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Y. Kyono, N. Sugiyama, K. Imami, K. Miyazaki, M. Ohira, M. Tomita, and Y. Ishihama,Ishihama % V8&'()*+,x¯4V8n&»¼g½»r/0hC-J J. Mass Spectrom. Soc. Jpn., 58, 129῍138 (2010).
2)

H. Nakagami, N. Sugiyama, K. Mochida, A. Daudi, Y. Yoshida, T. Toyoda, M. Tomita, Y. Ishihama,Ishihama
and K. Shirasu, Large-scale comparative phosphoproteomics identiﬁes conserved phosphorylationsites in plants, Plant Physiol., 153, 1161῍1174 (2010).
ῌ 122 ῌ3)

Y. Kyono, N. Sugiyama, M. Tomita, and Y. Ishihama,Ishihama Chemical dephosphorylation for identiﬁcation of multiply phosphorylated peptides and phosphorylation site determination, RapidCommun. Mass Spectrom., 24, 2277῍2282 (2010).

4)

H. Imamura, N. Yachie, R. Saito, Y. Ishihama,Ishihama and M. Tomita, Towards the systematic discovery ofsignal transduction networks using phosphorylation dynamics data, BMC Bioinformatics, 11, 232(2010).

5)

K. Fujiwara, Y. Ishihama,
Ishihama K. Nakahigashi, T. Soga, and H. Taguchi, A systematic survey of in vivo
obligate chaperonin-dependent substrates, EMBO J., 29, 1552῍1564 (2010).

6)

M. Iwasaki, S. Miwa, T. Ikegai, M. Tomita, N. Tanaka, and Y. Ishihama,Ishihama One-dimensional capillaryliquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale, Anal. Chem., 82, 2616῍2620 (2010).

7)

K. Imami, M. Tomita, and Y. Ishihama,
Ishihama Quantitative proteome and phosphoproteome analyses ofcultured cells based on SILAC labeling without requirement of serum dialysis, Mol. BioSyst., 6(3),594῍602 (2010).

8)

K. Shinoda, M. Tomita, and Y. Ishihama,
Ishihama emPAI Calcῌfor the estimation of protein abundancefrom large-scale identiﬁcation data by liquid chromatography-tandem mass spectrometry, Bioinformatics, 26(4), 576῍577 (2010).

9)T. Masuda, N. Saito, M. Tomita, and Y. Ishihama,Ishihama Unbiased quantitation of Escherichia coli
membrane proteome using phase-transfer surfactants, Mol. Cell. Proteomics, 8, 2770῍2777 (2009).

10)

T. Umezawa, N. Sugiyama, M. Mizoguchi, S. Hayashi, F. Myouga, K. Yamaguchi-Shinozaki, Y.
Ishihama, T. Hirayama, and K. Shinozaki, Type 2C protein phosphatases directly regulate abscisicIshihama
acid-activated protein kinases in Arabidopsis, Proc. Natl. Acad. Sci. U.S.A., 106(41), 17588῍17593(2009).

11)

N. Yachie, R. Saito, J. Sugahara, M. Tomita, and Y. Ishihama,Ishihama In silico analysis of phosphoproteome
data suggests a rich-get-richer process of phosphosite accumulation over evolution, Mol. Cell.
Proteomics, 8(5), 1061῍1071 (2009).

12)

A. Ravichandran, N. Sugiyama, M. Tomita, S. Swarup, and Y. Ishihama,
Ishihama Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species, Proteomics, 9(10), 2764῍
2775 (2009).

13)A. Nock, J. M. Ascano, T. Jones, M. Barrero, N. Sugiyama, M. Tomita, Y. Ishihama,
Ishihama and S. Malik,Identiﬁcation of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor
FoxA2, J. Biol. Chem., 284(30), 19915῍19926 (2009).

14)

M. Iwasaki, T. Masuda, M. Tomita, and Y. Ishihama,Ishihama Chemical cleavage-assisted tryptic digestion
for membrane proteome analysis, J. Proteome Res., 8(6), 3169῍3175 (2009).

15)

N. Sugiyama, H. Nakagami, K. Mochida, A. Daudi, M. Tomita, K. Shirasu, and Y. Ishihama,Ishihama
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis, Mol. Syst. Biol., 4, 193 (2008).

16)

K. Shinoda, M. Tomita, and Y. Ishihama,
Ishihama Aligning LC peaks by converting gradient retention times
to retention index of peptide in proteomic experiments, Bioinformatics (Oxford, England), 24(14),1590῍1595 (2008).

17)

K. Shinoda, M. Sugimoto, M. Tomita, and Y. Ishihama,Ishihama Informatics for peptide retention properties
in proteomic LC-MS, Proteomics, 8(4), 787῍798 (2008).

18)

K. Sagane, Y. Ishihama,Ishihama and H. Sugimoto, LGI1 and LGI4 bind to ADAM22, ADAM23 and ADAM
11, Int. J. Biol. Sci., 4(6), 387῍396 (2008).

19)

K. Miyamoto, T. Hara, H. Kobayashi, H. Morisaka, D. Tokuda, K. Horie, K. Koduki, S. Makino, O.
Nunez, C. Yang, T. Kawabe, T. Ikegami, H. Takubo, Y. Ishihama,Ishihama and N. Tanaka, High-e$ciency
liquid chromatographic separation utilizing long monolithic silica capillary columns, Anal. Chem.,ῌ 123 ῌ80(22), 8741῍8750 (2008).
20)

T. Masuda, M. Tomita, and Y. Ishihama,Ishihama Phase transfer surfactant-aided trypsin digestion formembrane proteome analysis, J. Proteome Res., 7(2), 731῍740 (2008).

21)

Y. Kyono, N. Sugiyama, K. Imami, M. Tomita, and Y. Ishihama,
Ishihama Successive and selective release ofphosphorylated peptides captured by hydroxy acid-modiﬁed metal oxide chromatography, J.
Proteome Res., 7(10), 4585῍4593 (2008).

22)

Y. Ishihama,Ishihama T. Schmidt, J. Rappsilber, M. Mann, F. U. Hartl, M. J. Kerner, and D. Frishman, Protein
abundance proﬁling of the Escherichia coli cytosol, BMC Genomics, 9, 102(2008).

23)

K. Imami, N. Sugiyama, Y. Kyono, M. Tomita, and Y. Ishihama,
Ishihama Automated phosphoproteome
analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18
biphasic column, Anal. Sci., 24(1), 161῍166 (2008).

24)

K. Imami, Y. Ishihama,Ishihama and S. Terabe, On-line selective enrichment and ion-pair reaction forstructural determination of sulfated glycopeptides by capillary electrophoresis-mass spectrometry, J. Chromatogr. A, 1194(2), 237῍242 (2008).

25)

N. Sugiyama, T. Masuda, K. Shinoda, A. Nakamura, M. Tomita, and Y. Ishihama,Ishihama Phosphopeptide
enrichment by aliphatic hydroxy acid-modiﬁed metal oxide chromatography for nano-LC-MS/MS
in proteomics applications, Mol. Cell. Proteomics, 6(6), 1103῍1109 (2007).

26)

T. Sato, Y. Ishihama,Ishihama and Y. Oda, Quantitative proteomics of mouse brain and speciﬁc proteininteraction studies using stable isotope labeling, Methods Mol. Biol., 359, 53῍70 (2007).

27)

J. Rappsilber, M. Mann, and Y. Ishihama,Ishihama Protocol for micro-puriﬁcation, enrichment, prefractionation and storage of peptides for proteomics using StageTips, Nat. Protoc., 2(8), 1896῍1906(2007).

28)

M. R. Monton, M. Tomita, T. Soga, and Y. Ishihama,Ishihama Polymer entrapment in polymerized silicatefor preparing highly stable capillary coatings for CE and CE-MS, Anal. Chem., 79(20), 7838῍7844(2007).

29)

Y. Kotake, K. Sagane, T. Owa, Y. Mimori-Kiyosue, H. Shimizu, M. Uesugi, Y. Ishihama,Ishihama M. Iwata,and Y. Mizui, Splicing factor SF3b as a target of the antitumor natural product pladienolide, Nat.
Chem. Biol., 3(9), 570῍575 (2007).

30)

Y. Ishihama,Ishihama F. Y. Wei, K. Aoshima, T. Sato, J. Kuromitsu, and Y. Oda, Enhancement of thee$ciency of phosphoproteomic identiﬁcation by removing phosphates after phosphopeptide
enrichment, J. Proteome Res., 6(3), 1139῍1144 (2007).

31)

K. Imami, M. R. Monton, Y. Ishihama,Ishihama and S. Terabe, Simple on-line sample preconcentration
technique for peptides based on dynamic pH junction in capillary electrophoresis-mass spectrometry, J. Chromatogr. A, 1148(2), 250῍255 (2007).

32)

M. Hashimoto, Y. Ishihama,Ishihama M. Tomita, and T. Soga, Microelectrospray interface with coaxial
sheath ﬂow for high-resolution capillary electrophoresis/mass spectrometry separation, RapidCommun. Mass Spectrom., 21(22), 3579῍3584 (2007).

33)

Y. Wakabayashi, M. Kobayashi, S. Akashi-Takamura, N. Tanimura, K. Konno, K. Takahashi, T.
Ishii, T. Mizutani, H. Iba, T. Kouro, S. Takaki, K. Takatsu, Y. Oda, Y. Ishihama,Ishihama S.-I. Saitoh, and K.
Miyake, A protein associated with toll-like receptor 4 (PRAT4A) regulates cell surface expressionof TLR4, J. Immunol., 177(3), 1772῍1779 (2006).

34)

H. Saito, Y. Oda, T. Sato, J. Kuromitsu, and Y. Ishihama,Ishihama Multiplexed two-dimensional liquid
chromatography for MALDI and nanoelectrospray ionization mass spectrometry in proteomics, J.
Proteome Res., 5(7), 1803῍1807 (2006).

35)

K. Murata, N. Mano, N. Asakawa, and Y. Ishihama,Ishihama Simpliﬁed gradient generator for micro- and36)

Y. Ishihama,Ishihama J. Rappsilber, and M. Mann, Modular stop and go extraction tips with stacked disksnano-liquid chromatography, J. Chromatogr. A, 1123(1), 47῍52 (2006).

ῌ 124 ῌfor parallel and multidimensional peptide fractionation in proteomics, J. Proteome Res., 5(4), 988῍994 (2006).
37)

M. Kokubu, Y. Ishihama,Ishihama T. Sato, T. Nagasu, and Y. Oda, Speciﬁcity of immobilized metal
a$nity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis,Anal. Chem., 77(16), 5144῍5154 (2005).

38)

M. J. Kerner,῎ D. J. Naylor, ῎ Y. Ishihama,῎Ishihama T. Maier,῎ H. C. Chang, A. P. Stines, C. Georgopoulos, D.
Frishman, M. Hayer-Hartl, M. Mann, and F. U. Hartl, Proteome-wide analysis of chaperonindependent protein folding in Escherichia coli, Cell, 122(2), 209῍220 (2005) (῎ shared ﬁrst authors).

39)

Y. Ishihama,Ishihama T. Sato, T. Tabata, N. Miyamoto, K. Sagane, T. Nagasu, and Y. Oda, Quantitativemouse brain proteomics using culture-derived isotope tags as internal standards, Nat. Biotechnol.,23(5), 617῍621 (2005).

40)

Y. Ishihama,Ishihama Y. Oda, T. Tabata, T. Sato, T. Nagasu, J. Rappsilber, and M. Mann, Exponentially
modiﬁed protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein, Mol. Cell. Proteomics, 4(9), 1265῍1272(2005).

41)

H. Katayama, T. Tabata, Y. Ishihama,Ishihama T. Sato, Y. Oda, and T. Nagasu, E$cient in-gel digestion
procedure using 5-cyclohexyl-1-pentyl-beta-9-maltoside as an additive for gel-based membraneproteomics, Rapid Commun. Mass Spectrom., 18(20), 2388῍2394 (2004).

42)

J. Rappsilber,῎ Y. Ishihama,῎Ishihama and M. Mann, Stop and go extraction tips for matrix-assisted laser
desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics, Anal.
Chem., 75(3), 663῍670 (2003) (῎ shared ﬁrst authors).

43)

E. Lasonder, Y. Ishihama,Ishihama J. S. Andersen, A. M. Vermunt, A. Pain, R. W. Sauerwein, W. M. Eling, N.
Hall, A. P. Waters, H. G. Stunnenberg, and M. Mann, Analysis of the Plasmodium falciparum
proteome by high-accuracy mass spectrometry, Nature, 419(6906), 537῍542 (2002).

44)

Y. Ishihama,Ishihama J. Rappsilber, J. S. Andersen, and M. Mann, Microcolumns with self-assembled particle

45)

Y. Ishihama,Ishihama H. Katayama, N. Asakawa, and Y. Oda, Highly robust stainless steel tips as micro-frits for proteomics, J. Chromatogr. A, 979(1῍2), 233῍239 (2002).

electrospray emitters, Rapid Commun. Mass Spectrom., 16(10), 913῍918 (2002).
46)

H. Katayama, Y. Ishihama,Ishihama Y. Oda, and N. Asakawa, Electrophoretic mobility-assisted identiﬁcation of proteins by nanoelectrospray capillary electrophoresis/mass spectrometry under methanolic conditions, Rapid Commun. Mass Spectrom., 14(14), 1167῍1178 (2000).

47)

Y. Ishihama,Ishihama H. Katayama, and N. Asakawa, Surfactants usable for electrospray ionization mass
spectrometry, Anal. Biochem., 287(1), 45῍54 (2000).

ῌ῏῎῍1)

K. Imami, M. Tomita, and Y. Ishihama,Ishihama Development of dual stable isotope labeling by amino acids
in cell culture and application to quantitative proteomics, J. Mass Spectrom. Soc. Jpn., 58(2), 81῍87(2010).

2)

T. Masuda and Y. Ishihama,
Ishihama Sample preparation methods for large-scale analysis of membraneproteins using shotgun proteomics, J. Mass Spectrom. Soc. Jpn., 57(3), 145῍151 (2009).

3)

Y. Ishihama,
Ishihama  StageTip  BUNSEKI KAGAKU, 57(12),1011῍1018 (2008).
4)

Y. Ishihama,
Ishihama Optimization of nano-liquid chromatography coupled with mass spectrometry forproteomics, J. Mass Spectrom. Soc. Jpn., 55(3), 157῍164 (2007).

ῌ 125 ῌ