ExMS: Data analysis for HX-MS experiments

Journal of the American Society for Mass Spectrometry

Volumn 22, Issue 11, 2011, Pages 1906-1915

  Kan, Zhong Yuan ^a   Mayne, Leland ^a   Sevugan Chetty, Palaniappan ^b   Englander, S Walter ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

Author keywords

HDX; Hydrogen exchange; Proteins

Indexed keywords

COMPUTER PROGRAM; DESKTOP COMPUTER; FUNCTIONAL PROPERTIES; H-D EXCHANGE; HDX; HIGH RESOLUTION; HYDROGEN EXCHANGE; MANUAL CHECKING; MASS SPECTRA; MULTI-MODAL; OPEN SOURCES; OPERATOR INTERVENTIONS; PEPTIDE FRAGMENTS; PROCESS DATA; STEP-BY-STEP; STRUCTURAL HETEROGENEITY; TIME COURSE; TIME POINTS;

DATA REDUCTION; HYDROGEN; ISOTOPES; MASS SPECTROMETERS; MASS SPECTROMETRY;

PEPTIDES;

PEPTIDE FRAGMENT;

ARTICLE; AUTOMATION; BIOINFORMATICS; CHROMATOGRAPHY; COMPUTER PROGRAM; DATA ANALYSIS; DYNAMICS; INFORMATION PROCESSING; LEARNING ALGORITHM; MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTON TRANSPORT; STATIC ELECTRICITY; TANDEM MASS SPECTROMETRY;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DEUTERIUM EXCHANGE MEASUREMENT; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; REPRODUCIBILITY OF RESULTS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 80755144074     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0236-3     Document Type: Article

References (14)

1. Mayne, L.; Kan, Z.; Chetty, SP.; Ricciuti, A.; Walters, BT.; Englander, S. W. Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation/mass spectrometry method. J. Am. Soc. Mass Spectrom. (2011). doi: 10.1007/s13361-011-0235-4
2. JJ Englander C Del Mar W Li SW Englander JS Kim DD Stranz Y Hamuro VL Woods 2003 Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry Proc. Natl. Acad. Sci. USA 100 7057 7062 10.1073/pnas.1232301100 1:CAS:528:DC%2BD3sXkslOntbY%3D (Pubitemid 36706392)
3. GW Slysz CA Baker BM Bozsa A Dang AJ Percy M Bennett DC Schriemer 2009 Hydra: Software for tailored processing of H/D exchange data from MS or tandem MS analyses Bmc Bioinformatics 10 162 10.1186/1471-2105-10-162
4. BD Pascal MJ Chalmers SA Busby PR Griffin 2009 HD desktop: An integrated platform for the analysis and visualization of H/D exchange data J. Am. Soc. Mass Spectrom. 20 601 610 10.1016/j.jasms.2008.11.019 1:CAS:528: DC%2BD1MXjs1ansbw%3D
5. Pascal, B. D.; Chalmers, M. J.; Busby, S. A.; Mader, C. C.; Southern, M. R.; Tsinoremas, N. F.; Griffin, P. R. The deuterator: Software for the determination of backbone amide deuterium levels from H/D exchange MS data. Bmc Bioinformatics 8, 156 (2007).
6. Nikamanon, P.; Pun, E.; Chou, W.; Koter, M. D.; Gershon, P. D. Tof2H. A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. Bmc Bioinformatics 9, 387 (2008).
7. XH Lou M Kirchner BY Renard U Kothe S Boppel C Graf CT Lee JAJ Steen H Steen MP Mayer FA Hamprecht 2010 Deuteration distribution estimation with improved sequence coverage for HX/MS experiments Bioinformatics 26 1535 1541 10.1093/bioinformatics/btq165 1:CAS:528:DC%2BC3cXnsVOksbw%3D
8. DD Weis TE Wales JR Engen M Hotchko LF Ten Eyck 2006 Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis J. Am. Soc. Mass Spectrom. 17 1498 1509 10.1016/j.jasms.2006.05.014 1:CAS:528:DC%2BD28XhtFersL3J (Pubitemid 44635272)
9. 2H exchange mass spectrometry (DXMS) J. Mol. Biol. 327 1065 1076 10.1016/S0022-2836(03)00234-1 1:CAS:528:DC%2BD3sXitlWgtr8%3D (Pubitemid 36363713)
10. 2H mass spectrometry experiments Protein Sci 15 583 601 10.1110/ps.051774906 1:CAS:528:DC%2BD28XitlGlur8%3D
11. M Palmblad J Buijs P Hakansson 2001 Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions J. Am. Soc. Mass Spectrom. 12 1153 1162 10.1016/S1044-0305(01)00301-4 1:CAS:528:DC%2BD3MXotFynt7w%3D (Pubitemid 34552641)
12. JK Chik JLV Graaf DC Schriemer 2006 Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data Anal. Chem. 78 207 214 10.1021/ac050988l 1:CAS:528:DC%2BD2MXht1WisLzF (Pubitemid 43050156)
13. A Kreshuk M Stankiewicz X Lou M Kirchner FA Hamprecht MP Mayer 2011 Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HEXICON Int. J. Mass Spectrom. 302 125 131 10.1016/j.ijms.2010.08.025 1:CAS:528:DC%2BC3MXkslGrurs%3D
14. Y Bai JS Milne L Mayne SW Englander 1993 Primary structure effects on peptide group hydrogen exchange Proteins 17 75 86 10.1002/prot.340170110 1:CAS:528:DyaK2cXitl2nu74%3D (Pubitemid 23261059)