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ArticlesPeer ReviewedFull Text
Improved prediction of protein-protein interactions using AlphaFold2
Author / Creator:Bryant, Patrick ; Pozzati, Gabriele ; Elofsson, Arne
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-03, Vol.13 (1), p.1265-1265, Article 1265
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Philosopher: a versatile toolkit for shotgun proteomics data analysis
Author / Creator:da Veiga Leprevost, Felipe ; Haynes, Sarah E. ; Avtonomov, Dmitry M. ; Chang, Hui-Yin ; Shanmugam, Avinash K. ; Mellacheruvu, Dattatreya ; Kong, Andy T. ; Nesvizhskii, Alexey I.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-09, Vol.17 (9), p.869-870
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Large-scale integration of the plasma proteome with genetics and disease
Author / Creator:Ferkingstad, Egil ; Sulem, Patrick ; Atlason, Bjarni A. ; Sveinbjornsson, Gardar ; Magnusson, Magnus I. ; Styrmisdottir, Edda L. ; Gunnarsdottir, Kristbjorg ; Helgason, Agnar ; Oddsson, Asmundur ; Halldorsson, Bjarni V. ; Jensson, Brynjar O. ; Zink, Florian ; Halldorsson, Gisli H. ; Masson, Gisli ; Arnadottir, Gudny A. ; Katrinardottir, Hildigunnur ; Juliusson, Kristinn ; Magnusson, Magnus K. ; Magnusson, Olafur Th ; Fridriksdottir, Run ; Saevarsdottir, Saedis ; Gudjonsson, Sigurjon A. ; Stacey, Simon N. ; Rognvaldsson, Solvi ; Eiriksdottir, Thjodbjorg ; Olafsdottir, Thorunn A. ; Steinthorsdottir, Valgerdur ; Tragante, Vinicius ; Ulfarsson, Magnus O. ; Stefansson, Hreinn ; Jonsdottir, Ingileif ; Holm, Hilma ; Rafnar, Thorunn ; Melsted, Pall ; Saemundsdottir, Jona ; Norddahl, Gudmundur L. ; Lund, Sigrun H. ; Gudbjartsson, Daniel F. ; Thorsteinsdottir, Unnur ; Stefansson, Kari
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2021-12, Vol.53 (12), p.1712-1721
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ArticlesPeer ReviewedFull Text
Hierarchical graph learning for protein–protein interaction
Author / Creator:Gao, Ziqi ; Jiang, Chenran ; Zhang, Jiawen ; Jiang, Xiaosen ; Li, Lanqing ; Zhao, Peilin ; Yang, Huanming ; Huang, Yong ; Li, Jia
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-02, Vol.14 (1), p.1093-1093, Article 1093
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DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
Author / Creator:Demichev, Vadim ; Messner, Christoph B. ; Vernardis, Spyros I. ; Lilley, Kathryn S. ; Ralser, Markus
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-01, Vol.17 (1), p.41-44
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ArticlesPeer ReviewedFull Text
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
Author / Creator:Searle, Brian C. ; Pino, Lindsay K. ; Egertson, Jarrett D. ; Ting, Ying S. ; Lawrence, Robert T. ; MacLean, Brendan X. ; Villén, Judit ; MacCoss, Michael J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-12, Vol.9 (1), p.5128-12, Article 5128
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ArticlesPeer ReviewedFull Text
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
Author / Creator:Kong, Andy T ; Leprevost, Felipe V ; Avtonomov, Dmitry M ; Mellacheruvu, Dattatreya ; Nesvizhskii, Alexey I
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-05, Vol.14 (5), p.513-520
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diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition
Author / Creator:Meier, Florian ; Brunner, Andreas-David ; Frank, Max ; Ha, Annie ; Bludau, Isabell ; Voytik, Eugenia ; Kaspar-Schoenefeld, Stephanie ; Lubeck, Markus ; Raether, Oliver ; Bache, Nicolai ; Aebersold, Ruedi ; Collins, Ben C. ; Röst, Hannes L. ; Mann, Matthias
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-12, Vol.17 (12), p.1229-1236
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ArticlesPeer ReviewedFull Text
Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine
Author / Creator:Chi, Hao ; Liu, Chao ; Yang, Hao ; Zeng, Wen-Feng ; Wu, Long ; Zhou, Wen-Jing ; Wang, Rui-Min ; Niu, Xiu-Nan ; Ding, Yue-He ; Zhang, Yao ; Wang, Zhao-Wei ; Chen, Zhen-Lin ; Sun, Rui-Xiang ; Liu, Tao ; Tan, Guang-Ming ; Dong, Meng-Qiu ; Xu, Ping ; Zhang, Pei-Heng ; He, Si-Min
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2018-12, Vol.36 (11), p.1059-1061
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ArticlesPeer ReviewedFull Text
Standardized annotation of translated open reading frames
Author / Creator:Mudge, Jonathan M. ; Ruiz-Orera, Jorge ; Prensner, John R. ; Brunet, Marie A. ; Calvet, Ferriol ; Jungreis, Irwin ; Gonzalez, Jose Manuel ; Magrane, Michele ; Martinez, Thomas F. ; Schulz, Jana Felicitas ; Yang, Yucheng T. ; Albà, M. Mar ; Aspden, Julie L. ; Baranov, Pavel V. ; Bazzini, Ariel A. ; Bruford, Elspeth ; Martin, Maria Jesus ; Calviello, Lorenzo ; Carvunis, Anne-Ruxandra ; Chen, Jin ; Couso, Juan Pablo ; Deutsch, Eric W. ; Flicek, Paul ; Frankish, Adam ; Gerstein, Mark ; Hubner, Norbert ; Ingolia, Nicholas T. ; Kellis, Manolis ; Menschaert, Gerben ; Moritz, Robert L. ; Ohler, Uwe ; Roucou, Xavier ; Saghatelian, Alan ; Weissman, Jonathan S. ; van Heesch, Sebastiaan
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-07, Vol.40 (7), p.994-999
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ArticlesPeer ReviewedFull Text
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
Author / Creator:Vizcaíno, Juan A ; Deutsch, Eric W ; Wang, Rui ; Csordas, Attila ; Reisinger, Florian ; Ríos, Daniel ; Dianes, José A ; Sun, Zhi ; Farrah, Terry ; Bandeira, Nuno ; Binz, Pierre-Alain ; Xenarios, Ioannis ; Eisenacher, Martin ; Mayer, Gerhard ; Gatto, Laurent ; Campos, Alex ; Chalkley, Robert J ; Kraus, Hans-Joachim ; Albar, Juan Pablo ; Martinez-Bartolomé, Salvador ; Apweiler, Rolf ; Omenn, Gilbert S ; Martens, Lennart ; Jones, Andrew R ; Hermjakob, Henning
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2014-03, Vol.32 (3), p.223-226
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ArticlesPeer ReviewedFull Text
MaxDIA enables library-based and library-free data-independent acquisition proteomics
Author / Creator:Sinitcyn, Pavel ; Hamzeiy, Hamid ; Salinas Soto, Favio ; Itzhak, Daniel ; McCarthy, Frank ; Wichmann, Christoph ; Steger, Martin ; Ohmayer, Uli ; Distler, Ute ; Kaspar-Schoenefeld, Stephanie ; Prianichnikov, Nikita ; Yılmaz, Şule ; Rudolph, Jan Daniel ; Tenzer, Stefan ; Perez-Riverol, Yasset ; Nagaraj, Nagarjuna ; Humphrey, Sean J. ; Cox, Jürgen
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2021-12, Vol.39 (12), p.1563-1573
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ArticlesPeer ReviewedFull Text
The Perseus computational platform for comprehensive analysis of (prote)omics data
Author / Creator:Tyanova, Stefka ; Temu, Tikira ; Sinitcyn, Pavel ; Carlson, Arthur ; Hein, Marco Y ; Geiger, Tamar ; Mann, Matthias ; Cox, Jürgen
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2016-09, Vol.13 (9), p.731-740
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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
Author / Creator:Tyanova, Stefka ; Temu, Tikira ; Cox, Juergen
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2016-12, Vol.11 (12), p.2301-2319
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A dream of single-cell proteomics
Author / Creator:Marx, Vivien
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-09, Vol.16 (9), p.809-812
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Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
Author / Creator:Yu, Fengchao ; Teo, Guo Ci ; Kong, Andy T. ; Fröhlich, Klemens ; Li, Ginny Xiaohe ; Demichev, Vadim ; Nesvizhskii, Alexey I.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-07, Vol.14 (1), p.4154-4154, Article 4154
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ArticlesPeer ReviewedFull Text
Global detection of human variants and isoforms by deep proteome sequencing
Author / Creator:Sinitcyn, Pavel ; Richards, Alicia L. ; Weatheritt, Robert J. ; Brademan, Dain R. ; Marx, Harald ; Shishkova, Evgenia ; Meyer, Jesse G. ; Hebert, Alexander S. ; Westphall, Michael S. ; Blencowe, Benjamin J. ; Cox, Jürgen ; Coon, Joshua J.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2023-12, Vol.41 (12), p.1776-1786
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Quantitative single-cell proteomics as a tool to characterize cellular hierarchies
Author / Creator:Schoof, Erwin M. ; Furtwängler, Benjamin ; Üresin, Nil ; Rapin, Nicolas ; Savickas, Simonas ; Gentil, Coline ; Lechman, Eric ; Keller, Ulrich auf dem ; Dick, John E. ; Porse, Bo T.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-06, Vol.12 (1), p.3341-3341, Article 3341
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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
Author / Creator:Ouspenskaia, Tamara ; Law, Travis ; Clauser, Karl R. ; Klaeger, Susan ; Sarkizova, Siranush ; Aguet, François ; Li, Bo ; Christian, Elena ; Knisbacher, Binyamin A. ; Le, Phuong M. ; Hartigan, Christina R. ; Keshishian, Hasmik ; Apffel, Annie ; Oliveira, Giacomo ; Zhang, Wandi ; Chen, Sarah ; Chow, Yuen Ting ; Ji, Zhe ; Jungreis, Irwin ; Shukla, Sachet A. ; Justesen, Sune ; Bachireddy, Pavan ; Kellis, Manolis ; Getz, Gad ; Hacohen, Nir ; Keskin, Derin B. ; Carr, Steven A. ; Wu, Catherine J. ; Regev, Aviv
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-02, Vol.40 (2), p.209-217
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ArticlesPeer ReviewedFull Text
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry
Author / Creator:Tran, Ngoc Hieu ; Qiao, Rui ; Xin, Lei ; Chen, Xin ; Liu, Chuyi ; Zhang, Xianglilan ; Shan, Baozhen ; Ghodsi, Ali ; Li, Ming
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-01, Vol.16 (1), p.63-66
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Improved prediction of protein-protein interactions using AlphaFold2

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Philosopher: a versatile toolkit for shotgun proteomics data analysis

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Large-scale integration of the plasma proteome with genetics and disease

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Hierarchical graph learning for protein–protein interaction

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DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

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Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

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MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

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diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

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Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

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Standardized annotation of translated open reading frames

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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

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MaxDIA enables library-based and library-free data-independent acquisition proteomics

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The Perseus computational platform for comprehensive analysis of (prote)omics data

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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

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A dream of single-cell proteomics

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Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

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Global detection of human variants and isoforms by deep proteome sequencing

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Quantitative single-cell proteomics as a tool to characterize cellular hierarchies

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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

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Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry

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