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For: Gessner C, Steinchen W, Bédard S, J Skinner J, Woods VL, Walsh TJ, Bange G, Pantazatos DP. Computational method allowing Hydrogen-Deuterium Exchange Mass Spectrometry at single amide Resolution. Sci Rep 2017. [PMID: 28630467 PMCID: PMC5476592 DOI: 10.1038/s41598-017-03922-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
Number Cited by Other Article(s)
1
Eilers K, Hoong Yam JK, Liu X, Goh YF, To KN, Paracuellos P, Morton R, Brizuela J, Hui Yong AM, Givskov M, Freibert SA, Bange G, Rice SA, Steinchen W, Filloux A. The dual GGDEF/EAL domain enzyme PA0285 is a Pseudomonas species housekeeping phosphodiesterase regulating early attachment and biofilm architecture. J Biol Chem 2024;300:105659. [PMID: 38237678 PMCID: PMC10874727 DOI: 10.1016/j.jbc.2024.105659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/23/2023] [Accepted: 01/04/2024] [Indexed: 02/15/2024]  Open
2
Anderson KW, Hudgens JW. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023;34:2672-2679. [PMID: 37930109 PMCID: PMC10704588 DOI: 10.1021/jasms.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
3
Kurooka N, Eguchi J, Wada J. Role of glycosylphosphatidylinositol-anchored high-density lipoprotein binding protein 1 in hypertriglyceridemia and diabetes. J Diabetes Investig 2023;14:1148-1156. [PMID: 37448184 PMCID: PMC10512915 DOI: 10.1111/jdi.14056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]  Open
4
Developments in rapid hydrogen-deuterium exchange methods. Essays Biochem 2023;67:165-174. [PMID: 36636941 DOI: 10.1042/ebc20220174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
5
Tajoddin NN, Konermann L. Structural Dynamics of a Thermally Stressed Monoclonal Antibody Characterized by Temperature-Dependent H/D Exchange Mass Spectrometry. Anal Chem 2022;94:15499-15509. [DOI: 10.1021/acs.analchem.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
6
Anderson KW, Hudgens JW. Chromatography at -30 °C for Reduced Back-Exchange, Reduced Carryover, and Improved Dynamic Range for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022;33:1282-1292. [PMID: 35732031 PMCID: PMC9264389 DOI: 10.1021/jasms.2c00096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
7
Abe H, Yoshiichi Y, Kishimura H. Hydrogen/deuterium Exchange in 1-Alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide-based Solutions. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
8
Tran MH, Schoeder CT, Schey KL, Meiler J. Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook. Front Immunol 2022;13:859964. [PMID: 35720345 PMCID: PMC9204306 DOI: 10.3389/fimmu.2022.859964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]  Open
9
Stofella M, Skinner SP, Sobott F, Houwing-Duistermaat J, Paci E. High-Resolution Hydrogen-Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022;33:813-822. [PMID: 35385652 PMCID: PMC9074100 DOI: 10.1021/jasms.2c00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
10
Advances in Mass Spectrometry-based Epitope Mapping of Protein Therapeutics. J Pharm Biomed Anal 2022;215:114754. [DOI: 10.1016/j.jpba.2022.114754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
11
Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022;33:215-237. [PMID: 35077179 DOI: 10.1021/jasms.1c00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
12
Smit JH, Krishnamurthy S, Srinivasu BY, Parakra R, Karamanou S, Economou A. Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal Chem 2021;93:12840-12847. [PMID: 34523340 DOI: 10.1021/acs.analchem.1c02155] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021;122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
14
Salmas RE, Borysik AJ. Characterization and Management of Noise in HDX-MS Data Modeling. Anal Chem 2021;93:7323-7331. [PMID: 33961396 DOI: 10.1021/acs.analchem.1c00894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
15
Di Muzio M, Wildner S, Huber S, Hauser M, Vejvar E, Auzinger W, Regl C, Laimer J, Zennaro D, Wopfer N, Huber CG, van Ree R, Mari A, Lackner P, Ferreira F, Schubert M, Gadermaier G. Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in IgE cross-reactivity of allergenic lipid transfer proteins. J Biol Chem 2021;295:17398-17410. [PMID: 33453986 DOI: 10.1074/jbc.ra120.014243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Indexed: 01/30/2023]  Open
16
Puchała W, Burdukiewicz M, Kistowski M, Dąbrowska KA, Badaczewska-Dawid AE, Cysewski D, Dadlez M. HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments. Bioinformatics 2021;36:4516-4518. [PMID: 32579220 PMCID: PMC7575049 DOI: 10.1093/bioinformatics/btaa587] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 02/03/2023]  Open
17
HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation. Commun Biol 2021;4:199. [PMID: 33589746 PMCID: PMC7884430 DOI: 10.1038/s42003-021-01709-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]  Open
18
Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020;93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
19
Tajoddin NN, Konermann L. Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments. Anal Chem 2020;92:10058-10067. [DOI: 10.1021/acs.analchem.0c01828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
20
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020;120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
21
Wollenberg DTW, Pengelley S, Mouritsen JC, Suckau D, Jørgensen CI, Jørgensen TJD. Avoiding H/D Scrambling with Minimal Ion Transmission Loss for HDX-MS/MS-ETD Analysis on a High-Resolution Q-TOF Mass Spectrometer. Anal Chem 2020;92:7453-7461. [PMID: 32427467 DOI: 10.1021/acs.analchem.9b05208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
22
Zhang Z. Complete Extraction of Protein Dynamics Information in Hydrogen/Deuterium Exchange Mass Spectrometry Data. Anal Chem 2020;92:6486-6494. [DOI: 10.1021/acs.analchem.9b05724] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
23
Babić D, Kazazić S, Smith DM. Resolution of protein hydrogen/deuterium exchange by fitting amide exchange probabilities to the peptide isotopic envelopes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019;33:1248-1257. [PMID: 31034666 DOI: 10.1002/rcm.8460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/13/2019] [Accepted: 04/10/2019] [Indexed: 05/11/2023]
24
Huang L, So PK, Yao ZP. Protein dynamics revealed by hydrogen/deuterium exchange mass spectrometry: Correlation between experiments and simulation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019;33 Suppl 3:83-89. [PMID: 30321473 DOI: 10.1002/rcm.8307] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 05/09/2023]
25
Estimating Constraints for Protection Factors from HDX-MS Data. Biophys J 2019;116:1194-1203. [PMID: 30885379 PMCID: PMC6451051 DOI: 10.1016/j.bpj.2019.02.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/21/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]  Open
26
Anderson KW, Gallagher ES, Hudgens JW. Automated Removal of Phospholipids from Membrane Proteins for H/D Exchange Mass Spectrometry Workflows. Anal Chem 2018;90:6409-6412. [PMID: 29723469 DOI: 10.1021/acs.analchem.8b00429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
27
Kazazić S, Karačić Z, Sabljić I, Agić D, Tomin M, Abramić M, Dadlez M, Tomić A, Tomić S. Conservation of the conformational dynamics and ligand binding within M49 enzyme family. RSC Adv 2018;8:13310-13322. [PMID: 35542530 PMCID: PMC9079729 DOI: 10.1039/c7ra13059g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 12/25/2022]  Open
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