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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: zhu y. 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 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: zhu y. 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: zhu y. 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.
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: zhu y. 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: zhu y. 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.
π-HuB: the proteomic navigator of the human body.
He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y; π-HuB Consortium. He F, et al. Among authors: zhu y. Nature. 2024 Dec;636(8042):322-331. doi: 10.1038/s41586-024-08280-5. Epub 2024 Dec 11. Nature. 2024. PMID: 39663494 Review.
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