The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
Vizcaíno, Juan Antonio, Côté, Richard G, Csordas, Attila, Dianes, José A, Fabregat, Antonio, Foster, Joseph M, Griss, Johannes, Alpi, Emanuele, Birim, Melih, Contell, Javier, O'Kelly, Gavin, Schoenegger, Andreas, Ovelleiro, David, Pérez-Riverol, Yasset, Reisinger, Florian, Ríos, Daniel, Wang, Rui, Hermjakob, Henning
Published in Nucleic acids research (01.01.2013)
Published in Nucleic acids research (01.01.2013)
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Journal Article
Tissue-based absolute quantification using large-scale TMT and LFQ experiments
Wang, Hong, Dai, Chengxin, Pfeuffer, Julianus, Sachsenberg, Timo, Sanchez, Aniel, Bai, Mingze, Perez-Riverol, Yasset
Published in Proteomics (Weinheim) (01.10.2023)
Published in Proteomics (Weinheim) (01.10.2023)
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Journal Article
Universal Spectrum Identifier for mass spectra
Deutsch, Eric W., Perez-Riverol, Yasset, Carver, Jeremy, Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Binz, Pierre-Alain, Pullman, Benjamin, Sun, Zhi, Shofstahl, Jim, Bittremieux, Wout, Mak, Tytus D., Klein, Joshua, Zhu, Yunping, Lam, Henry, Vizcaíno, Juan Antonio, Bandeira, Nuno
Published in Nature methods (01.07.2021)
Published in Nature methods (01.07.2021)
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Journal Article
MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets
Choi, Meena, Carver, Jeremy, Chiva, Cristina, Tzouros, Manuel, Huang, Ting, Tsai, Tsung-Heng, Pullman, Benjamin, Bernhardt, Oliver M., Hüttenhain, Ruth, Teo, Guo Ci, Perez-Riverol, Yasset, Muntel, Jan, Müller, Maik, Goetze, Sandra, Pavlou, Maria, Verschueren, Erik, Wollscheid, Bernd, Nesvizhskii, Alexey I., Reiter, Lukas, Dunkley, Tom, Sabidó, Eduard, Bandeira, Nuno, Vitek, Olga
Published in Nature methods (01.10.2020)
Published in Nature methods (01.10.2020)
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Journal Article
Open source libraries and frameworks for biological data visualisation: A guide for developers
Wang, Rui, Perez-Riverol, Yasset, Hermjakob, Henning, Vizcaíno, Juan Antonio
Published in Proteomics (Weinheim) (01.04.2015)
Published in Proteomics (Weinheim) (01.04.2015)
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Journal Article
The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
Griss, Johannes, Jones, Andrew R., Sachsenberg, Timo, Walzer, Mathias, Gatto, Laurent, Hartler, Jürgen, Thallinger, Gerhard G., Salek, Reza M., Steinbeck, Christoph, Neuhauser, Nadin, Cox, Jürgen, Neumann, Steffen, Fan, Jun, Reisinger, Florian, Xu, Qing-Wei, del Toro, Noemi, Pérez-Riverol, Yasset, Ghali, Fawaz, Bandeira, Nuno, Xenarios, Ioannis, Kohlbacher, Oliver, Vizcaíno, Juan Antonio, Hermjakob, Henning
Published in Molecular & cellular proteomics (01.10.2014)
Published in Molecular & cellular proteomics (01.10.2014)
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Journal Article
An integrated landscape of protein expression in human cancer
Jarnuczak, Andrew F., Najgebauer, Hanna, Barzine, Mitra, Kundu, Deepti J., Ghavidel, Fatemeh, Perez-Riverol, Yasset, Papatheodorou, Irene, Brazma, Alvis, Vizcaíno, Juan Antonio
Published in Scientific data (23.04.2021)
Published in Scientific data (23.04.2021)
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Journal Article
The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): an open community for bioinformatics training and research
Bittremieux, Wout, Bouyssié, David, Dorfer, Viktoria, Locard-Paulet, Marie, Perez-Riverol, Yasset, Schwämmle, Veit, Uszkoreit, Julian, Van Den Bossche, Tim
Published in Rapid communications in mass spectrometry (16.04.2021)
Published in Rapid communications in mass spectrometry (16.04.2021)
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Journal Article
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
Van Puyvelde, Bart, Daled, Simon, Willems, Sander, Gabriels, Ralf, Gonzalez de Peredo, Anne, Chaoui, Karima, Mouton-Barbosa, Emmanuelle, Bouyssié, David, Boonen, Kurt, Hughes, Christopher J., Gethings, Lee A., Perez-Riverol, Yasset, Bloomfield, Nic, Tate, Stephen, Schiltz, Odile, Martens, Lennart, Deforce, Dieter, Dhaenens, Maarten
Published in Scientific data (30.03.2022)
Published in Scientific data (30.03.2022)
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Journal Article
Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation
Ramos, Yassel, González, Annia, Sosa‐Acosta, Patricia, Perez‐Riverol, Yasset, García, Yairet, Castellanos‐Serra, Lila, Gil, Jeovanis, Sánchez, Aniel, González, Luis J., Besada, Vladimir
Published in Journal of separation science (01.12.2019)
Published in Journal of separation science (01.12.2019)
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Journal Article
Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations]
Gruening, Bjorn, Sallou, Olivier, Moreno, Pablo, da Veiga Leprevost, Felipe, Ménager, Hervé, Søndergaard, Dan, Röst, Hannes, Sachsenberg, Timo, O'Connor, Brian, Madeira, Fábio, Dominguez Del Angel, Victoria, Crusoe, Michael R, Varma, Susheel, Blankenberg, Daniel, Jimenez, Rafael C, Perez-Riverol, Yasset
Published in F1000 research (01.01.2018)
Published in F1000 research (01.01.2018)
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Journal Article
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Perez-Riverol, Yasset, Bai, Jingwen, Bandla, Chakradhar, García-Seisdedos, David, Hewapathirana, Suresh, Kamatchinathan, Selvakumar, Kundu, Deepti J, Prakash, Ananth, Frericks-Zipper, Anika, Eisenacher, Martin, Walzer, Mathias, Wang, Shengbo, Brazma, Alvis, Vizcaíno, Juan Antonio
Published in Nucleic acids research (07.01.2022)
Published in Nucleic acids research (07.01.2022)
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Journal Article
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Perez-Riverol, Yasset, Csordas, Attila, Bai, Jingwen, Bernal-Llinares, Manuel, Hewapathirana, Suresh, Kundu, Deepti J, Inuganti, Avinash, Griss, Johannes, Mayer, Gerhard, Eisenacher, Martin, Pérez, Enrique, Uszkoreit, Julian, Pfeuffer, Julianus, Sachsenberg, Timo, Yılmaz, Şule, Tiwary, Shivani, Cox, Jürgen, Audain, Enrique, Walzer, Mathias, Jarnuczak, Andrew F, Ternent, Tobias, Brazma, Alvis, Vizcaíno, Juan Antonio
Published in Nucleic acids research (08.01.2019)
Published in Nucleic acids research (08.01.2019)
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Journal Article
2016 update of the PRIDE database and its related tools
Vizcaíno, Juan Antonio, Csordas, Attila, del-Toro, Noemi, Dianes, José A, Griss, Johannes, Lavidas, Ilias, Mayer, Gerhard, Perez-Riverol, Yasset, Reisinger, Florian, Ternent, Tobias, Xu, Qing-Wei, Wang, Rui, Hermjakob, Henning
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Journal Article
The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
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
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Journal Article
2016 update of the PRIDE database and its related tools
Vizcaíno, Juan Antonio, Csordas, Attila, Del-Toro, Noemi, Dianes, José A, Griss, Johannes, Lavidas, Ilias, Mayer, Gerhard, Perez-Riverol, Yasset, Reisinger, Florian, Ternent, Tobias, Xu, Qing-Wei, Wang, Rui, Hermjakob, Henning
Published in Nucleic acids research (15.12.2016)
Published in Nucleic acids research (15.12.2016)
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Journal Article
The ProteomeXchange consortium at 10 years: 2023 update
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
Published in Nucleic acids research (06.01.2023)
Published in Nucleic acids research (06.01.2023)
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Journal Article
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
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
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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Journal Article