds. Plenum Press, New York) (1991) pp. 201-210.
• S. Aduru and B.T. Chait "Californium-252 plasma desorption mass spectrometry of oligosaccharides and glycoconjugates: Control of ionization and fragmentation". Anal Chem 63 (1991) 1621-1625.
• S.K. Chowdhury, B.T. Chait "Method for the Electrospray Ionization of Highly Conductive Aqueous Solutions" Anal Chem 63 (1991) 1660-1664.
• R.C. Beavis, B.T. Chait (1991) "Investigations of matrix isolated (UV) laser induced polymer sublimation using a time-of-flight mass spectrometer" in Methods and Mechanisms for Producing Ions from Large Molecules, (NATO Advanced Workshop, June 1990) ASI series, K.G. Standing and W. Ens (eds. Plenum Press, New York).
• V. Katta, B.T. Chait "A pulsed ion bombardment time-of-flight mass spectrometer with high sensitivity for the analysis of peptides" Int. J Mass Spectrom and Ion Processes 105 (1991) 129-145.
• L.R. Manning, S. Morgan, R.C. Beavis, B.T. Chait, J.M. Manning, J.R. Hess, M. Cross, D.M. Winslow "Preparation, properties, and plasma retention of human hemoglobin derivatives: comparison of uncrosslinked, carboxymethylated hemoglobin with crosslinked tetrameric hemoglobin" Proc Natl Acad Sci 88 (1991) 3329-3333.
• B.T. Chait "The analysis of synthetic peptides and problems by ²⁵²Cf plasma desorption mass spectrometry" in Mass Spectrometry of Peptides. Ed. D.M. Desiderio, CRC Press (1991) pp. 41-63.
• V. Katta, S.K. Chowdhury, B.T. Chait "Use of a single-quadrupole mass spectrometer for collision-induced dissociation studies of multiply charged peptide ions produced by electrospray ionization" Anal Chem 63(1991) 174-178

1990

• S.K. Chowdhury, B.T. Chait "Analysis of mixtures of closely related forms of bovine trypsin by electrospray ionization mass spectrometry. Use of charge state distributions to resolve ions of different forms" Biochem Biophys Res Commun 173 (1990) 927-931.
• R.A. Bradshaw, S. Raffioni, P. Luporini, B.T. Chait, T.D. Lee, J. Shively "Amino acid sequence - mass spectrometric analysis of mating pheromones of the ciliate Euplotes raikovi" In Analytical Biotechnology: Capillary Electrophoresis and Chromatography (Horvath, C. and Nikelly, J.C. Ed.) ACS Symposium Series vol. 434, (1990) pp. 153-161.
• S.K. Chowdhury, V. Katta, B.T. Chait "Probing conformational changes in proteins by mass spectrometry" J Am Chem Soc 112 (1990) 9012-9013.
• S. Pollack, S. Halpine, B.T. Chait, S. Birken "High resolution high performance liquid chromatography fingerprinting of purified human chorionic gonadotropin demonstrated that oxidation is a cause of hormone heterogeneity" Endocrinology 126 (1990) 199-208.
• S.K. Chowdhury, V. Katta, R.C. Beavis, B.T. Chait "Origin and Removal of adducts (Molecular mass = 98 u) attached to peptide and protein ions in electrospray ionization mass spectra" J Am Soc Mass Spectrom 1 (1990) 382-388.
• R.C. Beavis, B.T. Chait "High-accuracy molecular mass determination of proteins using matrix-assisted laser desorption mass spectrometry" Anal Chem 62 (1990) 1836-1840.
• R.C. Beavis, B.T. Chait "Rapid, sensitive analysis of protein mixtures by mass spectrometry" Proc Natl Acad Sci 87 (1990) 6873-6877.
• T.P. King, D. De Fa Wang, L. Kochoumian, B.T. Chait "Structural studies of a hornet venom allergen antigen 5, Dol m V and its sequence similarity with other proteins" Protein Seq Data Anal 3 (1990) 263-266.
• V. Katta, S.K. Chowdhury, B.T. Chait "Electrospray ionization: A new tool for the analysis of ionic transition-metal complexes" J Am Chem Soc 112 (1990) 5348-5349.
• J. Buck, G. Ritter, L. Dannecker, V. Katta, S.L. Cohen, B.T. Chait, U. Hammerling, "Retinol is essential for growth of activated human cells" J Exp Med 171 (1990) 1613-1624.
• B.T. Chait, R.C. Beavis "Matrix assisted UV laser desorption of biologically interesting molecules" in Secondary Mass Spectrometry, eds. A. Benninghoven, Evans, McKeegan, Storms and Werner. Wiley (1990) pp. 289-292.
• S.K. Chowdhury, V. Katta, B.T. Chait "Electrospray ionization mass spectrometric peptide mapping: A rapid, sensitive technique for protein structure analysis" Biochem Biophys Res Commun 167 (1990) 686-692.
• S.K. Chowdhury, V. Katta, B.T. Chait "An Electrospray-ionization mass spectrometer with new features" Rapid Commun Mass Spectrom 4(1990) 81-87.
• R.C. Beavis, B.T. Chait "Matrix assisted UV laser desorption of large biomolecules" in Ion Formation from Organic Solids, (1990) Eds. A. Hedin, A. Benninghoven and B.U.R. Sundqvist, John Wiley and Sons.

1989

• S.K. Chowdhury and B.T. Chait, "A mass spectrometric technique for detecting and identifying by-products in the synthesis of peptides", Anal. Biochem. 180 (1989) 387-395.
• R.C. Beavis, B.T. Chait "Matrix-assisted laser-desorption mass spectrometry using 355nm radiation" Rapid Commun Mass Spec 3(1989)436-439.
• B.T. Chait "²⁵²Cf plasma desorption mass spectrometry.Contributions from the Rockefeller University" Int J Mass Spectrom Ion Processes 92 (1989) 297.
• R.C. Beavis, B.T. Chait "Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins" Rapid Commun Mass Spec 3 (1989) 432-435.
• Y. Ito, J. Breslow, B.T. Chait, "Apolipoprotein C-111_o lacks carbohydrate residues: use of mass spectrometry to study apolipoprotein structure" J. Lipid Res 30 (1989) 1781-1788.
• C.J.A. Wallace, P. Mascagni, B.T. Chait, J.F. Collawn, Y. Peterson, A.E. Proudfoot and S.B.H. Kent, "Substitutions engineered by chemical synthesis at 3 conserved sites in mitochondrial cytochrome-C-Thermodynamic and functional consequences" J. Biol. Chem. 264 (1989) 5199-5209.
• D.L. Woo, I. Clarke-Lewis, B.T. Chait, S.B.H. Kent "Chemical synthesis in protein engineering: total synthesis, purification and covalent structural characterization of a mitogenic protein, human transforming growth factor-alpha" Protein Engineering 3 (1989) 29-37.
• S.K. Chowdhury, B.T. Chait "Recent developments in the mass spectrometry of peptides and proteins" Annual Reports in Medicinal Chem 24 (1989) 253-263.
• R.C. Beavis, B.T. Chait "Factors affecting the ultraviolet laser desorption of proteins" Rapid Commun Mass Spectrom 3 (1989) 233-237.
• S. Burman, D. Wellner, B.T. Chait, T. Chaudhary, E. Breslow "Complete Assignment of Neurophysin Disulfides indicates Pairing in Two Separate Domains" Proc Natl Acad Sci USA 86 (1989) 429-433.
• K.M. Khandke, T. Fairwell, B.T. Chait, T. Chaudhary, B.N. Manjula "Influence of ions on cyclization of the amino terminal glutamine residues of tryptic peptides of streptococcal PepM49 protein" Int J Peptide Protein Res 34 (1989) 118-123.

1988

• B.T. Chait "The use of ²⁵²Cf plasma desorption mass spectrometry for the analysis of synthetic peptides and proteins", (Chapter) "The analysis of peptides and proteins by mass spectrometry" Proceedings of the Fourth Texas Symposium, C.J. McNeal, (ed.), John Wiley & Sons, Inc. (1988) pp. 21-39.
• S. Raffioni, P. Luporini, B.T. Chait, S.S. Disper, R.A. Bradshaw, "Primary structure of the mating pheromone Er-1 of the ciliate Euplotes raikovi" J Biol Chem 263 (1988) 18152-18159.
• R.B. Merrifield, J. Singer, B.T. Chait "Mass spectrometric evaluation of synthetic peptides for deletions & insertions" Anal Biochem 174 (1988)399-414
• K. Furukawa, B.T. Chait, K.O. Lloyd, "Identification of N-glycolylenuraminic acid-containing gangliosides of cat and sheep erythrocytes: Californium-252 fission fragment mass spectrometry in the analysis of glycosphingo-lipids" J Biol Chem 263 (1988) 14939-14947.
• S. Burman, E. Breslow, B.T. Chait, T. Chaudhary "Application of high-performance liquid chromatography in neurophysin disulfide assignment" J Chromatog 443 (1988) 285-298.
• W. Ens, D.E. Main, K.G. Standing, B.T. Chait "Comparison of relative quasi-molecular ion yields for 8-keV ion and ²⁵²Cf fission fragment bombardment" Anal Chem 60 (1988) 1494-1498.
• J.F. Garcia-Bustos, B.T. Chait, A. Tomasz "Altered peptidoglycan structure in a pneumococcal transformant resistant to penicillin" J Bacteriol 170 (1988) 2143-2147.

1987

• B.T. Chait, "A study of the fragmentation of singly and multiply charged ions produced by 252Cf fission fragment bombardment of polypeptides bound to nitrocellulose", Int. J Mass Spectrom Ion Processes 78 (1987) 237-250.
• J.F. Garcia-Bustos, B.T. Chait, A. Tomasz "Structure of the peptide network of pneumococcal peptidoglycan" J Biol Chem 262 (1987) 15400-15405.
• S. Burman, E. Breslow, B.T. Chait, T. Chaudhary "Partial assignment of disulfide pairs in neurophysins" Biochem Biophys Res Comm 148 (1987) 827-833.
• J.A. Loo, E.R. Williams, J.I. Amster, J.J. Furlong, Bing H. Wang, F.W. McLafferty, B.T. Chait, F.H. Field "Californium-252 plasma desorption with Fourier transform mass spectrometry" Anal Chem 59 (1987) 1880-1882.
• F. Lafortune, R. Beavis, X. Tang, K.S. Standing, B.T. Chait "Narrowing the gap between keV and fission fragment secondary ion yields with nitrocellulose" Rapid Commun Mass Spectrom 1 (1987) 114-116.
• J.A. Loo, E.R. Williams, J.J.P. Furlong, B.H. Wang, F.W. McLafferty, B.T. Chait, F.H. Field "²⁵²Cf Plasma Desorption Fourier Transform Mass Spectrometry of Involatile Compounds" Int. J. Mass Spectrom & Ion Proc 78 (1987) 305-313.
• S.B.H. Kent, K.P. Parker, D.L Shiller, D.D.-L. Woo, I. Clarke-Lewis, B.T. Chait "Synthesis of characterization of peptides and proteins" Proceedings of 10^th American Peptide Symposium, (1987) St. Louis, MO.
• L.I. Grace, B.T. Chait, F.H. Field "A system for collecting high-resolution time-of-flight mass spectrometric data" Biomed & Environment Mass Spectrom 14 (1987) 295-299.

1986

• B.T. Chait, T. Chaudhary, F.H. Field, "Mass spectrometric characterization of microscale enzyme catalyzed reactions of surface-bound peptides and proteins" Methods in Protein Sequence Analysis (Kenneth A. Walsh, Editor) Humana Press, N.J. (1986) pp. 483-492.
• P.J. Gale, B.L. Bentz, B.T. Chait, F.H. Field, R.J. Cotter, "Reduction in liquid secondary ion mass spectrometry. Comparison of the fission fragment and liquid secondary ion mass spectra of organic dyestuffs" Anal Chem 58 (1986) 1070-1076.
• R. Bucala, P.C. Ulrich, B.T. Chait, F.A. Bencsath, A. Cerami, "Structures of lysine adducts with 16 α-hydroxyestrone & cortisol" J Steroid Biochem 25 (1986) 127-133.
• B.T. Chait, F.H. Field "A rapid, sensitive mass spectrometric method for investigating microscale chemical reactions of surface adsorbed peptides and proteins" Biochem & Biophys Res Commun 134 (1986) 420-426.

1985

• B.T. Chait, F.H. Field "A study of the metastable fragmentation of ions produced by ²⁵²Cf fission fragment bombardment of bovine insulin" Int J Mass Spec and Ion Proc 65 (1985) 169-180.
• B.T. Chait, F.H. Field "Mass spectrometry of microscale chemical reaction products produced at the surface of organic solids" J Am Chem Soc 107 (1985) 6743-6744.
• B.T. Chait "Ion bombardment MS: A sensitive probe of chemical reactions occurring at the surface of organic solids" Proc. 3^rd Int. Conf., Springer-Verlag Benninghoven, Ed. Springer Proc Phys 9 (Ion Form Org. Solids) (1985) 34-36.
• A.H. Fairlamb, P. Blackburn, P. Ulrich, B.T. Chait, A. Cerami "Trypanothione: A novel bis(glutathionyl) spermidine cofactor for glutathione reductase in trypanosomatids" Science 227 (1985) 1485-1487.

1984

• B.T. Chait and F.H. Field, "²⁵²Cf fission fragment ionization mass spectrometry of chlorophyll a" J. Am. Chem. Soc. 106 (1984) 1931-1938.
• A. Feinberg, P.D. Vidal, J.J. Fox, K.A. Watanabe, M.W. Chun, F.H. Field, F.A. Bencsath, B.T. Chait, F.S. Philips "Structures of metabolites isolated from urine of mice treated with antiviral agent, 1-(2-Fluoro-2-deoxy-b-arabinofuranosyl)-5-methyluracil" Drug Metabolism & Disposition 12 (1984) 784-786.
• B.T. Chait, J. Shpungin, F.H. Field "Fission fragment ionization mass spectrometry of polyethers" Int J Mass Spec & Ion Proc 58 (1984) 121-137.

1983

• B.T. Chait "Prompt and metastable decompositions in ²⁵²Cf fission fragment ionization mass spectrometry" Int J Mass Spec & Ion Phys 53 (1983) 227-242.

1982

• B.T. Chait, F.H. Field, "²⁵²Cf Fission fragment ionization mass spectrometry of chlorophyll a" J Am Chem Soc 104 (1982) 5519-5521.
• K.G. Standing, B.T. Chait, W. Ens, G. McIntosh, R. Beavis "Time-of-flight measurements of secondary organic ions produced by 1 keV to 16 keV primary ions" Nuclear Instruments and Methods in Physics Research 198 (1982) 33-38.
• B.T. Chait, B.F. Gisin, F.H. Field "Fission fragment ionization mass spectrometry of alamethicin I" J Am Chem Soc 104 (1982) 5157-5162.

1981

• B.T. Chait, F.H. Field "Fission fragment ionization mass spectrometry: metastable decompositions" Int J Mass Spec & Ion Phys 41 (1981) 17-29.
• W. Ens, K.G. Standing, B.T. Chait, F.H. Field "Comparison of mass spectra obtained with low-energy ion and high-energy californium-252 fission fragment bombardment" Anal Chem 53 (1981) 1241-1244.
• B.T. Chait, W.C. Agosta, F.H. Field "Fission fragment ionization ⁽²⁵²Cf) mass spectrometry. Positive and negative spectra & decomposition mechanisms for seven compounds" Int J Mass Spec & Ion Phys 39 (1981) 339-366.
• B.T. Chait, K.G. Standing "A time-of-flight mass spectrometer for measurement of secondary ion mass spectra" Int. J Mass Spectrom Ion Phys 40 (1981) 185-193.

1980

• R.F. Bonner, D.V. Bowen, B.T. Chait, A.B. Lipton, W.F. Sippach, F.H. Field "High performance digital timing system" Anal Chem 52 (1980) 1923-1928.

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