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MaxDIA enables library-based and library-free data-independent acquisition proteomics.
Sinitcyn P, Hamzeiy H, Salinas Soto F, Itzhak D, McCarthy F, Wichmann C, Steger M, Ohmayer U, Distler U, Kaspar-Schoenefeld S, Prianichnikov N, Yılmaz Ş, Rudolph JD, Tenzer S, Perez-Riverol Y, Nagaraj N, Humphrey SJ, Cox J. Sinitcyn P, et al. Nat Biotechnol. 2021 Dec;39(12):1563-1573. doi: 10.1038/s41587-021-00968-7. Epub 2021 Jul 8. Nat Biotechnol. 2021. PMID: 34239088 Free PMC article.
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. Vizcaíno JA, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29. Nucleic Acids Res. 2013. PMID: 23203882 Free PMC article.
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. Griss J, et al. Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30. Mol Cell Proteomics. 2014. PMID: 24980485 Free PMC article.
PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA. Perez-Riverol Y, et al. Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6. Mol Cell Proteomics. 2016. PMID: 26545397 Free PMC article.
A multicenter study benchmarks software tools for label-free proteome quantification.
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. Navarro P, et al. Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3. Nat Biotechnol. 2016. PMID: 27701404 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. 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.
107 results