One-Step Isolation of Protein C‑Terminal Peptides from V8 Protease-Digested Proteins by Metal Oxide-Based Ligand-Exchange Chromatography von Nishida, Hiroshi, Ishihama, Yasushi

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Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips von Rappsilber, Juri, Mann, Matthias, Ishihama, Yasushi

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Biotinylation-based proximity labelling proteomics: basics, applications and technical considerations von Niinae, Tomoya, Ishihama, Yasushi, Imami, Koshi

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Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis von Masuda, Takeshi, Tomita, Masaru, Ishihama, Yasushi

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The ProteomeXchange consortium at 10 years: 2023 update von Deutsch, Eric W, Bandeira, Nuno, Perez-Riverol, Yasset, Sharma, Vagisha, Carver, Jeremy J, Mendoza, Luis, Kundu, Deepti J, Wang, Shengbo, Bandla, Chakradhar, Kamatchinathan, Selvakumar, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan Antonio

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The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics von Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan A

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Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks von Wagih, Omar, Sugiyama, Naoyuki, Ishihama, Yasushi, Beltrao, Pedro

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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition von Deutsch, Eric W, Csordas, Attila, Sun, Zhi, Jarnuczak, Andrew, Perez-Riverol, Yasset, Ternent, Tobias, Campbell, David S, Bernal-Llinares, Manuel, Okuda, Shujiro, Kawano, Shin, Moritz, Robert L, Carver, Jeremy J, Wang, Mingxun, Ishihama, Yasushi, Bandeira, Nuno, Hermjakob, Henning, Vizcaíno, Juan Antonio

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Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid von Battellino, Taylor, Ogata, Kosuke, Spicer, Victor, Ishihama, Yasushi, Krokhin, Oleg

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PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy von Shiba-Fukushima, Kahori, Imai, Yuzuru, Yoshida, Shigeharu, Ishihama, Yasushi, Kanao, Tomoko, Sato, Shigeto, Hattori, Nobutaka

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CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides von Ogata, Kosuke, Ishihama, Yasushi

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Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis von Umezawa, Taishi, Sugiyama, Naoyuki, Mizoguchi, Masahide, Hayashi, Shimpei, Myouga, Fumiyoshi, Yamaguchi-Shinozaki, Kazuko, Ishihama, Yasushi, Hirayama, Takashi, Shinozaki, Kazuo

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Analytical Platforms for Mass Spectrometry-Based Proteomics von ISHIHAMA, Yasushi

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Stop and Go Extraction Tips for Matrix-Assisted Laser Desorption/Ionization, Nanoelectrospray, and LC/MS Sample Pretreatment in Proteomics von Rappsilber, Juri, Ishihama, Yasushi, Mann, Matthias

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Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis von Imami, Koshi, Milek, Miha, Bogdanow, Boris, Yasuda, Tomoharu, Kastelic, Nicolai, Zauber, Henrik, Ishihama, Yasushi, Landthaler, Markus, Selbach, Matthias

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emPAI Calc—for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry von Shinoda, Kosaku, Tomita, Masaru, Ishihama, Yasushi

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Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer von Oka, Miho, Xu, Liu, Suzuki, Toshihiro, Yoshikawa, Toshiaki, Sakamoto, Hiromi, Uemura, Hayato, Yoshizawa, Akiyasu C, Suzuki, Yutaka, Nakatsura, Tetsuya, Ishihama, Yasushi, Suzuki, Ayako, Seki, Masahide

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Peptide probes containing a non‐hydrolyzable phosphotyrosine‐mimetic residue for enrichment of protein tyrosine phosphatases von Tsumagari, Kazuya, Niinae, Tomoya, Otaka, Akira, Ishihama, Yasushi

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Protein abundance profiling of the Escherichia coli cytosol von Ishihama, Yasushi, Schmidt, Thorsten, Rappsilber, Juri, Mann, Matthias, Hartl, F Ulrich, Kerner, Michael J, Frishman, Dmitrij

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Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics von Masuda, Takeshi, Sugiyama, Naoyuki, Tomita, Masaru, Ohtsuki, Sumio, Ishihama, Yasushi

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