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The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.
Klein J, Lam H, Mak TD, Bittremieux W, Perez-Riverol Y, Gabriels R, Shofstahl J, Hecht H, Binz PA, Kawano S, Van Den Bossche T, Carver J, Neely BA, Mendoza L, Suomi T, Claeys T, Payne T, Schulte D, Sun Z, Hoffmann N, Zhu Y, Neumann S, Jones AR, Bandeira N, Vizcaíno JA, Deutsch EW. Klein J, et al. Among authors: kawano s. Anal Chem. 2024 Nov 19;96(46):18491-18501. doi: 10.1021/acs.analchem.4c04091. Epub 2024 Nov 8. Anal Chem. 2024. PMID: 39514576 Free PMC article.
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. Deutsch EW, et al. Among authors: kawano s. Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18. Nucleic Acids Res. 2017. PMID: 27924013 Free PMC article.
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Deutsch EW, et al. Among authors: kawano s. J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15. J Proteome Res. 2017. PMID: 28849660 Free PMC article.
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Deutsch EW, et al. Among authors: kawano s. Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152. doi: 10.1093/nar/gkz984. Nucleic Acids Res. 2020. PMID: 31686107 Free PMC article.
Universal Spectrum Identifier for mass spectra.
Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N. Deutsch EW, et al. Among authors: kawano s. Nat Methods. 2021 Jul;18(7):768-770. doi: 10.1038/s41592-021-01184-6. Epub 2021 Jun 28. Nat Methods. 2021. PMID: 34183830 Free PMC article.
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.
LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA. LeDuc RD, et al. Among authors: kawano s. J Proteome Res. 2022 Apr 1;21(4):1189-1195. doi: 10.1021/acs.jproteome.1c00771. Epub 2022 Mar 15. J Proteome Res. 2022. PMID: 35290070 Free PMC article.
The ProteomeXchange consortium at 10 years: 2023 update.
Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Deutsch EW, et al. Among authors: kawano s. Nucleic Acids Res. 2023 Jan 6;51(D1):D1539-D1548. doi: 10.1093/nar/gkac1040. Nucleic Acids Res. 2023. PMID: 36370099 Free PMC article.
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.
Deutsch EW, Vizcaíno JA, Jones AR, Binz PA, Lam H, Klein J, Bittremieux W, Perez-Riverol Y, Tabb DL, Walzer M, Ricard-Blum S, Hermjakob H, Neumann S, Mak TD, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Bandeira N, Carver J, Pullman B, Sun Z, Hoffmann N, Shofstahl J, Zhu Y, Licata L, Quaglia F, Tosatto SCE, Orchard SE. Deutsch EW, et al. Among authors: kawano s. J Proteome Res. 2023 Feb 3;22(2):287-301. doi: 10.1021/acs.jproteome.2c00637. Epub 2023 Jan 10. J Proteome Res. 2023. PMID: 36626722 Free PMC article. Review.
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. Vos RA, et al. Among authors: kawano s. F1000Res. 2020 Feb 24;9:136. doi: 10.12688/f1000research.18236.1. eCollection 2020. F1000Res. 2020. PMID: 32308977 Free PMC article.
The jPOST environment: an integrated proteomics data repository and database.
Moriya Y, Kawano S, Okuda S, Watanabe Y, Matsumoto M, Takami T, Kobayashi D, Yamanouchi Y, Araki N, Yoshizawa AC, Tabata T, Iwasaki M, Sugiyama N, Tanaka S, Goto S, Ishihama Y. Moriya Y, et al. Among authors: kawano s. Nucleic Acids Res. 2019 Jan 8;47(D1):D1218-D1224. doi: 10.1093/nar/gky899. Nucleic Acids Res. 2019. PMID: 30295851 Free PMC article.
1,732 results