| The PRIDE database and related tools and resources in 2019: improving support for quantification data Y Perez-Riverol, A Csordas, J Bai, M Bernal-Llinares, S Hewapathirana, ... Nucleic acids research 47 (D1), D442-D450, 2019 | 5970 | 2019 |
| 2016 update of the PRIDE database and its related tools JA Vizcaíno, A Csordas, N Del-Toro, JA Dianes, J Griss, I Lavidas, ... Nucleic acids research 44 (D1), D447-D456, 2016 | 3673 | 2016 |
| The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences Y Perez-Riverol, J Bai, C Bandla, D García-Seisdedos, S Hewapathirana, ... Nucleic acids research 50 (D1), D543-D552, 2022 | 2180 | 2022 |
| The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013 JA Vizcaíno, RG Côté, A Csordas, JA Dianes, A Fabregat, JM Foster, ... Nucleic acids research 41 (D1), D1063-D1069, 2012 | 1976 | 2012 |
| The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition EW Deutsch, A Csordas, Z Sun, A Jarnuczak, Y Perez-Riverol, T Ternent, ... Nucleic acids research, gkw936, 2016 | 827 | 2016 |
| Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 754 | 2018 |
| The ProteomeXchange consortium in 2020: enabling ‘big data’approaches in proteomics EW Deutsch, N Bandeira, V Sharma, Y Perez-Riverol, JJ Carver, ... Nucleic acids research 48 (D1), D1145-D1152, 2020 | 603 | 2020 |
| A multicenter study benchmarks software tools for label-free proteome quantification P Navarro, J Kuharev, LC Gillet, OM Bernhardt, B MacLean, HL Röst, ... Nature biotechnology 34 (11), 1130-1136, 2016 | 308 | 2016 |
| BioContainers: An open-source and community-driven framework for software standardization FV Leprevost, BA Grüning, S Alves Aflitos, HL Röst, J Uszkoreit, ... Bioinformatics, 2017 | 230 | 2017 |
| Making proteomics data accessible and reusable: current state of proteomics databases and repositories Y Perez‐Riverol, E Alpi, R Wang, H Hermjakob, JA Vizcaíno Proteomics 15 (5-6), 930-950, 2015 | 196 | 2015 |
| Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets J Griss, Y Perez-Riverol, S Lewis, DL Tabb, JA Dianes, N Del-Toro, ... Nature methods 13 (8), 651-656, 2016 | 175 | 2016 |
| Discovering and linking public omics data sets using the Omics Discovery Index Y Perez-Riverol, M Bai, F da Veiga Leprevost, S Squizzato, YM Park, ... Nature biotechnology 35 (5), 406-409, 2017 | 161 | 2017 |
| The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience J Griss, AR Jones, T Sachsenberg, M Walzer, L Gatto, J Hartler, ... Molecular & Cellular Proteomics 13 (10), 2765-2775, 2014 | 144 | 2014 |
| PRIDE inspector toolsuite: moving toward a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets Y Perez-Riverol, QW Xu, R Wang, J Uszkoreit, J Griss, A Sanchez, ... Molecular & Cellular Proteomics 15 (1), 305-317, 2016 | 137 | 2016 |
| Four simple recommendations to encourage best practices in research software RC Jiménez, M Kuzak, M Alhamdoosh, M Barker, B Batut, M Borg, ... F1000Research 6, 2017 | 136* | 2017 |
| Ten simple rules for taking advantage of Git and GitHub Y Perez-Riverol, L Gatto, R Wang, T Sachsenberg, J Uszkoreit, ... PLoS computational biology 12 (7), e1004947, 2016 | 136 | 2016 |
| ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion N Hulstaert, J Shofstahl, T Sachsenberg, M Walzer, H Barsnes, L Martens, ... Journal of proteome research 19 (1), 537-542, 2019 | 133 | 2019 |
| PRIDE Inspector: a tool to visualize and validate MS proteomics data R Wang, A Fabregat, D Ríos, D Ovelleiro, JM Foster, RG Côté, J Griss, ... Nature biotechnology 30 (2), 135-137, 2012 | 125 | 2012 |
| The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium RG Côté, J Griss, JA Dianes, R Wang, JC Wright, HWP van den Toorn, ... Molecular & Cellular Proteomics 11 (12), 1682-1689, 2012 | 122 | 2012 |
| MaxDIA enables library-based and library-free data-independent acquisition proteomics P Sinitcyn, H Hamzeiy, F Salinas Soto, D Itzhak, F McCarthy, C Wichmann, ... Nature biotechnology 39 (12), 1563-1573, 2021 | 118 | 2021 |
Juan Antonio VizcainoProteomics Team Leader, EMBL-EBIVerified email at ebi.ac.uk
