35. mMass is a freely available software suitable for processing of
single spectra. It can be obtained from http://mmass.org/.
36. There are also other ways of data processing. Similar to mMass
processing is the use of the MagTran program written by
Zhongqi Zhang. Also, HX-Express2 (http://www.hxms.
com/HXExpress/) can be used for this purpose [32]. The
advantage of HX-Express 2 is its ability to detect and dissect
bimodal isotopic envelopes that are typical for mixed
EX1/EX2 exchange kinetics.
37. Script can be obtained at http://peterslab.org/downloads.php
under HDX tools section.
38. To run Python scripts directly, install python on your PC
(https://www.python.org/downloads/) and include it in the
PATH variable of the operating system (version used here was
2.7.12).
39. Script was written by Robert L. Campbell and is available here:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/.
Acknowledgments
Czech Science Foundation projects 16-24309S and 16-20860S are
gratefully acknowledged. Additional support was obtained from
EU/MEYS projects BioCeV (CZ.1.05/1.1.00/02.0109) and
NPU II (LQ1604). R.F. also thanks Charles University Grant
Agency (project 1618218) and SVV260427/2019.
References
1. Katta V, Chait BT, Carr S (1991) Conformational changes in proteins probed by hydrogenexchange electrospray-ionization mass spectrometry. Rapid Commun Mass Spectrom
5:214–217
2. Zhang Z, Smith DL (1993) Determination of
amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 2:522–531
3. Bai YW, Milne JS, Mayne L et al (1993) Primary structure effects on peptide group
hydrogen-exchange. Proteins 17:75–86
4. Engen JR, Wales TE (2015) Analytical aspects
of hydrogen exchange mass spectrometry.
Annu Rev Anal Chem 8:127–148
5. Oganesyan I, Lento C, Wilson DJ (2018) Contemporary hydrogen deuterium exchange mass
spectrometry. Methods 144:27–42
6. Sorokin VA, Gladchenko GO, Valeev VA
(1986) DNA protonation at low ionic strength
of solution. Die Makromol Chemie
187:1053–1063
7. Ma L, Fitzgerald MC (2003) A new H/D
exchange- and mass spectrometry-based
method for thermodynamic analysis of
protein-DNA interactions. Chem Biol
10:1205–1213
8. Sperry JB, Wilcox JM, Gross ML (2008)
Strong anion exchange for studying proteinDNA interactions by H/D exchange mass
spectrometry. J Am Soc Mass Spectrom
19:887–890
9. Sperry JB, Shi X, Rempel DL et al (2008) A
mass spectrometric approach to the study of
DNA-binding proteins: interaction of human
TRF2 with telomeric DNA. Biochemistry
47:1797–1807
10. Poliakov A, Jardine P, Prevelige PE (2008)
Hydrogen/deuterium exchange on protein
solutions containing nucleic acids: utility of
HDX-MS of Protein-DNA Complexes
217
single spectra. It can be obtained from http://mmass.org/.
36. There are also other ways of data processing. Similar to mMass
processing is the use of the MagTran program written by
Zhongqi Zhang. Also, HX-Express2 (http://www.hxms.
com/HXExpress/) can be used for this purpose [32]. The
advantage of HX-Express 2 is its ability to detect and dissect
bimodal isotopic envelopes that are typical for mixed
EX1/EX2 exchange kinetics.
37. Script can be obtained at http://peterslab.org/downloads.php
under HDX tools section.
38. To run Python scripts directly, install python on your PC
(https://www.python.org/downloads/) and include it in the
PATH variable of the operating system (version used here was
2.7.12).
39. Script was written by Robert L. Campbell and is available here:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/.
Acknowledgments
Czech Science Foundation projects 16-24309S and 16-20860S are
gratefully acknowledged. Additional support was obtained from
EU/MEYS projects BioCeV (CZ.1.05/1.1.00/02.0109) and
NPU II (LQ1604). R.F. also thanks Charles University Grant
Agency (project 1618218) and SVV260427/2019.
References
1. Katta V, Chait BT, Carr S (1991) Conformational changes in proteins probed by hydrogenexchange electrospray-ionization mass spectrometry. Rapid Commun Mass Spectrom
5:214–217
2. Zhang Z, Smith DL (1993) Determination of
amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 2:522–531
3. Bai YW, Milne JS, Mayne L et al (1993) Primary structure effects on peptide group
hydrogen-exchange. Proteins 17:75–86
4. Engen JR, Wales TE (2015) Analytical aspects
of hydrogen exchange mass spectrometry.
Annu Rev Anal Chem 8:127–148
5. Oganesyan I, Lento C, Wilson DJ (2018) Contemporary hydrogen deuterium exchange mass
spectrometry. Methods 144:27–42
6. Sorokin VA, Gladchenko GO, Valeev VA
(1986) DNA protonation at low ionic strength
of solution. Die Makromol Chemie
187:1053–1063
7. Ma L, Fitzgerald MC (2003) A new H/D
exchange- and mass spectrometry-based
method for thermodynamic analysis of
protein-DNA interactions. Chem Biol
10:1205–1213
8. Sperry JB, Wilcox JM, Gross ML (2008)
Strong anion exchange for studying proteinDNA interactions by H/D exchange mass
spectrometry. J Am Soc Mass Spectrom
19:887–890
9. Sperry JB, Shi X, Rempel DL et al (2008) A
mass spectrometric approach to the study of
DNA-binding proteins: interaction of human
TRF2 with telomeric DNA. Biochemistry
47:1797–1807
10. Poliakov A, Jardine P, Prevelige PE (2008)
Hydrogen/deuterium exchange on protein
solutions containing nucleic acids: utility of
HDX-MS of Protein-DNA Complexes
217