Akashi’s Group: Structural
Biology by Mass Spectrometry
Publication (2001~) Original articles and reviews in English
2024
1.
*Hiraoka, K., Usmanov, D., Ninomiya, S., Rankin-Turner, S., Akashi,
S. “Pulsed Nano-electrospray Ionization Applied to Solutions of Angiotensin
II, Bradykinin, and Gramicidin S in Water/Acetonitrile (1/1) with the Addition
of 1% Acetic Acid and 10 mM Ammonium Acetate.” Mass Spectrom.,
(Tokyo), 13(1), A0157 (2024).
2.
Konuma, T., Takai, T., Tsuchiya, C., Nishida, M., Hashiba,
M., Yamada, Y., Nagadoi, A., Chikaishi, E., Akagi, K., Akashi, S., Yamazaki, T., Akutsu,
H., *Ikegami, T. “NMR analysis of the homodimeric
structure of a D-Ala-D-Ala metallopeptidase, VanX,
from vancomycin-resistant bacteria.” Protein Sci., 33, e5002
(2024).
3.
Suzuki, N., *Konuma, T., Ikegami, T., *Akashi, S.,
“Biophysical insights into the dimer formation of human Sirtuin 2.” Protein
Sci., 3, e4994 (2024).
4.
*Hiraoka, K., Ninomiya, S., Rankin-Turner, S., Akashi, S.,
“Sodiation of melittin, cytochrome c, and ubiquitin
studied by electrospray mass spectrometry: stabilities of α-helix and β-sheet
in basic solutions.” Int. J. Mass Spectrom.,
498, 117212 (2024).
5.
*Ninomiya, S., Rankin-Turner, S., Akashi, S.,
*Hiraoka, K., “Solvent effect on the detection of peptides and proteins by nanoelectrospray ionization mass spectrometry: Anomalous
behavior of aqueous 2-propanol.” Anal. Biochem.,
688, 115461 (2024).
2023
6.
*Saikusa, K., Asakawa, D.,
Fuchigami, S., Akashi, S., “Evaluation for Ion Heating of H2A-H2B dimer
in Ion Mobility Spectrometry Mass Spectrometry.” Mass Spectrom.
(Tokyo), 12, A0131 (2023).
7.
*Hiraoka, K., Akashi, S., Rankin-Turner, S.,
Ninomiya, S., Site-specific deprotonation/sodiation
of gramicidin S studied by electrospray ionization/mass spectrometry. Int.
J. Mass Spectrom., 493, 117135 (2023).
8.
Ishimoto, N., Park, J.-H., Kawakami, K., Ikuta, T., Tajiri,
M., Mizutani, K., Akashi, S., Tame, J.R.H., Inoue, A., *Park, S.-Y.
Structural basis of chemokine receptor 1 ligand binding and activation.” Nat.
Commun., 14, 4107 (2023).
9.
Tajiri, M., Imai, S., Konuma, T., Shimamoto, K., Shimada, I., *Akashi,
S. “Evaluation of drug responses to human β2AR using native mass
spectrometry.” ACS Omega, 8, 24544-24551 (2023).
10.
*Liu, N., Konuma, T., Sharma, R., Wang, D., Zhao, N.,
Cao, L., Ju, Y., Liu, D., Wang, S., Bosch, A., Sun, Y., Zhang, S., Ji, D., Nagatoishi, S., Suzuki, N., Kikuchi, M., Wakamori, M., Zhao, C., Ren, C., Zhou, T.J., Xu, Y., Meslamani, J., Fu, S., Umehara, T., Tsumoto, K., Akashi,
S., Zeng, L., Roeder, R.G., Walsh, M.J., *Zhang, Q., *Zhou, M.M.” Histone
H3 lysine 27 crotonylation mediates gene transcriptional repression in
chromatin.” Mol. Cell, 83, 2206–2221 (2023).
11.
*Hiraoka, K., Usmanov, D. T., Ninomiya, S., Rankin-Turner,
S., Akashi, S. “Site-specific sodiation of
peptides studied by pulsed nanoelectrospray
ionization.” Int. J. Mass Spectrom., 490,
117073 (2023).
2022
12.
Azegami, N., Taguchi, N., Suzuki,
N., Sakata, Y., *Konuma, T., *Akashi, S. “Native mass
spectrometry of BRD4 bromodomains linked to a long disordered region.” Mass
Spectrom. (Tokyo), A0110 (2022).
13.
Nozawa, K., Takizawa, Y., Pierrakeas,
L., Saikusa, K., Akashi, S., Luk, E., *Kurumizaka, H. “Cryo-electron microscopy structure of the
H3-H4 octasome without histones H2A and H2B.” Proc.
Nat. Acad. Sci. USA, 119, e2206542119 (2022).
14.
Tanaka, T., Ekimoto, T., Nagatomo, M., Neyazaki,
M., Shimoji, E., Yamane, T., Kanagawa, S., Oi, R.,
Mihara, E., Takagi, J., Akashi, S., Ikeguchi,
M., *Nogi, T. “Hybrid in vitro/in silico analysis of low-affinity
protein-protein interactions that regulate signal transduction by Sema6D.” Protein
Sci., 31, e4452 (2022).
15.
Imaizumi, Y., Takanuki, K.,
Miyake, T., Takemoto, M., Hirata, K., Hirose, M., Oi, R., Kobayashi, T.,
Miyoshi, K., Aruga, R., Yokoyama, T., Katagiri, S.,
Matsuura, H., Iwasaki, K., Kato, T., Kaneko, M. K., Kato, Y., Tajiri, M.,
Akashi, S., Nureki, O., *Hizukuri,
Y., *Akiyama, Y., *Nogi, T. “Mechanistic insights into intramembrane
proteolysis by E. coli site-2 protease homolog RseP.”
Sci Adv., 8, eabp9011 (2022).
16.
Tajiri, M., Aoki, H., Shintani, A., Sue, K., *Akashi, S.,
*Furukawa, Y. “Metal distribution in Cu/Zn-superoxide dismutase revealed by
native mass spectrometry.” Free Radic. Biol. Med., 183,
60-68 (2022).
17.
*Hiraoka, K., Ninomiya, S., Rankin-Turner, S., Akashi, S.
“Comparative study of H3O+ (aq)
and NH4+ (aq) on
electrophoresis, protonating ability, and sodiation
of proteins.” Int. J. Mass Spectrom., 471,
116728 (2022).
2021
18.
Mylemans, B, Laier, I., Kamata, K., Akashi,
S., Noguchi, H., Tame, J.R.H., *Voet, A.R.D. “Structural plasticity of a
designer protein sheds light on β-propeller protein evolution.” FEBS J., 288, 530-545 (2021).
19.
Sakamoto, W., Azegami,
N., Konuma, T., *Akashi, S. “Single-Cell Native Mass
Spectrometry of Human Erythrocytes.” Anal.
Chem., 93, 6583-6588 (2021).
2020
20.
*Saikusa, K., Hidaka, H., Izumi,
S., Akashi, S. “Mass spectrometric characterization of histone H3
isolated from in-vitro reconstituted and acetylated nucleosome core particle.” Mass Spectrom.
(Tokyo), 9, A0090 (2020).
21.
Takano, K., Arai, S., Sakamoto, S., Ushijima, H., Ikegami,
T., Saikusa, K., Konuma, T., Hamachi. I.,
*Akashi, S. “Screening of Protein-Ligand Interactions under Crude
Conditions by Native Mass Spectrometry.” Anal.
Bioanal. Chem., 412, 4037-4043 (2020). Cover article.
22.
*Saikusa, K., Kato, D., Nagadoi, A., Kurumizaka, H., Akashi,
S. “Native mass spectrometry of protein and DNA complexes prepared in
non-volatile buffers.” J. Am. Soc.
Mass Spectrom., 31, 711-718 (2020).
2019
23.
Ushijima, H., Maekawa, R., Igarashi,E., *Akashi, S. “Rapid and
definitive analysis of in vitro DNA methylation by nanoelectrospray
ionization mass spectrometry.” J. Am.
Soc. Mass Spectrom., 30, 2335-2346 (2019). Open Access.
24.
*Mayanagi, K., Saikusa,
K., Miyazaki, N., Akashi, S., Iwasaki, K., Nishimura, Y., *Morikawa, K,
*Tsunaka, Y. “Structural visualization of key steps
in nucleosome reorganization by human FACT.” Sci. Rep., 9, 10183
(2019).
25.
Tamura, R., Oi, R., Akashi, S., Kaneko, M.K., Kato,
Y., *Nogi, T., “Application of the NZ-1 Fab as a crystallization chaperone for
PA tag-inserted target proteins.” Protein
Sci., 28, 823-836 (2019).
2018
26.
Hyodo, F., Sho, T., Basudev, M., Fujita, K., Tachibana, Y., Akashi,
S., Mano, M., Hishikawa, Y., Matsuo, M., Nakaji,
T., *Ueno, T., “Photo-induced In Vivo MRI Imaging with Rapid CO Release from an
MnCO-Protein Needle Composite.” Chemistry, 24, 11578-11583 (2018).
27.
Saikusa, K., Osakabe,
A., Kato, D., Fuchigami, S., Nagadoi, A., Nishimura,
Y., Kurumizaka, H., *Akashi, S., “Structural
Diversity of Nucleosomes Characterized by Native Mass Spectrometry.” Anal. Chem., 90, 8217-8226 (2018).
28.
Suzuki, R., Sakakura, M., Mori,
M., Fujii, M., Akashi, S., *Takahashi, H. “Methyl-selective isotope
labeling using a-ketoisovalerate
for the yeast Pichia pastoris recombinant protein expression system”, J. Biomol. NMR,
71, 213-223 (2018).
29.
Meyer, K., Addy, C., Akashi, S., Roper, D.I., *Tame,
J.R.H. “The crystal structure and oligomeric form of Escherichia coli L,D-carboxypeptidase A.” Biochem. Biophys. Res.
Commun. 499, 594-599 (2018).
30.
*Amino, Y., Wakabayashi, H., Akashi, S., Ishiwatari, Y. “Structural Analysis, CaSR
Activity Determination, and Taste Evaluation of γ-Glutamyl Peptides Comprising
Sulfur-Containing Amino Acids.” Biosci. Biotechnol. Biochem. 82, 383-394 (2018).
2017
31.
Kato, D., Osakabe, A., Arimura,
Y., Mizukami, Y., Horikoshi, N., Saikusa, K., Akashi,
S., Nishimura, Y., Park, S.-Y., Nogami, J., Maehara, K., Ohkawa, Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama,
M., *Kurumizaka, H., “Crystal structure of the
overlapping dinucleosome composed of hexasome and octasome.” Science, 356, 205-208 (2017).
32.
Nagae, M., Mishra, S.K., Neyazaki,
M., Oi, R., Ikeda, A., Matsugaki, N., Akashi, S.,
Manya, H., Mizuno, M., Yagi, H., Kato, K., Senda, T., Endo, T., Nogi, T.,
*Yamaguchi, Y. “3D structural analysis of Protein O-Mannosyl
Kinase POMK, a causative gene product of dystroglycanopathy.” Genes Cells, 22, 348–359 (2017).
2016
33.
Akashi, S., *Downard, K.M., “Effect of Charge on the Conformation of
Highly Basic Peptides including the Tail Regions of Histone Proteins by Ion
Mobility Mass Spectrometry”. Anal. Bioanal. Chem., 408, 6637-6648 (2016). Cover article.
34.
Lee, S.J.C., Choi, T.S. Lee, J.W., Lee, H.J., Mun D.-G., Akashi,
S., Lee, S.-W., *Lim, M.H., *Kim, H.I. “Structure and assembly mechanisms
of toxic human islet amyloid polypeptide oligomers associated with copper.” Chem. Sci., 7, 5398-5406 (2016).
35.
Ohtomo, H., Akashi, S.,
Moriwaki, Y., Okuwaki, M., Osakabe,
A., Nagata, K., Kurumizaka, H., *Nishimura, Y. “The
C-terminal acidic domain of histone chaperone human NAP1 is an efficient
binding-assistant for histone H2A-H2B but not H3-H4.” Genes Cells, 21,
252-263 (2016).
36.
*Tsuchida, D., Yamazaki, K, *Akashi, S.
“Comprehensive Characterization of Relationship Between Higher-Order Structure
and FcRn Binding Affinity of Stress-Exposed
Monoclonal Antibodies.” Pharm. Res.,
33, 994-1002 (2016).
2015
37.
Saikusa, K., Shimoyama. S., Asano,
Y., Nagadoi, A., Sato, M., Kurumizaka,
H., Nishimura, Y., *Akashi, S. “Charge-neutralization effect of the tail
regions on the histone H2A/H2B dimer structure.” Protein Sci., 24,
1224-1231 (2015).
38.
Saikusa, K., Nagadoi,
A., Hara, K., Fuchigami, S., Kurumizaka, H.,
Nishimura, Y., *Akashi, S. “Mass spectrometric approach for
characterizing the disordered tail regions of the histone H2A/H2B dimer.” Anal. Chem., 87, 2220-2227 (2015).
39.
*Downard, K.M., Maleknia, S., Saikusa, K., Akashi, S. “Stability of the βB2B3
Crystallin Heterodimer to Increased Oxidation by Radical Probe and Ion Mobility
Mass Spectrometry.” J. Struct. Biol.,
189, 20-27 (2015).
2014
40.
*Tsuchida, D., Yamazaki, K, *Akashi, S.
“Characterization of stress-exposed Granulocyte Colony Stimulating Factor
characterized using ELISA and hydrogen/deuterium exchange mass spectrometry.” J. Am. Soc. Mass Spectrom.,
25, 1747-1754 (2014).
41.
Sugiyama, K., Iyori, M., Sawaguchi, A., Akashi, S., Tame, J.R., *Park, S.Y.,
*Yoshida, S. “The crystal structure of the active domain of Anopheles
anti-platelet protein, a powerful anti-coagulant, in complex with an antibody.”
J. Biol. Chem., 289, 16303-16312 (2014).
2013
42.
Azegami, N., Saikusa
K., Todokoro Y, Kurumizaka
H, Nagadoi A, *Nishimura Y, *Akashi S.
“Conclusive evidence of the reconstituted hexasome
proved by native mass spectrometry.” Biochemistry,
52, 5155-5157 (2013). Highlighted
article.
43.
Saikusa, K., Fuchigami, S., Takahashi,
K., Asano, Y., Nagadoi, A., Tachiwana, H., Kurumizaka, H., Ikeguchi, M., *Nishimura, Y., *Akashi, S. “Gas-phase
structure of the histone multimers characterized by ion mobility mass
spectrometry and molecular dynamics simulation.” Anal. Chem., 85,
4165-4171 (2013).
44.
Saikusa, K., Kuwabara, N., Kokabu, Y., Inoue, Y., Sato, M., Iwasaki, H., Shimizu, T., Ikeguchi, M., *Akashi, S. “Characterisation
of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility
mass spectrometry and small-angle X-ray scattering.” Analyst, 138,
1441-1449 (2013).
2012
45.
Yoshida, H., Kawai, F., Obayashi, E., Akashi, S.,
Roper, D.I., Tame, J.R., *Park, S.Y. “Crystal Structures of Penicillin-Binding
Protein 3 (PBP3) from Methicillin-Resistant Staphylococcus aureus in the Apo
and Cefotaxime-Bound Forms.” J. Mol.
Biol., 423, 351-364 (2012).
46.
*Okuwaki, M., Sumi, A., Hisaoka, M., Saotome-Nakamura, A., Akashi, S.,
Nishimura, Y., Nagata, K. “Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin
family proteins NPM1, NPM2, and NPM3 during sperm chromatin remodeling.” Nuleic Acid Res., 40, 4861-4878 (2012).
47.
*Downard, K.M., Maleknia, S.D., Akashi,
S. “Impact of Limited Oxidation on Protein Ion Mobility and Structure of
Importance to Footprinting by Radical Probe Mass
Spectrometry.” Rapid Commun. Mass Spectrom., 26, 226-230 (2012).
2011
48.
Kokabu, Y., Murayama, Y.,
Kuwabara, N., Oroguchi, T., Hashimoto, H., Tsutsui,
Y., Nozaki, N., Akashi, S., Unzai, S.,
Shimizu, T., Iwasaki, H., Sato, M., *Ikeguchi, M.
“Fission yeast Swi5-Sfr1 complex, an activator of Rad51 recombinase, forms an
extremely elongated Dogleg-shaped structure.” J. Biol. Chem., 286, 43569-43576 (2011).
49.
*Downard, K.M., Kokabu, Y., Ikeguchi, M., Akashi, S., ”Homology Modelled
Structure of the βB2B3-Crystallin Heterodimer Studied by Ion Mobility and
Radical Probe Mass Spectrometry.” FEBS
J., 278, 4044-4054 (2011).
50.
Horikoshi, N.,Tachiwana, H.,
Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi,
S., Nishimura, Y., Kagawa, W., *Kurumizaka, H.
“Structural and biochemical analyses of the human PAD4 variant encoded by a
functional haplotype gene.” Acta Crystallogr D Biol Crystallogr.
67, 112-118 (2011).
2010
51.
Domann, P.J., Akashi, S., Barbas, C., Huang, L., Lau,
W., Legido-Quigley, C., McClean, S., Neusüss, C., Perrett, D., Quaglia, M., Rapp, E., Smallshaw, L., Smith, N.W., Smyth, W.F., *Taylor, C.F.;
Minimum Information About a Proteomics Experiment (MIAPE). “Guidelines for
reporting the use of capillary electrophoresis in proteomics.” Nat. Biotechnol.,
28, 654-655 (2010).
52.
Shimoyama, S., Nagadoi,
A., Tachiwana, H., Yamada, M., Sato, M., Kurumizaka, H., *Nishimura, Y., *Akashi, S. “Deimination stabilizes histone H2A/H2B
dimers as revealed by electrospray ionization mass spectrometry.” J. Mass Spectrom.,
45, 900-908 (2010).
53.
Hara, K., *Hashimoto H., Murakumo,
Y., Kobayashi, S., Kogame, T., Unzai,
S., Akashi, S., Takeda, S., Shimizu, T., Sato, M. “Crystal structure of
human REV7 in complex with a human REV3 fragment and structural implication of
the interaction between DNA polymerase z and REV1” J. Biol. Chem., 285, 12299-12307 (2010).
54.
Oda, T., Hashimoto, H., Kuwabara, N., Akashi, S.,
Hayashi, K., Kojima, C., Wong, H.L., Kawasaki, T., Shimamoto, K., Sato, M.,
*Shimizu, T. “The structure of the N-terminal regulatory domain of a plant
NADPH oxidase and its functional implications.” J. Biol. Chem., 285,
1435-1445 (2010).
2009
55.
Hara, K., Shimizu, T., Unzai, S., Akashi,
S., Sato, M., *Hashimoto, H. “Purification, crystallization and initial
X-ray diffraction study of human REV7 in complex with a REV3 fragment.” Acta Crystallogr
Sect F Struct Biol Cryst Commun., 65, 1302-1305 (2009).
56.
Miranda, F.F., Iwasaki, K., Akashi, S., Sumitomo, K.,
Kobayashi, M., Yamashita, I., *Tame, J.R., *Heddle, J.G. “A Self-Assembled
Protein Nanotube with High Aspect Ratio.” Small, 5, 2077-2084
(2009).
57.
*Akashi, S., Watanabe, M., Heddle, J.G., Unzai, S., Park, S.Y., *Tame, J.R.H. “RNA and protein
complexes of TRAP characterized by mass spectrometry.” Anal Chem., 81,
2218-2226 (2009).
58.
Watanabe, M., Heddle, J.G., Kikuchi, K., Unzai,
S., Akashi, S., Park, S.Y., *Tame, J.R.H. “The nature of the
TRAP-Anti-TRAP complex.” Proc Nat Acad Sci USA, 106,
2176-2181 (2009).
2008
59.
*Akashi, S., Nagakura,
S., Yamamoto, S., Okuda, M., Ohkuma, Y.,
*Nishimura, Y. “Structural characterization of human general transcription
factor TFIIF in solution.” Protein
Sci., 17, 389-400 (2008).
60.
Sperry, J., Shi, X., Rempel, D., Nishimura, Y., Akashi,
S., *Gross, M. ”A Mass Spectrometric Approach to the Study of DNA-Binding
Proteins: The Interaction of Human
TRF2 with Telomeric DNA.” Biochemistry,
47, 1797-1807 (2008).
61.
Hiraki, T., Shibayama, N., Akashi, S., *Park, S.Y.
”Crystal Structures of the Clock Protein EA4 from the Silkworm Bombyx mori.” J. Mol. Biol., 377, 630-635 (2008).
62.
Shi, X., Takamizawa, A., Nishimura, Y., Hiraoka, K., *Akashi, S.,
“Thermal unfolding of proteins probed by laser spray mass spectrometry.” Rapid Commun. Mass Spectrom.,
22, 1430-1436 (2008).
2007
63.
Nakamura, M., Takamizawa, A., Yamada, H., *Hiraoka, K., Akashi,
S., “Denaturation of a-lactalbumin and ubiquitin
studied by electrospray and laser spray.” Rapid Commun. Mass Spectrom., 21, 1635-1643 (2007).
64.
*Heddle, J.G., Okajima, T., Scott, D.J., Akashi, S.,
Park, S.Y., *Tame, J.R.H. “Dynamic Allostery in the Ring Protein TRAP.” J. Mol. Biol., 371, 154-167 (2007).
2006
65.
*Akashi, S. “Investigation of Molecular Interaction
within Biological Macromolecular Complexes by Mass Spectrometry.” Med. Res. Rev., 26, 339-368 (2006).
66.
Shi, X., Takamizawa, A., Nishimura, Y., Hiraoka, K., *Akashi, S.
”Evaluation of Binding Affinity of Protein–Mutant DNA Complexes in Solution by
Laser Spray Mass Spectrometry.” J. Am.
Soc. Mass Spectrom., 17, 611-620 (2006).
67.
*Akashi, S., Suzuki, K., Arai, A., Yamada, N.,
Suzuki, E.-I., Hirayama, K., Nakamura, S. and Nishimura, Y. “Top-down analysis
of basic proteins by microchip capillary electrophoresis mass spectrometry.” Rapid Commun. Mass Spectrom.,
20, 1932-1938 (2006).
68.
Shi, X., Takamizawa, A., Nishimura, Y., Hiraoka, K., *Akashi, S.
“Stability Analsysis for double-stranded DNA
oligomers and their non-covalent complexes with drugs by laser spray.” J. Mass Spectrom.,
41, 1086-1095 (2006).
2005
69.
Itoh, Y., Unzai, S., Sato, M., Nagadoi, A., Okuda, M., *Nishimura, Y., *Akashi, S.
“Investigation of molecular size of Transcription Factor TFIIE in solution.” Proteins, 61, 633-641 (2005).
70.
*Akashi, S., Osawa, R., and *Nishimura, Y.
“Evaluation of protein-DNA binding affinity by electrospray ionization mass
spectrometry.” J. Am. Soc. Mass Spectrom., 16,
116-125 (2005).
71.
Takamizawa, A., Akashi, S., *Hiraoka, K. ”Comparative
study of laser spray and electrospray using an orthogonal TOF mass
spectrometer.” J. Mass Spectrom. Soc. Jpn. 53, 100-107 (2005).
2004
72.
Takamizawa, A., Itoh, Y., Osawa, R., Iwasaki, N.,
Nishimura, Y, Akashi, S., *Hiraoka, K.” Selective dissociation of
non-covalent bonds in biological molecules by laser spray.” J. Mass Spectrom.
39, 1053-1058 (2004).
2002
73.
*Akashi, S., Takio, K. “Melittin-Diacylphosphatidylcholine
Interaction Examined by Electrospray Ionization Fourier Transform Ion Cyclotron
Resonance Mass Spectrometry.” J. Mass Spectrom. Soc. Jpn. 50, 67-71 (2002).
2001
74.
*Akashi, S., Takio, K. “Structure of Melittin Bound
to Phospholipid Micelles Studied using Hydrogen-Deuterium Exchange and
Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass
Spectrometry.” J. Am. Soc. Mass Spectrom., 12,
1247-1253 (2001).
75.
Mandell, J. G., Baerga-Ortiz, A., Akashi, S., Takio,
K., *Komives, E.A. “Solvent Accessibility of the Thrombin-thrombomodulin
Interface.” J. Mol. Biol. 306,
575-589 (2001).
和文論文、総説、総合論文、解説 等 (1997~)
1.
明石知子 講義「ネイティブ質量分析でできること」ぶんせき、日本分析化学会、5月号、157-161 (2024).
2.
明石知子、七種和美 「タンパク質複合体のイオンモビリティ質量分析」エアロゾル研究、28(2), 119-124 (2013).
3.
明石知子 「質量分析によるタンパク質複合体の相互作用解析」生物工学、日本生物工学会、89(7)、384-387 (2011).
4.
明石知子、渡邊真宏、Jonathan G. Heddle, 雲財悟、朴三用、Jeremy R. H. Tame 「質量分析によるタンパク質‐タンパク質およびタンパク質‐RNA複合体の構造研究 －X線結晶構造解析と質量分析で見えてくる生体超分子の構造－（MS71）」日本結晶学会誌 51(1) 105-106 (2009).
5.
明石知子、「巨大タンパク質複合体の質量分析」ぶんせき、日本分析化学会、8月号、422-427 (2009).
6.
明石知子、史向国、高見澤淳、西村善文、平岡賢三「レーザースプレー質量分析が可能にした生体高分子複合体の結合親和性の定量的な解析」J. Mass Spectrom. Soc. Jpn., 56(3), 155-161
(2008).
7.
明石知子「難結晶性生体超分子複合体の溶液構造を解析する –様々な手法を駆使して基本転写因子 TFIIE の構造を解析- 化学と生物、45, 86-87 (2007).
8.
明石知子、「生体高分子の質量分析による構造機能研究」YAKUGAKU ZASSHI 126,
915-929 (2006).
9.
明石知子 「プロテオミクス解析の分析技術 タンパク質の構造解析法としての質量分析」ぶんせき、日本分析化学会、8月号、426-431 (2005).
10. 伊藤喜之、西村善文、明石知子「非スプリット低流速 LC/MSによるペプチドの分析－もっと手軽に高感度な低流速LC/MS分析を行う－」Jasco Report, 45(2), 1-7 (2003).
11. 明石知子「田中耕一氏の発見が生命科学研究をどう変えたか」化学と教育、日本化学会、51, 296-297 (2003).
12. 明石知子「２つのソフトイオン化法の開発 -2002 年度ノーベル化学賞 田中耕一氏、John B. Fenn 教授の業績」化学と工業、日本化学会、55, 1332-1336 (2002).
13. 明石知子「田中耕一氏 2002 年度ノーベル化学賞受賞」ファルマシア、日本薬学会、38, 1183 (2002).
14. 明石知子、瀧尾擴士 「重水素交換と MS を組み合わせたタンパク質の高次構造解析」J. Mass Spectrom. Soc. Jpn. 48, 94-100
(2000).
15. 明石知子、「質量分析を用いたタンパク質の構造解析」J. Mass Spectrom. Soc. Jpn. 45, 1-23 (1997).
著書 (1997~)
1.
明石知子、田尻道子 “生命金属ダイナミクス: 生体内における金属の挙動と制御”、城宜嗣、津本浩平 監修 第7章 方法論 第9節 ネイティブ質量分析、エヌ・ティー・エス出版、p. 445-454 (2021) .（共著）
2.
明石知子 “現代質量分析学”、高山光男、早川滋雄、瀧浪欣彦、和田芳直編 第26章 生体超分子、化学同人、p. 383-392 (2013).（共著）
3.
明石知子 “試料分析講座 タンパク質分析”、日本分析化学会編 5.3 タンパク質複合体のネイティブ質量分析、丸善出版、p. 183-197 (2012). （共著）
4.
明石知子 “翻訳後修飾のプロテオミクス －質量分析装置を中心とした分析法の原理－”、平野久、大野茂男編 4章 4.13.2 質量分析法による脱イミノ化の検出、講談社、p. 171-174 (2011). （共著）
5.
明石知子 “生命科学のための機器分析実験ハンドブック”、西村善文編 第5章 2. エレクトロスプレーイオン化質量分析（ESI-MS） ～タンパク質複合体の分析～、羊土社、p. 189-193 (2007). （共著）
6.
明石知子 “ポストゲノムマススペクトロメトリー –生化学のための生体高分子解析”、化学フロンティア ⑩、丹羽利充編 part 3 プロテオーム解析に MS を応用する 5章 タンパク質の高次構造および相互作用部位の解析、化学同人、p. 145-155 (2003). （共著）
7.
明石知子 “プロテオミクス –方法とその病態解析への応用”、現代化学増刊42、鈴木紘一監修、平野久、鮎沢大編2. プロテオミクスにおける質量分析 2.2 FTICR MS と H/D 交換を用いたタンパク質の構造解析、東京化学同人、p.14-17 (2002). （共著）
8.
明石知子 “生命科学のための最新マススペクトロメトリー”、原田健一、田口良、橋本豊編 II-5 タンパク質の相互作用の解析 II-8 タンパク質-タンパク質相互作用部位の解析、講談社サイエンティフィク、p. 179-199 (2002). （共著）
9.
明石知子 “マススペクトロメトリーってなあに”、平山和雄、明石知子、高山光男、豊田岐聡、橋本豊、平岡賢三 編・著 4章4.5 試料の性質や研究対象に適した分析計の選択法は？、8章 MS/MS をわかりやすく説明すると、国際文献印刷、p.30-35, p.52-59 (2001). （共著）
10. 明石知子 ”バイオロジカルマススペクトロメトリー”、上野民夫、平山和雄、原田健一編 6. タンパク質 6.2 高次構造、東京化学同人、p. 139-144 (1997). （共著）