protamine sulfate. Rapid Commun Mass Spectrom 22:2423–2428
11. Roberts VA, Pique ME, Hsu S et al (2012)
Combining HD exchange mass spectroscopy
and computational docking reveals extended
DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res 40:6070–6081
12. Graham BW, Tao Y, Dodge KL et al (2016)
DNA interactions probed by hydrogendeuterium exchange (HDX) Fourier transform
ion cyclotron resonance mass spectrometry
confirm external binding sites on the minichromosomal maintenance (MCM) helicase. J Biol
Chem 291:12467–12480
13. Boura E, Silhan J, Herman P et al (2007) Both
the N-terminal loop and wing W2 of the forkhead domain of transcription factor Foxo4 are
important for DNA binding. J Biol Chem
282:8265–8275
14. Slavata L, Chmelik J, Kavan D et al (2019)
MS-based approaches enable the structural
characterization of transcription factor/DNA
response element complex. Biomol Ther 9:
E535
15. Anbanandam A, Albarado DC, Nguyen CT
et al (2006) Insights into transcription
enhancer factor 1 (TEF-1) activity from the
solution structure of the TEA domain. Proc
Natl Acad Sci U S A 103:17225–17230
16. Wang L, Pan H, Smith DL (2002) Hydrogen
exchange-mass spectrometry. Mol Cell Proteomics 1:132–138
17. Kadek A, Mrazek H, Halada P et al (2014)
Aspartic protease nepenthesin-1 as a tool for
digestion in hydrogen/deuterium exchange
mass spectrometry. Anal Chem 86:4287–4294
18. Kochert BA, Iacob RE, Wales TE et al (2018)
Hydrogen-deuterium exchange mass spectrometry to study protein complexes. In:
Methods in molecular biology (Clifton, N.J.).
Humana Press, New York, NY, pp 153–171
19. Rand KD, Zehl M, Jensen ON et al (2009)
Protein hydrogen exchange measured at
single-residue resolution by electron transfer
dissociation mass spectrometry. Anal Chem
81:5577–5584
20. Mistarz UH, Bellina B, Jensen PF et al (2018)
UV Photodissociation mass spectrometry accurately localize sites of backbone Deuteration in
peptides. Anal Chem 90:1077–1080
21. Mayne L, Kan ZY, Sevugan Chetty P et al
(2011) Many overlapping peptides for protein
hydrogen exchange experiments by the fragment separation-mass spectrometry method. J
Am Soc Mass Spectrom 22:1898–1905
22. Kan Z-Y, Walters BT, Mayne L et al (2013)
Protein hydrogen exchange at residue
resolution by proteolytic fragmentation mass
spectrometry analysis. Proc Natl Acad Sci U S
A 110:16438–16443
23. Cravello L, Lascoux D, Forest E (2003) Use of
different proteases working in acidic conditions
to improve sequence coverage and resolution
in hydrogen/deuterium exchange of large proteins. Rapid Commun Mass Spectrom
17:2387–2393
24. Rey M, Man P, Brandolin G et al (2009)
Recombinant immobilized rhizopuspepsin as
a new tool for protein digestion in hydrogen/
deuterium exchange mass spectrometry. Rapid
Commun Mass Spectrom 23:3431–3438
25. Kadek A, Tretyachenko V, Mrazek H et al
(2014) Expression and characterization of
plant aspartic protease nepenthesin-1 from
Nepenthes gracilis. Protein Expr Purif
95:121–128
26. Yang M, Hoeppner M, Rey M et al (2015)
Recombinant Nepenthesin II for hydrogen/
deuterium exchange mass spectrometry. Anal
Chem 87:6681–6687
27. Kadek A, Kavan D, Marcoux J et al (2017)
Interdomain electron transfer in cellobiose
dehydrogenase is governed by surface electrostatics. Biochim Biophys Acta Gen Subj
1861:157–167
28. Moroco JA, Engen JR (2015) Replication in
bioanalytical studies with HDX MS: aim as
high as possible. Bioanalysis 7:1065–1067
29. Houde D, Berkowitz SA, Engen JR (2011)
The utility of hydrogen/deuterium exchange
mass spectrometry in biopharmaceutical comparability studies. J Pharm Sci 100:2071–2086
30. Wales TE, Poe JA, Emert-Sedlak L et al (2016)
Hydrogen exchange mass spectrometry of
related proteins with divergent sequences: a
comparative study of HIV-1 Nef allelic variants. J Am Soc Mass Spectrom 27:1048–1061
31. Pascal BD, Willis S, Lauer JL et al (2012)
HDXWorkbench: software for the analysis of
H/D exchange MS data. J Am Soc Mass Spectrom 23:1512–1521
32. Guttman M, Weis DD, Engen JR et al (2013)
Analysis of overlapped and noisy hydrogen/
deuterium exchange mass spectra. J Am Soc
Mass Spectrom 24:1906–1912
33. Lindner R, Lou X, Reinstein J et al (2014)
Hexicon 2: automated processing of
hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. J Am Soc Mass Spectrom
25:1018–1028
34. Rey M, Sarpe V, Burns KM et al (2014) Mass
spec studio for integrative structural biology.
Structure 22:1538–1548
218
Ruzena Filandrova et al.
11. Roberts VA, Pique ME, Hsu S et al (2012)
Combining HD exchange mass spectroscopy
and computational docking reveals extended
DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res 40:6070–6081
12. Graham BW, Tao Y, Dodge KL et al (2016)
DNA interactions probed by hydrogendeuterium exchange (HDX) Fourier transform
ion cyclotron resonance mass spectrometry
confirm external binding sites on the minichromosomal maintenance (MCM) helicase. J Biol
Chem 291:12467–12480
13. Boura E, Silhan J, Herman P et al (2007) Both
the N-terminal loop and wing W2 of the forkhead domain of transcription factor Foxo4 are
important for DNA binding. J Biol Chem
282:8265–8275
14. Slavata L, Chmelik J, Kavan D et al (2019)
MS-based approaches enable the structural
characterization of transcription factor/DNA
response element complex. Biomol Ther 9:
E535
15. Anbanandam A, Albarado DC, Nguyen CT
et al (2006) Insights into transcription
enhancer factor 1 (TEF-1) activity from the
solution structure of the TEA domain. Proc
Natl Acad Sci U S A 103:17225–17230
16. Wang L, Pan H, Smith DL (2002) Hydrogen
exchange-mass spectrometry. Mol Cell Proteomics 1:132–138
17. Kadek A, Mrazek H, Halada P et al (2014)
Aspartic protease nepenthesin-1 as a tool for
digestion in hydrogen/deuterium exchange
mass spectrometry. Anal Chem 86:4287–4294
18. Kochert BA, Iacob RE, Wales TE et al (2018)
Hydrogen-deuterium exchange mass spectrometry to study protein complexes. In:
Methods in molecular biology (Clifton, N.J.).
Humana Press, New York, NY, pp 153–171
19. Rand KD, Zehl M, Jensen ON et al (2009)
Protein hydrogen exchange measured at
single-residue resolution by electron transfer
dissociation mass spectrometry. Anal Chem
81:5577–5584
20. Mistarz UH, Bellina B, Jensen PF et al (2018)
UV Photodissociation mass spectrometry accurately localize sites of backbone Deuteration in
peptides. Anal Chem 90:1077–1080
21. Mayne L, Kan ZY, Sevugan Chetty P et al
(2011) Many overlapping peptides for protein
hydrogen exchange experiments by the fragment separation-mass spectrometry method. J
Am Soc Mass Spectrom 22:1898–1905
22. Kan Z-Y, Walters BT, Mayne L et al (2013)
Protein hydrogen exchange at residue
resolution by proteolytic fragmentation mass
spectrometry analysis. Proc Natl Acad Sci U S
A 110:16438–16443
23. Cravello L, Lascoux D, Forest E (2003) Use of
different proteases working in acidic conditions
to improve sequence coverage and resolution
in hydrogen/deuterium exchange of large proteins. Rapid Commun Mass Spectrom
17:2387–2393
24. Rey M, Man P, Brandolin G et al (2009)
Recombinant immobilized rhizopuspepsin as
a new tool for protein digestion in hydrogen/
deuterium exchange mass spectrometry. Rapid
Commun Mass Spectrom 23:3431–3438
25. Kadek A, Tretyachenko V, Mrazek H et al
(2014) Expression and characterization of
plant aspartic protease nepenthesin-1 from
Nepenthes gracilis. Protein Expr Purif
95:121–128
26. Yang M, Hoeppner M, Rey M et al (2015)
Recombinant Nepenthesin II for hydrogen/
deuterium exchange mass spectrometry. Anal
Chem 87:6681–6687
27. Kadek A, Kavan D, Marcoux J et al (2017)
Interdomain electron transfer in cellobiose
dehydrogenase is governed by surface electrostatics. Biochim Biophys Acta Gen Subj
1861:157–167
28. Moroco JA, Engen JR (2015) Replication in
bioanalytical studies with HDX MS: aim as
high as possible. Bioanalysis 7:1065–1067
29. Houde D, Berkowitz SA, Engen JR (2011)
The utility of hydrogen/deuterium exchange
mass spectrometry in biopharmaceutical comparability studies. J Pharm Sci 100:2071–2086
30. Wales TE, Poe JA, Emert-Sedlak L et al (2016)
Hydrogen exchange mass spectrometry of
related proteins with divergent sequences: a
comparative study of HIV-1 Nef allelic variants. J Am Soc Mass Spectrom 27:1048–1061
31. Pascal BD, Willis S, Lauer JL et al (2012)
HDXWorkbench: software for the analysis of
H/D exchange MS data. J Am Soc Mass Spectrom 23:1512–1521
32. Guttman M, Weis DD, Engen JR et al (2013)
Analysis of overlapped and noisy hydrogen/
deuterium exchange mass spectra. J Am Soc
Mass Spectrom 24:1906–1912
33. Lindner R, Lou X, Reinstein J et al (2014)
Hexicon 2: automated processing of
hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. J Am Soc Mass Spectrom
25:1018–1028
34. Rey M, Sarpe V, Burns KM et al (2014) Mass
spec studio for integrative structural biology.
Structure 22:1538–1548
218
Ruzena Filandrova et al.