Ruedi Aebersold - Publications

Systems biology Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 

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Year Citation  Score
2024 Frommelt F, Fossati A, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M. DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature Methods. 21: 635-647. PMID 38532014 DOI: 10.1038/s41592-024-02211-y  0.329
2024 Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, ... Aebersold R, et al. The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of Proteome Research. PMID 38232391 DOI: 10.1021/acs.jproteome.3c00591  0.364
2023 Bludau I, Nicod C, Martelli C, Xue P, Heusel M, Fossati A, Uliana F, Frommelt F, Aebersold R, Collins BC. Rapid Profiling of Protein Complex Reorganization in Perturbed Systems. Journal of Proteome Research. PMID 37058003 DOI: 10.1021/acs.jproteome.3c00125  0.307
2023 Uliana F, Ciuffa R, Mishra R, Fossati A, Frommelt F, Keller S, Mehnert M, Birkeland ES, van Drogen F, Srejic N, Peter M, Tapon N, Aebersold R, Gstaiger M. Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration. Molecular Systems Biology. e11024. PMID 36896621 DOI: 10.15252/msb.202211024  0.32
2021 Omenn GS, Lane L, Overall CM, Paik YK, Cristea IM, Corrales FJ, Lindskog C, Weintraub S, Roehrl MHA, Liu S, Bandeira N, Srivastava S, Chen YJ, Aebersold R, Moritz RL, et al. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research. PMID 34670092 DOI: 10.1021/acs.jproteome.1c00590  0.316
2021 Zhu Y, Aebersold R, Mann M, Guo T. SnapShot: Clinical proteomics. Cell. 184: 4840-4840.e1. PMID 34478659 DOI: 10.1016/j.cell.2021.08.015  0.306
2021 Meier-Abt F, Lu J, Cannizzaro E, Pohly MF, Kummer S, Pfammatter S, Kunz L, Collins BC, Nadeu F, Lee KS, Xue P, Gwerder M, Roiss M, Hüllein J, Scheinost S, ... ... Aebersold R, et al. The Protein Landscape of Chronic Lymphocytic Leukemia (CLL). Blood. PMID 34189564 DOI: 10.1182/blood.2020009741  0.316
2021 Bludau I, Frank M, Dörig C, Cai Y, Heusel M, Rosenberger G, Picotti P, Collins BC, Röst H, Aebersold R. Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature Communications. 12: 3810. PMID 34155216 DOI: 10.1038/s41467-021-24030-x  0.32
2021 Mori M, Zhang Z, Banaei-Esfahani A, Lalanne JB, Okano H, Collins BC, Schmidt A, Schubert OT, Lee DS, Li GW, Aebersold R, Hwa T, Ludwig C. From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Molecular Systems Biology. 17: e9536. PMID 34032011 DOI: 10.15252/msb.20209536  0.328
2021 Fossati A, Li C, Uliana F, Wendt F, Frommelt F, Sykacek P, Heusel M, Hallal M, Bludau I, Capraz T, Xue P, Song J, Wollscheid B, Purcell AW, Gstaiger M, ... Aebersold R, et al. PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature Methods. PMID 33859439 DOI: 10.1038/s41592-021-01107-5  0.372
2021 Fossati A, Frommelt F, Uliana F, Martelli C, Vizovisek M, Gillet L, Collins B, Gstaiger M, Aebersold R. System-Wide Profiling of Protein Complexes Via Size Exclusion Chromatography-Mass Spectrometry (SEC-MS). Methods in Molecular Biology (Clifton, N.J.). 2259: 269-294. PMID 33687722 DOI: 10.1007/978-1-0716-1178-4_18  0.389
2020 Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Systems. 11: 589-607.e8. PMID 33333029 DOI: 10.1016/j.cels.2020.11.006  0.334
2020 Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, et al. Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project. Journal of Proteome Research. PMID 32931287 DOI: 10.1021/Acs.Jproteome.0C00485  0.457
2020 Zhu T, Zhu Y, Xuan Y, Gao H, Cai X, Piersma SR, Pham TV, Schelfhorst T, Haas RRGD, Bijnsdorp IV, Sun R, Yue L, Ruan G, Zhang Q, Hu M, ... ... Aebersold R, et al. DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. Genomics, Proteomics & Bioinformatics. PMID 32795611 DOI: 10.1016/J.Gpb.2019.11.008  0.451
2020 Poulos RC, Hains PG, Shah R, Lucas N, Xavier D, Manda SS, Anees A, Koh JMS, Mahboob S, Wittman M, Williams SG, Sykes EK, Hecker M, Dausmann M, Wouters MA, ... ... Aebersold R, et al. Strategies to enable large-scale proteomics for reproducible research. Nature Communications. 11: 3793. PMID 32732981 DOI: 10.1038/S41467-020-17641-3  0.387
2020 Buljan M, Ciuffa R, van Drogen A, Vichalkovski A, Mehnert M, Rosenberger G, Lee S, Varjosalo M, Pernas LE, Spegg V, Snijder B, Aebersold R, Gstaiger M. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. Molecular Cell. PMID 32707033 DOI: 10.1016/J.Molcel.2020.07.001  0.318
2020 Poghosyan E, Iacovache I, Faltova L, Leitner A, Yang P, Diener DR, Aebersold R, Zuber B, Ishikawa T. The structure and symmetry of the radial spoke protein complex in flagella. Journal of Cell Science. 133. PMID 32694165 DOI: 10.1242/Jcs.245233  0.311
2020 Bludau I, Heusel M, Frank M, Rosenberger G, Hafen R, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R. Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nature Protocols. PMID 32690956 DOI: 10.1038/S41596-020-0332-6  0.45
2020 Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nature Communications. 11: 3563. PMID 32678104 DOI: 10.1038/S41467-020-17387-Y  0.351
2020 Thomas SN, Friedrich B, Schnaubelt M, Chan DW, Zhang H, Aebersold R. Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes. Iscience. 23: 101079. PMID 32534439 DOI: 10.1016/J.Isci.2020.101079  0.407
2020 Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, et al. Publisher Correction: ChromID identifies the protein interactome at chromatin marks. Nature Biotechnology. 38: 757. PMID 32518402 DOI: 10.1038/S41587-020-0484-5  0.342
2020 Janacova L, Faktor J, Capkova L, Paralova V, Pospisilova A, Podhorec J, Ebhardt HA, Hrstka R, Nenutil R, Aebersold R, Bouchal P. SWATH-MS Analysis of FFPE Tissues Identifies Stathmin as a Potential Marker of Endometrial Cancer in Patients Exposed to Tamoxifen. Journal of Proteome Research. PMID 32343582 DOI: 10.1021/Acs.Jproteome.0C00064  0.318
2020 Bensimon A, Koch JP, Francica P, Roth SM, Riedo R, Glück AA, Orlando E, Blaukat A, Aebersold DM, Zimmer Y, Aebersold R, Medová M. Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. Molecular Oncology. PMID 32336009 DOI: 10.1002/1878-0261.12696  0.317
2020 Bludau I, Aebersold R. Proteomic and interactomic insights into the molecular basis of cell functional diversity. Nature Reviews. Molecular Cell Biology. PMID 32235894 DOI: 10.1038/S41580-020-0231-2  0.366
2020 Shao W, Caron E, Pedrioli P, Aebersold R. The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses. Methods in Molecular Biology (Clifton, N.J.). 2120: 173-181. PMID 32124319 DOI: 10.1007/978-1-0716-0327-7_12  0.339
2020 Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, et al. ChromID identifies the protein interactome at chromatin marks. Nature Biotechnology. PMID 32123383 DOI: 10.1038/S41587-020-0434-2  0.357
2020 Plank M, Perepelkina M, Müller M, Vaga S, Zou X, Bourgoint C, Berti M, Saarbach J, Haesendonckx S, Winssinger N, Aebersold R, Loewith R. Chemical genetics of AGC-kinases reveals shared targets of Ypk1, Protein Kinase A and Sch9. Molecular & Cellular Proteomics : McP. PMID 32102971 DOI: 10.1074/Mcp.Ra120.001955  0.324
2020 Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology. PMID 32094660 DOI: 10.1038/S41587-020-0457-8  0.317
2020 Sun R, Hunter C, Chen C, Ge W, Morrice N, Liang S, Zhu T, Yuan C, Ruan G, Zhang Q, Cai X, Yu X, Chen L, Dai S, Luan Z, ... Aebersold R, et al. Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS. Journal of Proteome Research. PMID 32053377 DOI: 10.1021/Acs.Jproteome.9B00671  0.439
2020 Heusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder MI, Liu Y, Collins BC, Gstaiger M, Kutay U, Aebersold R. A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Systems. PMID 32027860 DOI: 10.1016/J.Cels.2020.01.001  0.42
2020 Čuklina J, Pedrioli PGA, Aebersold R. Review of Batch Effects Prevention, Diagnostics, and Correction Approaches. Methods in Molecular Biology (Clifton, N.J.). 2051: 373-387. PMID 31552638 DOI: 10.1007/978-1-4939-9744-2_16  0.311
2019 Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Scientific Data. 6: 278. PMID 31757973 DOI: 10.1038/S41597-019-0294-0  0.483
2019 Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, ... ... Aebersold R, et al. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. Iscience. 21: 664-680. PMID 31733513 DOI: 10.1016/J.Isci.2019.10.059  0.6
2019 Zhu Y, Weiss T, Zhang Q, Sun R, Wang B, Yi X, Wu Z, Gao H, Cai X, Ruan G, Zhu T, Xu C, Lou S, Yu X, Gillet L, ... ... Aebersold R, et al. High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification. Molecular Oncology. PMID 31495056 DOI: 10.1002/1878-0261.12570  0.333
2019 Aebersold R, Blattmann P. Mass Spectrometric Exploration of the Biochemical Basis of Living Systems. Chimia. 73: 540-548. PMID 31431214 DOI: 10.2533/Chimia.2019.540  0.335
2019 Helleboid PY, Heusel M, Duc J, Piot C, Thorball CW, Coluccio A, Pontis J, Imbeault M, Turelli P, Aebersold R, Trono D. The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. The Embo Journal. e101220. PMID 31403225 DOI: 10.15252/Embj.2018101220  0.36
2019 Kaustov L, Lemak A, Wu H, Faini M, Fan L, Fang X, Zeng H, Duan S, Allali-Hassani A, Li F, Wei Y, Vedadi M, Aebersold R, Wang Y, Houliston S, et al. The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions. Nucleic Acids Research. PMID 31400120 DOI: 10.1093/Nar/Gkz697  0.308
2019 Bouchal P, Schubert OT, Faktor J, Capkova L, Imrichova H, Zoufalova K, Paralova V, Hrstka R, Liu Y, Ebhardt HA, Budinska E, Nenutil R, Aebersold R. Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Reports. 28: 832-843.e7. PMID 31315058 DOI: 10.1016/J.Celrep.2019.06.046  0.326
2019 Huttenhain R, Choi M, Martin de la Fuente L, Oehl K, Chang CY, Zimmermann AK, Malander S, Olsson H, Surinova S, Clough T, Heinzelmann-Schwarz V, Wild PJ, Dinulescu D, Niméus E, Vitek O, ... Aebersold R, et al. A targeted mass spectrometry strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancer. Molecular & Cellular Proteomics : McP. PMID 31289117 DOI: 10.1074/Mcp.Ra118.001221  0.388
2019 Paulitschke V, Eichhoff O, Gerner C, Paulitschke P, Bileck A, Mohr T, Cheng PF, Leitner A, Guenova E, Saulite I, Freiberger SN, Irmisch A, Knapp B, Zila N, Chatziisaak TP, ... ... Aebersold R, et al. Proteomic identification of a marker signature for MAPKi resistance in melanoma. The Embo Journal. e95874. PMID 31267558 DOI: 10.15252/Embj.201695874  0.312
2019 Shao W, Guo T, Toussaint NC, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser CD, Poyet C, ... ... Aebersold R, et al. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications. 10: 2524. PMID 31175306 DOI: 10.1038/S41467-019-10513-5  0.406
2019 Sajic T, Ciuffa R, Lemos V, Xu P, Leone V, Li C, Williams EG, Makris G, Banaei-Esfahani A, Heikenwalder M, Schoonjans K, Aebersold R. A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Scientific Reports. 9: 6913. PMID 31061415 DOI: 10.1038/S41598-019-43091-Z  0.382
2019 Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews PC, Bernfur K, Borchers CH, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis TN, et al. The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry. PMID 31045356 DOI: 10.1021/Acs.Analchem.9B00658  0.417
2019 Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals. Cell. PMID 31031010 DOI: 10.1016/J.Cell.2019.03.015  0.559
2019 Amon S, Meier-Abt F, Gillet LC, Dimitrieva S, Theocharides AP, Manz MG, Aebersold R. Sensitive quantitative proteomics of human hematopoietic stem and progenitor cells by data-independent acquisition mass spectrometry. Molecular & Cellular Proteomics : McP. PMID 30975897 DOI: 10.1074/Mcp.Tir119.001431  0.351
2019 Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J. The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis. Cell. PMID 30955883 DOI: 10.1016/J.Cell.2019.03.012  0.323
2019 Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, ... ... Aebersold R, et al. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology. PMID 30778230 DOI: 10.1038/S41587-019-0037-Y  0.338
2019 Blattmann P, Stutz V, Lizzo G, Richard J, Gut P, Aebersold R. Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Scientific Data. 6: 190011. PMID 30747917 DOI: 10.1038/Sdata.2019.11  0.448
2019 Sendoel A, Subasic D, Ducoli L, Keller M, Michel E, Kohler I, Singh KD, Zheng X, Brümmer A, Imig J, Kishore S, Wu Y, Kanitz A, Kaech A, Mittal N, ... ... Aebersold R, et al. MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death and Differentiation. PMID 30728462 DOI: 10.2210/Pdb6Fbl/Pdb  0.319
2019 Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R. Complex-centric proteome profiling by SEC-SWATH-MS. Molecular Systems Biology. 15: e8438. PMID 30642884 DOI: 10.15252/Msb.20188438  0.444
2019 Orlando E, Aebersold R. On the contribution of mass spectrometry-based platforms to the field of personalized oncology Trac Trends in Analytical Chemistry. 110: 129-142. DOI: 10.1016/J.Trac.2018.10.018  0.37
2018 Collins BC, Aebersold R. Proteomics goes parallel. Nature Biotechnology. 36: 1051-1053. PMID 30412198 DOI: 10.1038/Nbt.4288  0.344
2018 Schütz S, Michel E, Damberger FF, Oplová M, Peña C, Leitner A, Aebersold R, Allain FH, Panse VG. Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2. Nature Communications. 9: 3669. PMID 30201955 DOI: 10.1038/S41467-018-06160-X  0.389
2018 Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Molecular Systems Biology. 14: e8126. PMID 30104418 DOI: 10.15252/Msb.20178126  0.416
2018 Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E. A tissue-based draft map of the murine MHC class I immunopeptidome. Scientific Data. 5: 180157. PMID 30084848 DOI: 10.1038/Sdata.2018.157  0.347
2018 Williams EG, Wu Y, Ryu D, Kim JY, Lan J, Hasan M, Wolski W, Jha P, Halter C, Auwerx J, Aebersold R. Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. Molecular & Cellular Proteomics : McP. PMID 29945935 DOI: 10.1074/Mcp.Ra118.000554  0.393
2018 Sajic T, Liu Y, Arvaniti E, Surinova S, Williams EG, Schiess R, Hüttenhain R, Sethi A, Pan S, Brentnall TA, Chen R, Blattmann P, Friedrich B, Niméus E, Malander S, ... ... Aebersold R, et al. Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS. Cell Reports. 23: 2819-2831.e5. PMID 29847809 DOI: 10.1016/J.Celrep.2018.04.114  0.358
2018 Feller C, Aebersold R. A Proteomic Connectivity Map. Cell Systems. 6: 403-405. PMID 29698646 DOI: 10.1016/J.Cels.2018.04.007  0.329
2018 Hülsmann J, Kravic B, Weith M, Gstaiger M, Aebersold RH, Collins BC, Meyer H. AP-SWATH reveals direct involvement of VCP/p97 in integrated stress response signaling through facilitating CReP/PPP1R15B degradation. Molecular & Cellular Proteomics : McP. PMID 29599191 DOI: 10.1074/Mcp.Ra117.000471  0.33
2018 Buljan M, Blattmann P, Aebersold R, Boutros M. Systematic characterization of pan-cancer mutation clusters. Molecular Systems Biology. 14: e7974. PMID 29572294 DOI: 10.15252/Msb.20177974  0.371
2018 Uzozie AC, Aebersold R. Advancing translational research and precision medicine with targeted proteomics. Journal of Proteomics. PMID 29476807 DOI: 10.1016/J.Jprot.2018.02.021  0.41
2018 Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, et al. How many human proteoforms are there? Nature Chemical Biology. 14: 206-214. PMID 29443976 DOI: 10.1038/Nchembio.2576  0.702
2018 Eliseev B, Yeramala L, Leitner A, Karuppasamy M, Raimondeau E, Huard K, Alkalaeva E, Aebersold R, Schaffitzel C. Structure of a human cap-dependent 48S translation pre-initiation complex. Nucleic Acids Research. PMID 29401259 DOI: 10.1093/Nar/Gky054  0.301
2017 Clerici M, Faini M, Aebersold R, Jinek M. Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex. Elife. 6. PMID 29274231 DOI: 10.7554/Elife.33111  0.316
2017 Patel N, Stengel F, Aebersold R, Gold MG. Molecular basis of AKAP79 regulation by calmodulin. Nature Communications. 8: 1681. PMID 29162807 DOI: 10.1038/S41467-017-01715-W  0.323
2017 Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature Communications. 8: 1212. PMID 29089484 DOI: 10.1038/S41467-017-01422-6  0.404
2017 Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, ... ... Aebersold R, et al. The SysteMHC Atlas project. Nucleic Acids Research. PMID 28985418 DOI: 10.1093/Nar/Gkx664  0.387
2017 Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. Journal of Proteome Research. PMID 28938075 DOI: 10.1021/Acs.Jproteome.7B00467  0.393
2017 Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, ... ... Aebersold R, et al. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications. 8: 291. PMID 28827567 DOI: 10.1038/S41467-017-00249-5  0.614
2017 Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, ... Aebersold R, et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods. PMID 28825704 DOI: 10.1038/Nmeth.4398  0.454
2017 Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Reports. 20: 1229-1241. PMID 28768205 DOI: 10.1016/J.Celrep.2017.07.025  0.391
2017 Wu Y, Williams EG, Aebersold R. Application of SWATH Proteomics to Mouse Biology. Current Protocols in Mouse Biology. 7: 130-143. PMID 28628219 DOI: 10.1002/Cpmo.28  0.38
2017 Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nature Biotechnology. PMID 28604659 DOI: 10.1038/Nbt.3908  0.397
2017 Schubert OT, Röst HL, Collins BC, Rosenberger G, Aebersold R. Quantitative proteomics: challenges and opportunities in basic and applied research. Nature Protocols. 12: 1289-1294. PMID 28569762 DOI: 10.1038/Nprot.2017.040  0.35
2017 Caron E, Roncagalli R, Hase T, Wolski WE, Choi M, Menoita MG, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins BC, ... ... Aebersold R, et al. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports. 18: 3219-3226. PMID 28355572 DOI: 10.1016/J.Celrep.2017.03.019  0.391
2017 Dorn G, Leitner A, Boudet J, Campagne S, von Schroetter C, Moursy A, Aebersold R, Allain FH. Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS. Nature Methods. PMID 28346450 DOI: 10.1038/Nmeth.4235  0.386
2017 Yadav L, Tamene F, Göös H, van Drogen A, Katainen R, Aebersold R, Gstaiger M, Varjosalo M. Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. Cell Systems. PMID 28330616 DOI: 10.1016/J.Cels.2017.02.011  0.413
2017 Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg CH, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, ... ... Aebersold R, et al. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Molecular & Cellular Proteomics : McP. PMID 28292943 DOI: 10.1074/Mcp.M116.065326  0.602
2017 Röst HL, Aebersold R, Schubert OT. Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms. Methods in Molecular Biology (Clifton, N.J.). 1550: 289-307. PMID 28188537 DOI: 10.1007/978-1-4939-6747-6_20  0.444
2017 Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, ... ... Aebersold R, et al. Building ProteomeTools based on a complete synthetic human proteome. Nature Methods. PMID 28135259 DOI: 10.1038/Nmeth.4153  0.388
2017 Zhong Q, Guo T, Toussaint N, Wagner U, Charmpi K, Calzone L, Beyer A, Aebersold R, Wild PJ. Abstract 5565: Multi-omic profiling of prostate cancer evolution in 39 patients Cancer Research. 77: 5565-5565. DOI: 10.1158/1538-7445.Am2017-5565  0.331
2017 Dorn G, Leitner A, Boudet J, Campagne S, Schroetter Cv, Moursy A, Aebersold R, Allain FH-. Mapping protein-RNA interactions with single residue resolution by CLIR-MS/MS Protocol Exchange. DOI: 10.1038/Protex.2017.031  0.355
2016 Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R. System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects. Journal of Proteome Research. PMID 27936760 DOI: 10.1021/Acs.Jproteome.6B00815  0.314
2016 Magliarelli HF, Matondo M, Mészáros G, Goginashvili A, Erbs E, Zhang Z, Mihlan M, Wolfrum C, Aebersold R, Sumara I, Ricci R. Liver ubiquitome uncovers nutrient-stress-mediated trafficking and secretion of complement C3. Cell Death & Disease. 7: e2411. PMID 27735945 DOI: 10.1038/Cddis.2016.312  0.305
2016 Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. A High-Density Map for Navigating the Human Polycomb Complexome. Cell Reports. 17: 583-595. PMID 27705803 DOI: 10.1016/J.Celrep.2016.08.096  0.372
2016 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. A multicenter study benchmarks software tools for label-free proteome quantification. Nature Biotechnology. PMID 27701404 DOI: 10.1038/Nbt.3685  0.416
2016 Aebersold R, Mann M. Mass-spectrometric exploration of proteome structure and function. Nature. 537: 347-55. PMID 27629641 DOI: 10.1038/Nature19949  0.392
2016 Okada H, Ebhardt HA, Vonesch SC, Aebersold R, Hafen E. Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster. Nature Communications. 7: 12649. PMID 27582081 DOI: 10.1038/Ncomms12649  0.329
2016 Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, ... ... Aebersold R, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods. 13: 741-748. PMID 27575624 DOI: 10.1038/Nmeth.3959  0.39
2016 Van Eyk JE, Corrales FJ, Aebersold R, Cerciello F, Deutsch EW, Roncada P, Sanchez JC, Yamamoto T, Yang P, Zhang H, Omenn GS. Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. Journal of Proteome Research. 15: 3979-3987. PMID 27573249 DOI: 10.1021/Acs.Jproteome.6B00444  0.381
2016 Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. Journal of Proteome Research. 15: 3961-3970. PMID 27490519 DOI: 10.1021/Acs.Jproteome.6B00392  0.382
2016 Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nature Methods. PMID 27479329 DOI: 10.1038/Nmeth.3954  0.428
2016 M Uumlller DB, Schubert OT, R Oumlst H, Aebersold R, Vorholt JA. Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization. Molecular & Cellular Proteomics : McP. PMID 27457762 DOI: 10.1074/Mcp.M116.058164  0.331
2016 Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, ... ... Aebersold R, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. PMID 27453469 DOI: 10.1016/J.Cell.2016.06.041  0.573
2016 Williams EG, Wu Y, Jha P, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J. Systems proteomics of liver mitochondria function. Science (New York, N.Y.). 352: aad0189. PMID 27284200 DOI: 10.1126/Science.Aad0189  0.415
2016 Groner AC, Cato L, de Tribolet-Hardy J, Bernasocchi T, Janouskova H, Melchers D, Houtman R, Cato AC, Tschopp P, Gu L, Corsinotti A, Zhong Q, Fankhauser C, Fritz C, Poyet C, ... ... Aebersold R, et al. TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer. Cancer Cell. PMID 27238081 DOI: 10.1016/J.Ccell.2016.04.012  0.313
2016 Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell. 165: 535-50. PMID 27104977 DOI: 10.1016/J.Cell.2016.03.014  0.364
2016 Shao S, Guo T, Gross V, Lazarev A, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R. Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics using MicroPestle-assisted Pressure Cycling Technology. Journal of Proteome Research. PMID 27098501 DOI: 10.1021/Acs.Jproteome.5B01136  0.423
2016 Faini M, Stengel F, Aebersold R. The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology. Journal of the American Society For Mass Spectrometry. PMID 27056566 DOI: 10.1007/S13361-016-1382-4  0.397
2016 Blattmann P, Heusel M, Aebersold R. SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools. Plos One. 11: e0153160. PMID 27054327 DOI: 10.1371/Journal.Pone.0153160  0.392
2016 Gillet LC, Leitner A, Aebersold R. Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing. Annual Review of Analytical Chemistry (Palo Alto, Calif.). PMID 27049628 DOI: 10.1146/Annurev-Anchem-071015-041535  0.493
2016 Faridi P, Aebersold R, Caron E. A first dataset toward a standardized community-driven global mapping of the human immunopeptidome. Data in Brief. 7: 201-5. PMID 26958639 DOI: 10.1016/J.Dib.2016.02.016  0.334
2016 Liu Y, Aebersold R. The interdependence of transcript and protein abundance: new data-new complexities. Molecular Systems Biology. 12: 856. PMID 26792872 DOI: 10.15252/Msb.20156720  0.352
2016 Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, ... ... Aebersold R, et al. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clinical Chemistry. 62: 48-69. PMID 26719571 DOI: 10.1373/Clinchem.2015.250563  0.432
2015 Goh WW, Guo T, Aebersold R, Wong L. Quantitative proteomics signature profiling based on network contextualization. Biology Direct. 10: 71. PMID 26666224 DOI: 10.1186/S13062-015-0098-X  0.37
2015 Leitner A, Faini M, Stengel F, Aebersold R. Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines. Trends in Biochemical Sciences. PMID 26654279 DOI: 10.1016/J.Tibs.2015.10.008  0.404
2015 Schmidt A, Kochanowski K, Vedelaar S, Ahrné E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold R, Heinemann M. The quantitative and condition-dependent Escherichia coli proteome. Nature Biotechnology. PMID 26641532 DOI: 10.1038/Nbt.3418  0.433
2015 Caron E, Kowalewski DJ, Chiek Koh C, Sturm T, Schuster H, Aebersold R. Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Molecular & Cellular Proteomics : McP. 14: 3105-17. PMID 26628741 DOI: 10.1074/Mcp.O115.052431  0.371
2015 Schubert OT, Aebersold R. Microbial Proteome Profiling and Systems Biology: Applications to Mycobacterium tuberculosis. Advances in Experimental Medicine and Biology. 883: 235-54. PMID 26621471 DOI: 10.1007/978-3-319-23603-2_13  0.313
2015 Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Molecular Biology of the Cell. 26: 3926-31. PMID 26543201 DOI: 10.1091/Mbc.E15-07-0507  0.444
2015 Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R. xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nature Methods. PMID 26501516 DOI: 10.1038/Nmeth.3631  0.434
2015 Thomas S, Harlan R, Chen J, Aiyetan P, Liu Y, Sokoll LJ, Aebersold R, Chan DW, Zhang H. Multiplexed targeted mass spectrometry-based assays for the quantification of N-linked glycosite-containing peptides in serum. Analytical Chemistry. PMID 26451657 DOI: 10.1021/Acs.Analchem.5B02063  0.395
2015 Shao S, Guo T, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R. Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry. Proteomics. PMID 26287124 DOI: 10.1002/Pmic.201500161  0.348
2015 Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC, Zhou L. Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress. Journal of Proteome Research. PMID 26260330 DOI: 10.1021/Acs.Jproteome.5B00443  0.312
2015 Surinova S, Choi M, Tao S, Schüffler PJ, Chang CY, Clough T, Vysloužil K, Khoylou M, Srovnal J, Liu Y, Matondo M, Hüttenhain R, Weisser H, Buhmann JM, Hajdúch M, ... ... Aebersold R, et al. Prediction of colorectal cancer diagnosis based on circulating plasma proteins. Embo Molecular Medicine. PMID 26253081 DOI: 10.15252/Emmm.201404873  0.367
2015 Surinova S, Radová L, Choi M, Srovnal J, Brenner H, Vitek O, Hajdúch M, Aebersold R. Non-invasive prognostic protein biomarker signatures associated with colorectal cancer. Embo Molecular Medicine. 7: 1153-65. PMID 26253080 DOI: 10.15252/Emmm.201404874  0.335
2015 Nillegoda NB, Kirstein J, Szlachcic A, Berynskyy M, Stank A, Stengel F, Arnsburg K, Gao X, Scior A, Aebersold R, Guilbride DL, Wade RC, Morimoto RI, Mayer MP, Bukau B. Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nature. 524: 247-51. PMID 26245380 DOI: 10.1038/Nature14884  0.392
2015 Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. Molecular & Cellular Proteomics : McP. 14: 2800-13. PMID 26199342 DOI: 10.1074/Mcp.O114.042267  0.392
2015 Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, ... ... Aebersold R, et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods. PMID 26121405 DOI: 10.1038/Nmeth.3472  0.532
2015 Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics. PMID 26097198 DOI: 10.1002/Pmic.201500004  0.353
2015 Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R. Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis. Cell Host & Microbe. 18: 96-108. PMID 26094805 DOI: 10.1016/J.Chom.2015.06.001  0.424
2015 Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R. Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2. Molecular Cell. 58: 977-88. PMID 26028537 DOI: 10.1016/J.Molcel.2015.04.031  0.332
2015 Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. Journal of Proteome Research. PMID 25944384 DOI: 10.1021/Acs.Jproteome.5B00315  0.43
2015 Röst HL, Schmitt U, Aebersold R, Malmström L. Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. Plos One. 10: e0125108. PMID 25927999 DOI: 10.1371/Journal.Pone.0125108  0.385
2015 Oliveira AP, Ludwig C, Zampieri M, Weisser H, Aebersold R, Sauer U. Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Science Signaling. 8: rs4. PMID 25921291 DOI: 10.1126/Scisignal.2005768  0.35
2015 Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, ... ... Aebersold R, et al. A mass spectrometric-derived cell surface protein atlas. Plos One. 10: e0121314. PMID 25894527 DOI: 10.1371/Journal.Pone.0121314  0.372
2015 Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R. Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways. The Journal of Biological Chemistry. 290: 14963-78. PMID 25882841 DOI: 10.1074/Jbc.M114.627794  0.308
2015 Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N. Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome. Science (New York, N.Y.). 348: 303-8. PMID 25837512 DOI: 10.1126/Science.Aaa3872  0.309
2015 Röst HL, Rosenberger G, Aebersold R, Malmström L. Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (Oxford, England). 31: 2415-7. PMID 25788625 DOI: 10.1093/Bioinformatics/Btv152  0.384
2015 Suni V, Imanishi SY, Maiolica A, Aebersold R, Corthals GL. Confident site localization using a simulated phosphopeptide spectral library. Journal of Proteome Research. 14: 2348-59. PMID 25774671 DOI: 10.1021/Acs.Jproteome.5B00050  0.611
2015 Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature Medicine. 21: 407-13. PMID 25730263 DOI: 10.1038/Nm.3807  0.395
2015 Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nature Protocols. 10: 426-41. PMID 25675208 DOI: 10.1038/Nprot.2015.015  0.598
2015 Liu Y, Buil A, Collins BC, Gillet LC, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology. 11: 786. PMID 25652787 DOI: 10.15252/Msb.20145728  0.374
2015 Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R. Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Molecular & Cellular Proteomics : McP. 14: 739-49. PMID 25561506 DOI: 10.1074/Mcp.M113.035550  0.503
2015 Shao S, Guo T, Aebersold R. Mass spectrometry-based proteomic quest for diabetes biomarkers. Biochimica Et Biophysica Acta. 1854: 519-527. PMID 25556002 DOI: 10.1016/J.Bbapap.2014.12.012  0.325
2015 Bouyssié D, Dubois M, Nasso S, Gonzalez de Peredo A, Burlet-Schiltz O, Aebersold R, Monsarrat B. mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets. Molecular & Cellular Proteomics : McP. 14: 771-81. PMID 25505153 DOI: 10.1074/Mcp.O114.039115  0.367
2015 Sajic T, Liu Y, Aebersold R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics. Clinical Applications. 9: 307-21. PMID 25504613 DOI: 10.1002/Prca.201400117  0.462
2015 Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. Journal of Proteome Research. 14: 787-803. PMID 25495225 DOI: 10.1021/Pr500834Z  0.429
2015 Kuilman T, Maiolica A, Godfrey M, Scheidel N, Aebersold R, Uhlmann F. Identification of Cdk targets that control cytokinesis. The Embo Journal. 34: 81-96. PMID 25371407 DOI: 10.15252/Embj.201488958  0.326
2015 Cheng L, Liu Y, Chang C, Röst H, Aebersold R, Vitek O. Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition Bmc Bioinformatics. 16. DOI: 10.1186/1471-2105-16-S2-A4  0.303
2014 Gengenbacher M, Mouritsen J, Schubert OT, Aebersold R, Kaufmann SH. Mycobacterium tuberculosis in the Proteomics Era. Microbiology Spectrum. 2. PMID 26105825 DOI: 10.1128/Microbiolspec.Mgm2-0020-2013  0.419
2014 Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, ... ... Aebersold R, et al. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data. 1: 140031. PMID 25977788 DOI: 10.1038/Sdata.2014.31  0.478
2014 Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Molecular Systems Biology. 10: 767. PMID 25492886 DOI: 10.15252/Msb.20145112  0.338
2014 Joachimiak LA, Walzthoeni T, Liu CW, Aebersold R, Frydman J. The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. Cell. 159: 1042-55. PMID 25416944 DOI: 10.1016/J.Cell.2014.10.042  0.315
2014 Ebhardt HA, Nan J, Chaulk SG, Fahlman RP, Aebersold R. Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage. Rapid Communications in Mass Spectrometry : Rcm. 28: 2735-43. PMID 25380496 DOI: 10.1002/Rcm.7069  0.381
2014 Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N. The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature. 515: 283-6. PMID 25271403 DOI: 10.1038/Nature13895  0.315
2014 Wu Y, Williams EG, Dubuis S, Mottis A, Jovaisaite V, Houten SM, Argmann CA, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R. Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell. 158: 1415-30. PMID 25215496 DOI: 10.1016/J.Cell.2014.07.039  0.352
2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40Sâ‹…eIF1â‹…eIF3 translation initiation complex. Cell. 158: 1123-35. PMID 25171412 DOI: 10.1016/J.Cell.2014.07.044  0.306
2014 Birol M, Enchev RI, Padilla A, Stengel F, Aebersold R, Betzi S, Yang Y, Hoh F, Peter M, Dumas C, Echalier A. Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer. Plos One. 9: e105688. PMID 25144743 DOI: 10.1371/Journal.Pone.0105688  0.332
2014 Greco V, Pieragostino D, Piras C, Aebersold R, Wiltfang J, Caltagirone C, Bernardini S, Urbani A. Direct analytical sample quality assessment for biomarker investigation: qualifying cerebrospinal fluid samples. Proteomics. 14: 1954-62. PMID 25044759 DOI: 10.1002/Pmic.201300565  0.301
2014 Braun KA, Vaga S, Dombek KM, Fang F, Palmisano S, Aebersold R, Young ET. Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling. Science Signaling. 7: ra64. PMID 25005228 DOI: 10.1126/Scisignal.2005000  0.345
2014 Fengos G, Schmidt A, Martin K, Fluri E, Aebersold R, Iber D, Pertz O. Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Science. 12: 23. PMID 24987309 DOI: 10.1186/1477-5956-12-23  0.388
2014 Leitner A, Joachimiak LA, Unverdorben P, Walzthoeni T, Frydman J, Förster F, Aebersold R. Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 111: 9455-60. PMID 24938783 DOI: 10.1073/Pnas.1320298111  0.365
2014 Jünger MA, Aebersold R. Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic. Wiley Interdisciplinary Reviews. Developmental Biology. 3: 83-112. PMID 24902836 DOI: 10.1002/Wdev.121  0.452
2014 Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, ... ... Aebersold R, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics : McP. 13: 1905-13. PMID 24760958 DOI: 10.1074/Mcp.M113.035907  0.317
2014 Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics (Oxford, England). 30: 2511-3. PMID 24753486 DOI: 10.1093/Bioinformatics/Btu200  0.448
2014 Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Molecular & Cellular Proteomics : McP. 13: 1753-68. PMID 24741114 DOI: 10.1074/Mcp.M114.038273  0.345
2014 Maiolica A, de Medina-Redondo M, Schoof EM, Chaikuad A, Villa F, Gatti M, Jeganathan S, Lou HJ, Novy K, Hauri S, Toprak UH, Herzog F, Meraldi P, Penengo L, Turk BE, ... ... Aebersold R, et al. Modulation of the chromatin phosphoproteome by the Haspin protein kinase. Molecular & Cellular Proteomics : McP. 13: 1724-40. PMID 24732914 DOI: 10.1074/Mcp.M113.034819  0.335
2014 Toprak UH, Gillet LC, Maiolica A, Navarro P, Leitner A, Aebersold R. Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. Molecular & Cellular Proteomics : McP. 13: 2056-71. PMID 24623587 DOI: 10.1074/Mcp.O113.036475  0.385
2014 Roncagalli R, Hauri S, Fiore F, Liang Y, Chen Z, Sansoni A, Kanduri K, Joly R, Malzac A, Lähdesmäki H, Lahesmaa R, Yamasaki S, Saito T, Malissen M, Aebersold R, et al. Quantitative proteomics analysis of signalosome dynamics in primary T cells identifies the surface receptor CD6 as a Lat adaptor-independent TCR signaling hub. Nature Immunology. 15: 384-92. PMID 24584089 DOI: 10.1038/Ni.2843  0.302
2014 Politis A, Stengel F, Hall Z, Hernández H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R. A mass spectrometry-based hybrid method for structural modeling of protein complexes. Nature Methods. 11: 403-6. PMID 24509631 DOI: 10.1038/Nmeth.2841  0.415
2014 Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, ... ... Aebersold R, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular & Cellular Proteomics : McP. 13: 907-17. PMID 24443746 DOI: 10.1074/Mcp.M113.036095  0.404
2014 Chang CY, Sabidó E, Aebersold R, Vitek O. Targeted protein quantification using sparse reference labeling. Nature Methods. 11: 301-4. PMID 24441934 DOI: 10.1038/Nmeth.2806  0.426
2014 Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 14: 74-7. PMID 24420968 DOI: 10.1002/Pmic.201300246  0.339
2014 Greber BJ, Boehringer D, Leitner A, Bieri P, Voigts-Hoffmann F, Erzberger JP, Leibundgut M, Aebersold R, Ban N. Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature. 505: 515-9. PMID 24362565 DOI: 10.1038/Nature12890  0.338
2014 Leitner A, Walzthoeni T, Aebersold R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nature Protocols. 9: 120-37. PMID 24356771 DOI: 10.1038/Nprot.2013.168  0.456
2014 Kiel C, Ebhardt HA, Burnier J, Portugal C, Sabidó E, Zimmermann T, Aebersold R, Serrano L. Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. Journal of Proteome Research. 13: 300-13. PMID 24313378 DOI: 10.1021/Pr400878X  0.425
2014 Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Bühlmann P. Statistical approach to protein quantification. Molecular & Cellular Proteomics : McP. 13: 666-77. PMID 24255132 DOI: 10.1074/Mcp.M112.025445  0.464
2014 Vialas V, Sun Z, Loureiro y Penha CV, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Aebersold R, Moritz RL, Gil C. A Candida albicans PeptideAtlas. Journal of Proteomics. 97: 62-8. PMID 23811049 DOI: 10.1016/J.Jprot.2013.06.020  0.426
2014 Kalliomäki M, Kouvonen P, Koh C, Collins B, Malmström L, Aebersold R. P-003: Detection of bacterial and host proteins from a single colonic biopsy sample by a new mass spectrometry-based assay in pediatric ulcerative colitis Journal of Crohn's and Colitis. 8: S395. DOI: 10.1016/S1873-9946(14)50007-4  0.306
2014 Quandt A, Espona L, Balasko A, Weisser H, Brusniak MY, Kunszt P, Aebersold R, Malmström L. Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis Eupa Open Proteomics. 5: 21-31. DOI: 10.1016/J.Euprot.2014.10.001  0.381
2013 Hauri S, Wepf A, van Drogen A, Varjosalo M, Tapon N, Aebersold R, Gstaiger M. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Molecular Systems Biology. 9: 713. PMID 24366813 DOI: 10.1002/Msb.201304750  0.352
2013 Cerciello F, Choi M, Nicastri A, Bausch-Fluck D, Ziegler A, Vitek O, Felley-Bosco E, Stahel R, Aebersold R, Wollscheid B. Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring. Clinical Proteomics. 10: 16. PMID 24207061 DOI: 10.1186/1559-0275-10-16  0.302
2013 Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nature Methods. 10: 1246-53. PMID 24162925 DOI: 10.1038/Nmeth.2703  0.43
2013 Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nature Methods. 10: 1239-45. PMID 24162924 DOI: 10.1038/Nmeth.2702  0.594
2013 Liu Y, Hüttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Review of Molecular Diagnostics. 13: 811-25. PMID 24138574 DOI: 10.1586/14737159.2013.845089  0.387
2013 Kahraman A, Herzog F, Leitner A, Rosenberger G, Aebersold R, Malmström L. Cross-link guided molecular modeling with ROSETTA. Plos One. 8: e73411. PMID 24069194 DOI: 10.1371/Journal.Pone.0073411  0.412
2013 Pfaff J, Hennig J, Herzog F, Aebersold R, Sattler M, Niessing D, Meister G. Structural features of Argonaute-GW182 protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 110: E3770-9. PMID 24043833 DOI: 10.1073/Pnas.1308510110  0.383
2013 Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, ... ... Aebersold R, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nature Methods. 10: 730-6. PMID 23921808 DOI: 10.1038/Nmeth.2557  0.616
2013 Surinova S, Hüttenhain R, Chang CY, Espona L, Vitek O, Aebersold R. Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nature Protocols. 8: 1602-19. PMID 23887179 DOI: 10.1038/Nprot.2013.091  0.454
2013 Sabidó E, Wu Y, Bautista L, Porstmann T, Chang CY, Vitek O, Stoffel M, Aebersold R. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Molecular Systems Biology. 9: 681. PMID 23860498 DOI: 10.1038/Msb.2013.36  0.301
2013 Leitner A, Aebersold R. SnapShot: mass spectrometry for protein and proteome analyses. Cell. 154: 252-252.e1. PMID 23827686 DOI: 10.1016/J.Cell.2013.06.025  0.469
2013 Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Molecular & Cellular Proteomics : McP. 12: 2381-2. PMID 23756428 DOI: 10.1074/Mcp.E113.031658  0.412
2013 Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK, Claassen M, Campbell DS, Sun Z, Farrah T, Gengenbacher M, Maiolica A, Kaufmann SH, Moritz RL, Aebersold R. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host & Microbe. 13: 602-12. PMID 23684311 DOI: 10.1016/J.Chom.2013.04.008  0.447
2013 Varjosalo M, Keskitalo S, Van Drogen A, Nurkkala H, Vichalkovski A, Aebersold R, Gstaiger M. The protein interaction landscape of the human CMGC kinase group. Cell Reports. 3: 1306-20. PMID 23602568 DOI: 10.1016/J.Celrep.2013.03.027  0.383
2013 Gstaiger M, Aebersold R. Genotype-phenotype relationships in light of a modular protein interaction landscape. Molecular Biosystems. 9: 1064-7. PMID 23529396 DOI: 10.1039/C3Mb25583B  0.367
2013 Walzthoeni T, Leitner A, Stengel F, Aebersold R. Mass spectrometry supported determination of protein complex structure. Current Opinion in Structural Biology. 23: 252-60. PMID 23522702 DOI: 10.1016/J.Sbi.2013.02.008  0.458
2013 Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R. Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. Molecular & Cellular Proteomics : McP. 12: 1741-51. PMID 23462206 DOI: 10.1074/Mcp.M112.023754  0.493
2013 Varjosalo M, Sacco R, Stukalov A, van Drogen A, Planyavsky M, Hauri S, Aebersold R, Bennett KL, Colinge J, Gstaiger M, Superti-Furga G. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nature Methods. 10: 307-14. PMID 23455922 DOI: 10.1038/Nmeth.2400  0.458
2013 Stützer I, Selevsek N, Esterházy D, Schmidt A, Aebersold R, Stoffel M. Systematic proteomic analysis identifies β-site amyloid precursor protein cleaving enzyme 2 and 1 (BACE2 and BACE1) substrates in pancreatic β-cells. The Journal of Biological Chemistry. 288: 10536-47. PMID 23430253 DOI: 10.1074/Jbc.M112.444703  0.375
2013 Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, ... Aebersold R, et al. N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Molecular & Cellular Proteomics : McP. 12: 1005-16. PMID 23408683 DOI: 10.1074/Mcp.O112.026617  0.34
2013 Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L. An automated pipeline for high-throughput label-free quantitative proteomics. Journal of Proteome Research. 12: 1628-44. PMID 23391308 DOI: 10.1021/Pr300992U  0.411
2013 Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J. Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proceedings of the National Academy of Sciences of the United States of America. 110: 3645-50. PMID 23388641 DOI: 10.1073/Pnas.1216918110  0.38
2013 Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, ... ... Aebersold R, et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature. 494: 266-70. PMID 23334424 DOI: 10.1038/Nature11835  0.401
2013 Liu Y, Hüttenhain R, Surinova S, Gillet LC, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics. 13: 1247-56. PMID 23322582 DOI: 10.1002/Pmic.201200417  0.409
2013 Wong CC, Cociorva D, Miller CA, Schmidt A, Monell C, Aebersold R, Yates JR. Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods. Journal of Proteome Research. 12: 763-70. PMID 23298259 DOI: 10.1021/Pr300840J  0.419
2013 Bontron S, Jaquenoud M, Vaga S, Talarek N, Bodenmiller B, Aebersold R, De Virgilio C. Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A. Cell Reports. 3: 16-22. PMID 23273919 DOI: 10.1016/J.Celrep.2012.11.025  0.332
2013 Picotti P, Bodenmiller B, Aebersold R. Proteomics meets the scientific method. Nature Methods. 10: 24-7. PMID 23269373 DOI: 10.1038/Nmeth.2291  0.419
2013 Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. Journal of Proteome Research. 12: 23-7. PMID 23259511 DOI: 10.1021/Pr301151M  0.329
2012 Skoulidis F, Schiess R, Aebersold R, Venkitaraman AR. An integrated cross-species approach for the discovery of serum-based diagnostic biomarkers of PDAC using a genetically engineered murine model (GEMM). Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 30: 218. PMID 27983193 DOI: 10.1200/Jco.2012.30.4_Suppl.218  0.302
2012 Karlsson C, Malmström L, Aebersold R, Malmström J. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nature Communications. 3: 1301. PMID 23250431 DOI: 10.1038/Ncomms2297  0.408
2012 Clough T, Thaminy S, Ragg S, Aebersold R, Vitek O. Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. Bmc Bioinformatics. 13: S6. PMID 23176351 DOI: 10.1186/1471-2105-13-S16-S6  0.474
2012 Oliveira AP, Ludwig C, Picotti P, Kogadeeva M, Aebersold R, Sauer U. Regulation of yeast central metabolism by enzyme phosphorylation. Molecular Systems Biology. 8: 623. PMID 23149688 DOI: 10.1038/Msb.2012.55  0.351
2012 Ciferri C, Lander GC, Maiolica A, Herzog F, Aebersold R, Nogales E. Molecular architecture of human polycomb repressive complex 2. Elife. 1: e00005. PMID 23110252 DOI: 10.7554/Elife.00005  0.337
2012 Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bähler J. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell. 151: 671-83. PMID 23101633 DOI: 10.1016/J.Cell.2012.09.019  0.365
2012 Glatter T, Ludwig C, Ahrné E, Aebersold R, Heck AJ, Schmidt A. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. Journal of Proteome Research. 11: 5145-56. PMID 23017020 DOI: 10.1021/Pr300273G  0.448
2012 Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, Walzthoeni T, Leitner A, Beck M, Hartl FU, Ban N, Malmström L, Aebersold R. Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science (New York, N.Y.). 337: 1348-52. PMID 22984071 DOI: 10.1126/Science.1221483  0.643
2012 Bock T, Moest H, Omasits U, Dolski S, Lundberg E, Frei A, Hofmann A, Bausch-Fluck D, Jacobs A, Krayenbuehl N, Uhlen M, Aebersold R, Frei K, Wollscheid B. Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines. Journal of Proteome Research. 11: 4885-93. PMID 22909291 DOI: 10.1021/Pr300360A  0.302
2012 Bislev SL, Deutsch EW, Sun Z, Farrah T, Aebersold R, Moritz RL, Bendixen E, Codrea MC. A Bovine PeptideAtlas of milk and mammary gland proteomes. Proteomics. 12: 2895-9. PMID 22837157 DOI: 10.1002/Pmic.201200057  0.384
2012 Hood LE, Omenn GS, Moritz RL, Aebersold R, Yamamoto KR, Amos M, Hunter-Cevera J, Locascio L. New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics. 12: 2773-83. PMID 22807061 DOI: 10.1002/Pmic.201270086  0.456
2012 Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science Translational Medicine. 4: 142ra94. PMID 22786679 DOI: 10.1126/Scitranslmed.3003989  0.414
2012 Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, Förster F, Beck M, Aebersold R. False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nature Methods. 9: 901-3. PMID 22772729 DOI: 10.1038/Nmeth.2103  0.616
2012 Kohli BM, Pflieger D, Mueller LN, Carbonetti G, Aebersold R, Nitsch RM, Konietzko U. Interactome of the amyloid precursor protein APP in brain reveals a protein network involved in synaptic vesicle turnover and a close association with Synaptotagmin-1. Journal of Proteome Research. 11: 4075-90. PMID 22731840 DOI: 10.1021/Pr300123G  0.379
2012 Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nature Methods. 9: 555-66. PMID 22669653 DOI: 10.1038/Nmeth.2015  0.384
2012 Pulliainen AT, Pieles K, Brand CS, Hauert B, Böhm A, Quebatte M, Wepf A, Gstaiger M, Aebersold R, Dessauer CW, Dehio C. Bacterial effector binds host cell adenylyl cyclase to potentiate Gαs-dependent cAMP production. Proceedings of the National Academy of Sciences of the United States of America. 109: 9581-6. PMID 22635269 DOI: 10.1073/Pnas.1117651109  0.33
2012 Maiolica A, Jünger MA, Ezkurdia I, Aebersold R. Targeted proteome investigation via selected reaction monitoring mass spectrometry. Journal of Proteomics. 75: 3495-513. PMID 22579752 DOI: 10.1016/J.Jprot.2012.04.048  0.479
2012 Ebhardt HA, Sabidó E, Hüttenhain R, Collins B, Aebersold R. Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. Proteomics. 12: 1185-93. PMID 22577020 DOI: 10.1002/Pmic.201100543  0.428
2012 Röst H, Malmström L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Molecular & Cellular Proteomics : McP. 11: 540-9. PMID 22535207 DOI: 10.1074/Mcp.M111.013045  0.361
2012 Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure (London, England : 1993). 20: 814-25. PMID 22503819 DOI: 10.1016/J.Str.2012.03.007  0.313
2012 Waldemarson S, Krogh M, Alaiya A, Kirik U, Schedvins K, Auer G, Hansson KM, Ossola R, Aebersold R, Lee H, Malmström J, James P. Protein expression changes in ovarian cancer during the transition from benign to malignant. Journal of Proteome Research. 11: 2876-89. PMID 22471520 DOI: 10.1021/Pr201258Q  0.356
2012 Paik YK, Omenn GS, Uhlen M, Hanash S, Marko-Varga G, Aebersold R, Bairoch A, Yamamoto T, Legrain P, Lee HJ, Na K, Jeong SK, He F, Binz PA, Nishimura T, et al. Standard guidelines for the chromosome-centric human proteome project. Journal of Proteome Research. 11: 2005-13. PMID 22443261 DOI: 10.1021/Pr200824A  0.341
2012 Bensimon A, Heck AJ, Aebersold R. Mass spectrometry-based proteomics and network biology. Annual Review of Biochemistry. 81: 379-405. PMID 22439968 DOI: 10.1146/Annurev-Biochem-072909-100424  0.327
2012 Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, ... ... Aebersold R, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology. 30: 221-3. PMID 22398612 DOI: 10.1038/Nbt.2152  0.316
2012 Sabidó E, Quehenberger O, Shen Q, Chang CY, Shah I, Armando AM, Andreyev A, Vitek O, Dennis EA, Aebersold R. Targeted proteomics of the eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism. Molecular & Cellular Proteomics : McP. 11: M111.014746. PMID 22361236 DOI: 10.1074/Mcp.M111.014746  0.382
2012 Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL. PASSEL: the PeptideAtlas SRMexperiment library. Proteomics. 12: 1170-5. PMID 22318887 DOI: 10.1002/Pmic.201100515  0.377
2012 Lamond AI, Uhlen M, Horning S, Makarov A, Robinson CV, Serrano L, Hartl FU, Baumeister W, Werenskiold AK, Andersen JS, Vorm O, Linial M, Aebersold R, Mann M. Advancing cell biology through proteomics in space and time (PROSPECTS). Molecular & Cellular Proteomics : McP. 11: O112.017731. PMID 22311636 DOI: 10.1074/Mcp.O112.017731  0.601
2012 Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proceedings of the National Academy of Sciences of the United States of America. 109: 1380-7. PMID 22307589 DOI: 10.1073/Pnas.1120559109  0.498
2012 Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Förster F, Aebersold R. Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Molecular & Cellular Proteomics : McP. 11: M111.014126. PMID 22286754 DOI: 10.1074/Mcp.M111.014126  0.37
2012 Malmström L, Malmström J, Selevsek N, Rosenberger G, Aebersold R. Automated workflow for large-scale selected reaction monitoring experiments. Journal of Proteome Research. 11: 1644-53. PMID 22283722 DOI: 10.1021/Pr200844D  0.371
2012 Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Molecular & Cellular Proteomics : McP. 11: O111.016717. PMID 22261725 DOI: 10.1074/Mcp.O111.016717  0.43
2012 Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Røntved CM, Aebersold R, Moritz RL, Bendixen E. Quantotypic properties of QconCAT peptides targeting bovine host response to Streptococcus uberis. Journal of Proteome Research. 11: 1832-43. PMID 22256911 DOI: 10.1021/Pr201064G  0.4
2012 Chang CY, Picotti P, Hüttenhain R, Heinzelmann-Schwarz V, Jovanovic M, Aebersold R, Vitek O. Protein significance analysis in selected reaction monitoring (SRM) measurements. Molecular & Cellular Proteomics : McP. 11: M111.014662. PMID 22190732 DOI: 10.1074/Mcp.M111.014662  0.416
2012 Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Molecular & Cellular Proteomics : McP. 11: R111.014027. PMID 22180098 DOI: 10.1074/Mcp.R111.014027  0.445
2012 Sabidó E, Selevsek N, Aebersold R. Mass spectrometry-based proteomics for systems biology. Current Opinion in Biotechnology. 23: 591-7. PMID 22169889 DOI: 10.1016/J.Copbio.2011.11.014  0.377
2012 Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY. TraML--a standard format for exchange of selected reaction monitoring transition lists. Molecular & Cellular Proteomics : McP. 11: R111.015040. PMID 22159873 DOI: 10.1074/Mcp.R111.015040  0.354
2012 Malmström J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmström L, Björck L. Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics. The Journal of Biological Chemistry. 287: 1415-25. PMID 22117078 DOI: 10.1074/Jbc.M111.267674  0.384
2012 Ludwig C, Claassen M, Schmidt A, Aebersold R. Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Molecular & Cellular Proteomics : McP. 11: M111.013987. PMID 22101334 DOI: 10.1074/Mcp.M111.013987  0.489
2012 Claassen M, Reiter L, Hengartner MO, Buhmann JM, Aebersold R. Generic comparison of protein inference engines. Molecular & Cellular Proteomics : McP. 11: O110.007088. PMID 22057310 DOI: 10.1074/Mcp.O110.007088  0.439
2012 Bernhardt OM, Selevsek N, Gillet LC, Rinner O, Picotti P, Aebersold R, Reiter L. Spectronaut A fast and efficient algorithm for MRM-like processing of data independent acquisition (SWATH-MS) data F1000research. 5. DOI: 10.7490/F1000Research.1096450.1  0.356
2012 Aebersold R. 83 Mass Spectrometric Strategies for Protein Biomarker Discovery and Validation European Journal of Cancer. 48: S20. DOI: 10.1016/S0959-8049(12)70787-6  0.321
2011 Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B. openBIS: a flexible framework for managing and analyzing complex data in biology research. Bmc Bioinformatics. 12: 468. PMID 22151573 DOI: 10.1186/1471-2105-12-468  0.319
2011 Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R. The quantitative proteome of a human cell line. Molecular Systems Biology. 7: 549. PMID 22068332 DOI: 10.1038/Msb.2011.82  0.605
2011 Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M. Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology. 7: 547. PMID 22068330 DOI: 10.1038/Msb.2011.79  0.332
2011 Esterházy D, Stützer I, Wang H, Rechsteiner MP, Beauchamp J, Döbeli H, Hilpert H, Matile H, Prummer M, Schmidt A, Lieske N, Boehm B, Marselli L, Bosco D, Kerr-Conte J, ... Aebersold R, et al. Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass. Cell Metabolism. 14: 365-77. PMID 21907142 DOI: 10.1016/J.Cmet.2011.06.018  0.332
2011 Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & Cellular Proteomics : McP. 10: M111.007690. PMID 21876204 DOI: 10.1074/Mcp.M111.007690  0.436
2011 Ritz D, Vuk M, Kirchner P, Bug M, Schütz S, Hayer A, Bremer S, Lusk C, Baloh RH, Lee H, Glatter T, Gstaiger M, Aebersold R, Weihl CC, Meyer H. Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations. Nature Cell Biology. 13: 1116-23. PMID 21822278 DOI: 10.1038/Ncb2301  0.344
2011 Hyung SW, Lee MY, Yu JH, Shin B, Jung HJ, Park JM, Han W, Lee KM, Moon HG, Zhang H, Aebersold R, Hwang D, Lee SW, Yu MH, Noh DY. A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers. Molecular & Cellular Proteomics : McP. 10: M111.011023. PMID 21799047 DOI: 10.1074/Mcp.M111.011023  0.332
2011 Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, Serrano L. Quantification of mRNA and protein and integration with protein turnover in a bacterium. Molecular Systems Biology. 7: 511. PMID 21772259 DOI: 10.1038/Msb.2011.38  0.444
2011 Schmidt A, Beck M, Malmström J, Lam H, Claassen M, Campbell D, Aebersold R. Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Molecular Systems Biology. 7: 510. PMID 21772258 DOI: 10.1038/Msb.2011.37  0.649
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, et al. The human proteome project: current state and future direction. Molecular & Cellular Proteomics : McP. 10: M111.009993. PMID 21742803 DOI: 10.1074/Mcp.M111.009993  0.658
2011 Kälin M, Cima I, Schiess R, Fankhauser N, Powles T, Wild P, Templeton A, Cerny T, Aebersold R, Krek W, Gillessen S. Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome. European Urology. 60: 1235-43. PMID 21741162 DOI: 10.1016/J.Eururo.2011.06.038  0.318
2011 Higdon R, Reiter L, Hather G, Haynes W, Kolker N, Stewart E, Bauman AT, Picotti P, Schmidt A, van Belle G, Aebersold R, Kolker E. IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics. Journal of Proteomics. 75: 116-21. PMID 21718813 DOI: 10.1016/J.Jprot.2011.06.003  0.471
2011 Kahraman A, Malmström L, Aebersold R. Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics (Oxford, England). 27: 2163-4. PMID 21666267 DOI: 10.1093/Bioinformatics/Btr348  0.362
2011 Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & Cellular Proteomics : McP. 10: M110.006353. PMID 21632744 DOI: 10.1074/Mcp.M110.006353  0.585
2011 Bensimon A, Aebersold R, Shiloh Y. Beyond ATM: the protein kinase landscape of the DNA damage response. Febs Letters. 585: 1625-39. PMID 21570395 DOI: 10.1016/J.Febslet.2011.05.013  0.353
2011 Hoofnagle AN, Aebersold R, Anderson NL, Felsenfeld A, Liebler DC. Painting a moving picture: large-scale proteomics efforts and their potential for changing patient care. Clinical Chemistry. 57: 1357-60. PMID 21540400 DOI: 10.1373/Clinchem.2010.158311  0.399
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, et al. The human proteome project: Current state and future direction. Molecular & Cellular Proteomics : McP. PMID 21531903 DOI: 10.1074/mcp.O111.009993  0.626
2011 Farrah T, Deutsch EW, Aebersold R. Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods in Molecular Biology (Clifton, N.J.). 728: 349-74. PMID 21468960 DOI: 10.1007/978-1-61779-068-3_23  0.346
2011 Ossola R, Schiess R, Picotti P, Rinner O, Reiter L, Aebersold R. Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites. Methods in Molecular Biology (Clifton, N.J.). 728: 179-94. PMID 21468948 DOI: 10.1007/978-1-61779-068-3_11  0.391
2011 Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature Methods. 8: 430-5. PMID 21423193 DOI: 10.1038/Nmeth.1584  0.574
2011 Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. Bmc Bioinformatics. 12: 78. PMID 21414234 DOI: 10.1186/1471-2105-12-78  0.404
2011 Selevsek N, Matondo M, Sanchez Carbayo M, Aebersold R, Domon B. Systematic quantification of peptides/proteins in urine using selected reaction monitoring. Proteomics. 11: 1135-47. PMID 21360671 DOI: 10.1002/Pmic.201000599  0.478
2011 Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R. Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology. 7: 464. PMID 21283140 DOI: 10.1038/Msb.2010.122  0.382
2011 Lam H, Aebersold R. Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics. Methods (San Diego, Calif.). 54: 424-31. PMID 21277371 DOI: 10.1016/J.Ymeth.2011.01.007  0.404
2011 Scherrer T, Femmer C, Schiess R, Aebersold R, Gerber AP. Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins. Genome Biology. 12: R3. PMID 21232131 DOI: 10.1186/Gb-2011-12-1-R3  0.334
2011 Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R. The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage. Proteomics. 11: 154-8. PMID 21182202 DOI: 10.1002/Pmic.201000459  0.391
2011 Yan W, Luo J, Robinson M, Eng J, Aebersold R, Ranish J. Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures. Molecular & Cellular Proteomics : McP. 10: M110.005611. PMID 21169564 DOI: 10.1074/Mcp.M110.005611  0.304
2011 Surinova S, Schiess R, Hüttenhain R, Cerciello F, Wollscheid B, Aebersold R. On the development of plasma protein biomarkers. Journal of Proteome Research. 10: 5-16. PMID 21142170 DOI: 10.1021/Pr1008515  0.351
2011 Bodenmiller B, Aebersold R. Phosphoproteome resource for systems biology research. Methods in Molecular Biology (Clifton, N.J.). 694: 307-22. PMID 21082442 DOI: 10.1007/978-1-60761-977-2_19  0.327
2011 Beck M, Claassen M, Aebersold R. Comprehensive proteomics. Current Opinion in Biotechnology. 22: 3-8. PMID 20888217 DOI: 10.1016/j.copbio.2010.09.002  0.585
2011 Pan S, Chen R, Aebersold R, Brentnall TA. Mass spectrometry based glycoproteomics--from a proteomics perspective. Molecular & Cellular Proteomics : McP. 10: R110.003251. PMID 20736408 DOI: 10.1074/Mcp.R110.003251  0.401
2011 Kiyonami R, Schoen A, Prakash A, Peterman S, Zabrouskov V, Picotti P, Aebersold R, Huhmer A, Domon B. Increased selectivity, analytical precision, and throughput in targeted proteomics. Molecular & Cellular Proteomics : McP. 10: M110.002931. PMID 20664071 DOI: 10.1074/Mcp.M110.002931  0.355
2010 Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, ... ... Aebersold R, et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Science Signaling. 3: rs4. PMID 21177495 DOI: 10.1126/Scisignal.2001182  0.323
2010 Bensimon A, Schmidt A, Ziv Y, Elkon R, Wang SY, Chen DJ, Aebersold R, Shiloh Y. ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Science Signaling. 3: rs3. PMID 21139141 DOI: 10.1126/Scisignal.2001034  0.334
2010 Bohn S, Beck F, Sakata E, Walzthoeni T, Beck M, Aebersold R, Förster F, Baumeister W, Nickell S. Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proceedings of the National Academy of Sciences of the United States of America. 107: 20992-7. PMID 21098295 DOI: 10.1073/Pnas.1015530107  0.64
2010 Bodenmiller B, Aebersold R. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. Methods in Enzymology. 470: 317-34. PMID 20946816 DOI: 10.1016/S0076-6879(10)70013-6  0.422
2010 Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nature Reviews. Molecular Cell Biology. 11: 789-801. PMID 20944666 DOI: 10.1038/Nrm2973  0.445
2010 Nilsson T, Mann M, Aebersold R, Yates JR, Bairoch A, Bergeron JJ. Mass spectrometry in high-throughput proteomics: ready for the big time. Nature Methods. 7: 681-5. PMID 20805795 DOI: 10.1038/Nmeth0910-681  0.402
2010 Przybylski C, Jünger MA, Aubertin J, Radvanyi F, Aebersold R, Pflieger D. Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-Orbitrap instrument. Journal of Proteome Research. 9: 5118-32. PMID 20734990 DOI: 10.1021/Pr1003888  0.438
2010 Mirzaei H, Rogers RS, Grimes B, Eng J, Aderem A, Aebersold R. Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry. Molecular Biosystems. 6: 2004-14. PMID 20694217 DOI: 10.1039/C005242F  0.445
2010 Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nature Biotechnology. 28: 710-21. PMID 20622845 DOI: 10.1038/Nbt.1661  0.398
2010 Duncan MW, Aebersold R, Caprioli RM. The pros and cons of peptide-centric proteomics. Nature Biotechnology. 28: 659-64. PMID 20622832 DOI: 10.1038/Nbt0710-659  0.327
2010 Lam H, Aebersold R. Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 25.5. PMID 20393975 DOI: 10.1002/0471140864.Ps2505S60  0.401
2010 Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, Beck M, Aebersold R. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Molecular & Cellular Proteomics : McP. 9: 1634-49. PMID 20360032 DOI: 10.1074/Mcp.R000001-Mcp201  0.61
2010 Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS. Orm family proteins mediate sphingolipid homeostasis. Nature. 463: 1048-53. PMID 20182505 DOI: 10.1038/Nature08787  0.367
2010 Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. A guided tour of the Trans-Proteomic Pipeline. Proteomics. 10: 1150-9. PMID 20101611 DOI: 10.1002/Pmic.200900375  0.389
2010 Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R. Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics. 10: 1190-5. PMID 20082347 DOI: 10.1002/Pmic.200900567  0.326
2010 Lam H, Aebersold R. Spectral library searching for peptide identification via tandem MS. Methods in Molecular Biology (Clifton, N.J.). 604: 95-103. PMID 20013366 DOI: 10.1007/978-1-60761-444-9_7  0.391
2010 Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nature Methods. 7: 43-6. PMID 19966807 DOI: 10.1038/Nmeth.1408  0.415
2010 Lam H, Deutsch EW, Aebersold R. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. Journal of Proteome Research. 9: 605-10. PMID 19916561 DOI: 10.1021/Pr900947U  0.35
2010 Wiedl T, Arni S, Roschitzki B, Grossmann J, Soltermann A, Hillinger S, Aebersold R, Weder W. Abstract 5576: Activity based protein profiling of human lung adenocarcinoma biopsies Cancer Research. 70: 5576-5576. DOI: 10.1158/1538-7445.Am10-5576  0.34
2009 Brentnall TA, Pan S, Bronner MP, Crispin DA, Mirzaei H, Cooke K, Tamura Y, Nikolskaya T, Jebailey L, Goodlett DR, McIntosh M, Aebersold R, Rabinovitch PS, Chen R. Proteins That Underlie Neoplastic Progression of Ulcerative Colitis. Proteomics. Clinical Applications. 3: 1326. PMID 20098637 DOI: 10.1002/Prca.200900061  0.585
2009 Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, ... ... Aebersold R, et al. Proteome organization in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1235-40. PMID 19965468 DOI: 10.1126/Science.1176343  0.412
2009 Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, et al. Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. Plos Biology. 7: e1000236. PMID 19885390 DOI: 10.1371/Journal.Pbio.1000236  0.365
2009 Beck M, Malmström JA, Lange V, Schmidt A, Deutsch EW, Aebersold R. Visual proteomics of the human pathogen Leptospira interrogans. Nature Methods. 6: 817-23. PMID 19838170 DOI: 10.1038/Nmeth.1390  0.584
2009 Hüttenhain R, Malmström J, Picotti P, Aebersold R. Perspectives of targeted mass spectrometry for protein biomarker verification. Current Opinion in Chemical Biology. 13: 518-25. PMID 19818677 DOI: 10.1016/J.Cbpa.2009.09.014  0.401
2009 Schmidt A, Claassen M, Aebersold R. Directed mass spectrometry: towards hypothesis-driven proteomics. Current Opinion in Chemical Biology. 13: 510-7. PMID 19775930 DOI: 10.1016/J.Cbpa.2009.08.016  0.422
2009 Gstaiger M, Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nature Reviews. Genetics. 10: 617-27. PMID 19687803 DOI: 10.1038/Nrg2633  0.448
2009 Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R. Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes & Development. 23: 1929-43. PMID 19684113 DOI: 10.1101/Gad.532109  0.416
2009 Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell. 138: 795-806. PMID 19664813 DOI: 10.1016/J.Cell.2009.05.051  0.442
2009 Jeong SK, Kwon MS, Lee EY, Lee HJ, Cho SY, Kim H, Yoo JS, Omenn GS, Aebersold R, Hanash S, Paik YK. BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. Proteomics. 9: 3729-40. PMID 19639590 DOI: 10.1002/Pmic.200800593  0.421
2009 Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling. 2: ra39. PMID 19638616 DOI: 10.1126/Scisignal.2000316  0.371
2009 Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular & Cellular Proteomics : McP. 8: 2405-17. PMID 19608599 DOI: 10.1074/Mcp.M900317-Mcp200  0.452
2009 Malmström J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature. 460: 762-5. PMID 19606093 DOI: 10.1038/Nature08184  0.643
2009 Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N, Aebersold R, Lam H, Martin DB. MaRiMba: a software application for spectral library-based MRM transition list assembly. Journal of Proteome Research. 8: 4396-405. PMID 19603829 DOI: 10.1021/Pr900010H  0.413
2009 Claassen M, Aebersold R, Buhmann JM. Proteome coverage prediction with infinite Markov models. Bioinformatics (Oxford, England). 25: i154-60. PMID 19477982 DOI: 10.1093/Bioinformatics/Btp233  0.42
2009 Aebersold R. A stress test for mass spectrometry-based proteomics. Nature Methods. 6: 411-2. PMID 19448640 DOI: 10.1038/Nmeth.F.255  0.355
2009 Domon B, Bodenmiller B, Carapito C, Hao Z, Huehmer A, Aebersold R. Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. Journal of Proteome Research. 8: 2633-9. PMID 19435317 DOI: 10.1021/Pr800834E  0.406
2009 Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts JD, Aebersold R. Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Molecular & Cellular Proteomics : McP. 8: 1934-46. PMID 19411281 DOI: 10.1074/Mcp.M800569-Mcp200  0.394
2009 Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Molecular Oncology. 3: 33-44. PMID 19383365 DOI: 10.1016/J.Molonc.2008.12.001  0.392
2009 Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/J.Molonc.2008.11.003  0.301
2009 Pan S, Chen R, Reimel BA, Crispin DA, Mirzaei H, Cooke K, Coleman JF, Lane Z, Bronner MP, Goodlett DR, McIntosh MW, Traverso W, Aebersold R, Brentnall TA. Quantitative proteomics investigation of pancreatic intraepithelial neoplasia. Electrophoresis. 30: 1132-44. PMID 19373808 DOI: 10.1002/Elps.200800752  0.587
2009 Carapito C, Klemm C, Aebersold R, Domon B. Systematic LC-MS analysis of labile post-translational modifications in complex mixtures. Journal of Proteome Research. 8: 2608-14. PMID 19284785 DOI: 10.1021/Pr800871N  0.438
2009 Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, Aebersold R, Hafen E. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. Bmc Bioinformatics. 10: 59. PMID 19210778 DOI: 10.1186/1471-2105-10-59  0.379
2009 Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M. Quantitative interaction proteomics using mass spectrometry. Nature Methods. 6: 203-5. PMID 19198594 DOI: 10.1038/Nmeth.1302  0.481
2009 Glatter T, Wepf A, Aebersold R, Gstaiger M. An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Molecular Systems Biology. 5: 237. PMID 19156129 DOI: 10.1038/Msb.2008.75  0.476
2009 Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M. Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature. 458: 228-32. PMID 19145231 DOI: 10.1038/Nature07643  0.348
2009 Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA. A human proteome detection and quantitation project. Molecular & Cellular Proteomics : McP. 8: 883-6. PMID 19131327 DOI: 10.1074/Mcp.R800015-Mcp200  0.443
2009 Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L. Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics (Oxford, England). 25: 682-3. PMID 19129212 DOI: 10.1093/Bioinformatics/Btp005  0.565
2009 Yan W, Aebersold R, Raines EW. Evolution of organelle-associated protein profiling. Journal of Proteomics. 72: 4-11. PMID 19110081 DOI: 10.1016/J.Jprot.2008.11.017  0.458
2009 Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA. Mass spectrometry based targeted protein quantification: methods and applications. Journal of Proteome Research. 8: 787-97. PMID 19105742 DOI: 10.1021/Pr800538N  0.638
2009 Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. Journal of Proteome Research. 8: 887-99. PMID 19072539 DOI: 10.1021/Pr800535H  0.387
2009 Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R. Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Molecular & Cellular Proteomics : McP. 8: 624-38. PMID 19036722 DOI: 10.1074/Mcp.M800172-Mcp200  0.336
2009 Urwyler S, Nyfeler Y, Ragaz C, Lee H, Mueller LN, Aebersold R, Hilbi H. Proteome analysis of Legionella vacuoles purified by magnetic immunoseparation reveals secretory and endosomal GTPases. Traffic (Copenhagen, Denmark). 10: 76-87. PMID 18980612 DOI: 10.1111/J.1600-0854.2008.00851.X  0.372
2009 Goudreault M, D'Ambrosio LM, Kean MJ, Mullin MJ, Larsen BG, Sanchez A, Chaudhry S, Chen GI, Sicheri F, Nesvizhskii AI, Aebersold R, Raught B, Gingras AC. A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Molecular & Cellular Proteomics : McP. 8: 157-71. PMID 18782753 DOI: 10.1074/Mcp.M800266-Mcp200  0.585
2009 Schiess R, Cima I, Wild PJ, Kalin M, Ossola R, Templeton A, Gillessen S, Cerny T, Moch H, Krek W, Aebersold R. Abstract C28: Discovery of new protein biomarkers for prostate cancer diagnosis using a Pten‐dependent mouse model and their validation in human patients Cancer Research. 69. DOI: 10.1158/0008-5472.Fbcr09-C28  0.333
2009 Brentnall TA, Pan S, Bronner MP, Crispin DA, Mirzaei H, Cooke K, Tamura Y, Nikolskaya T, JeBailey L, Goodlett DR, McIntosh M, Aebersold R, Rabinovitch PS, Chen R. Proteins that underlie neoplastic progression of ulcerative colitis Proteomics - Clinical Applications. 3: 1326-1337. DOI: 10.1002/prca.200900061  0.515
2008 Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS, Vitek O, Zhang H, Aebersold R, Watts JD. Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clinical Proteomics. 4: 105. PMID 20157627 DOI: 10.1007/S12014-008-9018-8  0.469
2008 Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. Bmc Bioinformatics. 9: 542. PMID 19087345 DOI: 10.1186/1471-2105-9-542  0.428
2008 Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R. PhosphoPep--a database of protein phosphorylation sites in model organisms. Nature Biotechnology. 26: 1339-40. PMID 19060867 DOI: 10.1038/Nbt1208-1339  0.337
2008 Tress ML, Bodenmiller B, Aebersold R, Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biology. 9: R162. PMID 19017398 DOI: 10.1186/gb-2008-9-11-r162  0.304
2008 Gavin AC, Aebersold R, Heck AJ. Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology. Molecular & Cellular Proteomics : McP. 7: 2288-91. PMID 18996833 DOI: 10.1074/Mcp.H800011-Mcp200  0.306
2008 Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R. A database of mass spectrometric assays for the yeast proteome. Nature Methods. 5: 913-4. PMID 18974732 DOI: 10.1038/Nmeth1108-913  0.396
2008 Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular Systems Biology. 4: 222. PMID 18854821 DOI: 10.1038/Msb.2008.61  0.417
2008 Chi Y, Welcker M, Hizli AA, Posakony JJ, Aebersold R, Clurman BE. Identification of CDK2 substrates in human cell lysates. Genome Biology. 9: R149. PMID 18847512 DOI: 10.1186/Gb-2008-9-10-R149  0.371
2008 Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. Building consensus spectral libraries for peptide identification in proteomics. Nature Methods. 5: 873-5. PMID 18806791 DOI: 10.1038/Nmeth.1254  0.363
2008 Hwang D, Zhang N, Lee H, Yi E, Zhang H, Lee IY, Hood L, Aebersold R. MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics (Oxford, England). 24: 2641-2. PMID 18805798 DOI: 10.1093/Bioinformatics/Btn491  0.541
2008 Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA, Nickson J, et al. Guidelines for reporting the use of mass spectrometry in proteomics. Nature Biotechnology. 26: 860-1. PMID 18688232 DOI: 10.1038/Nbt0808-860  0.364
2008 Ramos H, Shannon P, Aebersold R. The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics (Oxford, England). 24: 2110-1. PMID 18635572 DOI: 10.1093/Bioinformatics/Btn363  0.425
2008 Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, et al. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biology. 9: R93. PMID 18522751 DOI: 10.1186/Gb-2008-9-6-R93  0.396
2008 Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Molecular & Cellular Proteomics : McP. 7: 2138-50. PMID 18511481 DOI: 10.1074/Mcp.M700498-Mcp200  0.396
2008 Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. Embo Reports. 9: 429-34. PMID 18451766 DOI: 10.1038/Embor.2008.56  0.405
2008 Lange V, Malmström JA, Didion J, King NL, Johansson BP, Schäfer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, Bühlmann P, Björck L, Domon B, Aebersold R. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Molecular & Cellular Proteomics : McP. 7: 1489-500. PMID 18408245 DOI: 10.1074/Mcp.M800032-Mcp200  0.486
2008 Yan W, Hwang D, Aebersold R. Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. Methods in Molecular Biology (Clifton, N.J.). 432: 389-401. PMID 18370032 DOI: 10.1007/978-1-59745-028-7_26  0.483
2008 Soltermann A, Ossola R, Kilgus-Hawelski S, von Eckardstein A, Suter T, Aebersold R, Moch H. N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics. Cancer. 114: 124-33. PMID 18327805 DOI: 10.1002/Cncr.23349  0.372
2008 Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R. Identification of cross-linked peptides from large sequence databases. Nature Methods. 5: 315-8. PMID 18327264 DOI: 10.1038/Nmeth.1192  0.582
2008 Deutsch EW, Lam H, Aebersold R. Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiological Genomics. 33: 18-25. PMID 18212004 DOI: 10.1152/Physiolgenomics.00298.2007  0.375
2008 Zou Z, Ibisate M, Zhou Y, Aebersold R, Xia Y, Zhang H. Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format. Analytical Chemistry. 80: 1228-34. PMID 18197692 DOI: 10.1021/Ac701950H  0.311
2008 Mueller LN, Brusniak MY, Mani DR, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. Journal of Proteome Research. 7: 51-61. PMID 18173218 DOI: 10.1021/Pr700758R  0.398
2008 Mirzaei H, McBee JK, Watts J, Aebersold R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Molecular & Cellular Proteomics : McP. 7: 813-23. PMID 18089551 DOI: 10.1074/Mcp.M700495-Mcp200  0.341
2008 Pflieger D, Jünger MA, Müller M, Rinner O, Lee H, Gehrig PM, Gstaiger M, Aebersold R. Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Molecular & Cellular Proteomics : McP. 7: 326-46. PMID 17956857 DOI: 10.1074/Mcp.M700282-Mcp200  0.459
2008 Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Molecular & Cellular Proteomics : McP. 7: 71-87. PMID 17872894 DOI: 10.1074/Mcp.M700128-Mcp200  0.396
2008 Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. Journal of Proteome Research. 7: 96-103. PMID 17711323 DOI: 10.1021/Pr070244J  0.589
2008 Rinner O, Seebacher J, Walzthoeni T, Mueller L, Beck M, Schmidt A, Mueller M, Aebersold R. Erratum: Corrigendum: Identification of cross-linked peptides from large sequence databases Nature Methods. 5: 748-748. DOI: 10.1038/Nmeth0808-748A  0.521
2007 Aebersold R, Griffin TJ, Donohoe S. Isotope-coded affinity tagging of proteins. Csh Protocols. 2007: pdb.prot4728. PMID 21357116 DOI: 10.1101/Pdb.Prot4728  0.636
2007 Ahrens CH, Brunner E, Hafen E, Aebersold R, Basler K. A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics. Fly. 1: 182-6. PMID 18820430 DOI: 10.4161/Fly.4532  0.478
2007 Chen R, Pan S, Aebersold R, Brentnall TA. Proteomics studies of pancreatic cancer. Proteomics. Clinical Applications. 1: 1582-1591. PMID 18633454 DOI: 10.1002/Prca.200700414  0.316
2007 Bodenmiller B, Malmstrom J, Gerrits B, Campbell D, Lam H, Schmidt A, Rinner O, Mueller LN, Shannon PT, Pedrioli PG, Panse C, Lee HK, Schlapbach R, Aebersold R. PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology. 3: 139. PMID 17940529 DOI: 10.1038/Msb4100182  0.414
2007 Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/Nbt1347  0.306
2007 Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods. 4: 787-97. PMID 17901868 DOI: 10.1038/Nmeth1088  0.394
2007 Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M. SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics. 7: 3470-80. PMID 17726677 DOI: 10.1002/Pmic.200700057  0.417
2007 Noll H, Alcedo J, Daube M, Frei E, Schiltz E, Hunt J, Humphries T, Matranga V, Hochstrasser M, Aebersold R, Lee H, Noll M. The toposome, essential for sea urchin cell adhesion and development, is a modified iron-less calcium-binding transferrin. Developmental Biology. 310: 54-70. PMID 17707791 DOI: 10.1016/J.Ydbio.2007.07.016  0.314
2007 Malmström J, Lee H, Aebersold R. Advances in proteomic workflows for systems biology. Current Opinion in Biotechnology. 18: 378-84. PMID 17698335 DOI: 10.1016/J.Copbio.2007.07.005  0.452
2007 Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/Nbt1329  0.404
2007 Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Molecular & Cellular Proteomics : McP. 6: 1809-17. PMID 17644760 DOI: 10.1074/Mcp.M700132-Mcp200  0.407
2007 Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S, Flory MR, Lee H, Watts J, Goodlett DR, Aebersold R, et al. Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Molecular & Cellular Proteomics : McP. 6: 1741-8. PMID 17617667 DOI: 10.1074/Mcp.M600470-Mcp200  0.583
2007 Gingras AC, Gstaiger M, Raught B, Aebersold R. Analysis of protein complexes using mass spectrometry. Nature Reviews. Molecular Cell Biology. 8: 645-54. PMID 17593931 DOI: 10.1038/Nrm2208  0.617
2007 Zhou Y, Aebersold R, Zhang H. Isolation of N-linked glycopeptides from plasma. Analytical Chemistry. 79: 5826-37. PMID 17591751 DOI: 10.1021/Ac0623181  0.362
2007 Picotti P, Aebersold R, Domon B. The implications of proteolytic background for shotgun proteomics. Molecular & Cellular Proteomics : McP. 6: 1589-98. PMID 17533221 DOI: 10.1074/Mcp.M700029-Mcp200  0.481
2007 Chen R, Brentnall TA, Pan S, Cooke K, Moyes KW, Lane Z, Crispin DA, Goodlett DR, Aebersold R, Bronner MP. Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Molecular & Cellular Proteomics : McP. 6: 1331-42. PMID 17496331 DOI: 10.1074/Mcp.M700072-Mcp200  0.54
2007 Lu Y, Bottari P, Aebersold R, Turecek F, Gelb MH. Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Methods in Molecular Biology (Clifton, N.J.). 359: 159-76. PMID 17484117 DOI: 10.1007/978-1-59745-255-7_11  0.478
2007 Ranish JA, Brand M, Aebersold R. Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition. Methods in Molecular Biology (Clifton, N.J.). 359: 17-35. PMID 17484108 DOI: 10.1007/978-1-59745-255-7_2  0.423
2007 Zosso D, Podvinec M, Müller M, Aebersold R, Peitsch MC, Schwede T. Tandem mass spectrometry protein identification on a PC grid. Studies in Health Technology and Informatics. 126: 3-12. PMID 17476042  0.323
2007 Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, ... ... Aebersold R, et al. A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology. 25: 576-83. PMID 17450130 DOI: 10.1038/Nbt1300  0.646
2007 Tian Y, Zhou Y, Elliott S, Aebersold R, Zhang H. Solid-phase extraction of N-linked glycopeptides. Nature Protocols. 2: 334-9. PMID 17406594 DOI: 10.1038/Nprot.2007.42  0.335
2007 Bodenmiller B, Mueller LN, Pedrioli PG, Pflieger D, Jünger MA, Eng JK, Aebersold R, Tao WA. An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells. Molecular Biosystems. 3: 275-86. PMID 17372656 DOI: 10.1039/B617545G  0.575
2007 Rinner O, Mueller LN, Hubálek M, Müller M, Gstaiger M, Aebersold R. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nature Biotechnology. 25: 345-52. PMID 17322870 DOI: 10.1038/Nbt1289  0.458
2007 Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. Development and validation of a spectral library searching method for peptide identification from MS/MS Proteomics. 7: 655-667. PMID 17295354 DOI: 10.1002/Pmic.200600625  0.396
2007 Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R. Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nature Methods. 4: 231-7. PMID 17293869 DOI: 10.1038/Nmeth1005  0.362
2007 Chen R, Pan S, Cooke K, Moyes KW, Bronner MP, Goodlett DR, Aebersold R, Brentnall TA. Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas. 34: 70-9. PMID 17198186 DOI: 10.1097/01.Mpa.0000240615.20474.Fd  0.491
2007 Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R. Computational prediction of proteotypic peptides for quantitative proteomics. Nature Biotechnology. 25: 125-31. PMID 17195840 DOI: 10.1038/Nbt1275  0.703
2007 Pan S, Aebersold R. Quantitative proteomics by stable isotope labeling and mass spectrometry Methods in Molecular Biology (Clifton, N.J.). 367: 209-218. PMID 17185778 DOI: 10.1385/1-59745-275-0:209  0.471
2007 Schmidt A, Aebersold R. High-accuracy proteome maps of human body fluids. Genome Biology. 7: 242. PMID 17140426 DOI: 10.1186/Gb-2006-7-11-242  0.327
2007 Jasavala R, Martinez H, Thumar J, Andaya A, Gingras AC, Eng JK, Aebersold R, Han DK, Wright ME. Identification of putative androgen receptor interaction protein modules: cytoskeleton and endosomes modulate androgen receptor signaling in prostate cancer cells. Molecular & Cellular Proteomics : McP. 6: 252-71. PMID 17052974 DOI: 10.1074/Mcp.M600169-Mcp200  0.533
2007 Wang P, Tang H, Fitzgibbon MP, McIntosh M, Coram M, Zhang H, Yi E, Aebersold R. A statistical method for chromatographic alignment of LC-MS data. Biostatistics (Oxford, England). 8: 357-67. PMID 16880200 DOI: 10.1093/Biostatistics/Kxl015  0.421
2007 Omenn GS, Aebersold R, Paik Y. HUPO Plasma Proteome Project 2007 Workshop Report Molecular & Cellular Proteomics. 6: 2252-2253. DOI: 10.1074/Mcp.H700012-Mcp200  0.417
2006 Shiio Y, Aebersold R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nature Protocols. 1: 139-45. PMID 17406225 DOI: 10.1038/Nprot.2006.22  0.501
2006 Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 6: 6146-57. PMID 17133367 DOI: 10.1002/Pmic.200600159  0.615
2006 King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biology. 7: R106. PMID 17101051 DOI: 10.1186/Gb-2006-7-11-R106  0.603
2006 Zhang H, Liu AY, Loriaux P, Wollscheid B, Zhou Y, Watts JD, Aebersold R. Mass spectrometric detection of tissue proteins in plasma. Molecular & Cellular Proteomics : McP. 6: 64-71. PMID 17030953 DOI: 10.1074/Mcp.M600160-Mcp200  0.354
2006 Seebacher J, Mallick P, Zhang N, Eddes JS, Aebersold R, Gelb MH. Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing. Journal of Proteome Research. 5: 2270-82. PMID 16944939 DOI: 10.1021/Pr060154Z  0.635
2006 Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R. Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. Journal of Proteome Research. 5: 2241-9. PMID 16944936 DOI: 10.1021/Pr0600632  0.395
2006 Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R. The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). Omics : a Journal of Integrative Biology. 10: 145-51. PMID 16901219 DOI: 10.1089/Omi.2006.10.145  0.307
2006 Domon B, Aebersold R. Challenges and opportunities in proteomics data analysis. Molecular & Cellular Proteomics : McP. 5: 1921-6. PMID 16896060 DOI: 10.1074/Mcp.R600012-Mcp200  0.309
2006 Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R. Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nature Methods. 3: 533-9. PMID 16791211 DOI: 10.1038/Nmeth891  0.399
2006 Zhang H, Aebersold R. Isolation of glycoproteins and identification of their N-linked glycosylation sites. Methods in Molecular Biology (Clifton, N.J.). 328: 177-85. PMID 16785649 DOI: 10.1385/1-59745-026-X:177  0.421
2006 Chen R, Pan S, Yi EC, Donohoe S, Bronner MP, Potter JD, Goodlett DR, Aebersold R, Brentnall TA. Quantitative proteomic profiling of pancreatic cancer juice. Proteomics. 6: 3871-9. PMID 16739137 DOI: 10.1002/Pmic.200500702  0.579
2006 Bradshaw RA, Burlingame AL, Carr S, Aebersold R. Reporting protein identification data: The next generation of guidelines Molecular and Cellular Proteomics. 5: 787-788. PMID 16670253 DOI: 10.1074/Mcp.E600005-Mcp200  0.303
2006 Domon B, Aebersold R. Mass spectrometry and protein analysis. Science (New York, N.Y.). 312: 212-7. PMID 16614208 DOI: 10.1126/Science.1124619  0.468
2006 Hardwidge PR, Donohoe S, Aebersold R, Finlay BB. Proteomic analysis of the binding partners to enteropathogenic Escherichia coli virulence proteins expressed in Saccharomyces cerevisiae. Proteomics. 6: 2174-9. PMID 16552782 DOI: 10.1002/Pmic.200500523  0.464
2006 Maccarana M, Olander B, Malmström J, Tiedemann K, Aebersold R, Lindahl U, Li JP, Malmström A. Biosynthesis of dermatan sulfate: chondroitin-glucuronate C5-epimerase is identical to SART2. The Journal of Biological Chemistry. 281: 11560-8. PMID 16505484 DOI: 10.1074/Jbc.M513373200  0.344
2006 Gan RR, Yi EC, Chiu Y, Lee H, Kao YC, Wu TH, Aebersold R, Goodlett DR, Ng WV. Proteome analysis of Halobacterium sp. NRC-1 facilitated by the biomodule analysis tool BMSorter. Molecular & Cellular Proteomics : McP. 5: 987-97. PMID 16497792 DOI: 10.1074/Mcp.M500367-Mcp200  0.565
2006 Shiio Y, Rose DW, Aur R, Donohoe S, Aebersold R, Eisenman RN. Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. Molecular and Cellular Biology. 26: 1386-97. PMID 16449650 DOI: 10.1128/Mcb.26.4.1386-1397.2006  0.337
2006 Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R. Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics. 6: 738-41. PMID 16411267 DOI: 10.1002/Pmic.200500868  0.385
2006 Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Research. 34: D655-8. PMID 16381952 DOI: 10.1093/Nar/Gkj040  0.698
2006 Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Molecular & Cellular Proteomics : McP. 5: 652-70. PMID 16352522 DOI: 10.1074/Mcp.M500319-Mcp200  0.4
2006 Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B. Signal maps for mass spectrometry-based comparative proteomics. Molecular & Cellular Proteomics : McP. 5: 423-32. PMID 16269421 DOI: 10.1074/Mcp.M500133-Mcp200  0.604
2005 Toigo M, Donohoe S, Sperrazzo G, Jarrold B, Wang F, Hinkle R, Dolan E, Isfort RJ, Aebersold R. ICAT-MS-MS time course analysis of atrophying mouse skeletal muscle cytosolic subproteome. Molecular Biosystems. 1: 229-41. PMID 16880987 DOI: 10.1039/B507839C  0.449
2005 Keller A, Eng J, Zhang N, Li XJ, Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Molecular Systems Biology. 1: 2005.0017. PMID 16729052 DOI: 10.1038/Msb4100024  0.433
2005 Corthals GL, Aebersold R, Goodlett DR. Identification of phosphorylation sites using microimmobilized metal affinity chromatography. Methods in Enzymology. 405: 66-81. PMID 16413311 DOI: 10.1016/S0076-6879(05)05004-4  0.687
2005 Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS. Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. Journal of Proteome Research. 4: 2273-82. PMID 16335976 DOI: 10.1021/Pr050193V  0.424
2005 Chen SS, Deutsch EW, Yi EC, Li XJ, Goodlett DR, Aebersold R. Improving mass and liquid chromatography based identification of proteins using bayesian scoring. Journal of Proteome Research. 4: 2174-84. PMID 16335964 DOI: 10.1021/Pr050251C  0.677
2005 Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R. Human proteome organisation proteomics standards initiative pre-congress initiative Proteomics. 5: 4651-4652. PMID 16287159 DOI: 10.1002/Pmic.200500727  0.414
2005 Chen SS, Aebersold R. LC-MS solvent composition monitoring and chromatography alignment using mobile phase tracer molecules. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 829: 107-14. PMID 16242386 DOI: 10.1016/J.Jchromb.2005.09.039  0.565
2005 Chen R, Yi EC, Donohoe S, Pan S, Eng J, Cooke K, Crispin DA, Lane Z, Goodlett DR, Bronner MP, Aebersold R, Brentnall TA. Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology. 129: 1187-97. PMID 16230073 DOI: 10.1053/J.Gastro.2005.08.001  0.504
2005 Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R. ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics. 5: 4096-106. PMID 16196091 DOI: 10.1002/Pmic.200401260  0.378
2005 Bradshaw RA, Burlingame AL, Carr S, Aebersold R. Protein identification: The good, the bad, and the ugly Molecular and Cellular Proteomics. 4: 1221-1222. PMID 16160099  0.304
2005 Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, ... Aebersold R, et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5: 3226-45. PMID 16104056 DOI: 10.1002/Pmic.200500358  0.485
2005 Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nature Methods. 2: 591-8. PMID 16094384 DOI: 10.1038/Nmeth776  0.679
2005 Gingras AC, Caballero M, Zarske M, Sanchez A, Hazbun TR, Fields S, Sonenberg N, Hafen E, Raught B, Aebersold R. A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Molecular & Cellular Proteomics : McP. 4: 1725-40. PMID 16085932 DOI: 10.1074/Mcp.M500231-Mcp200  0.622
2005 Aebersold R, Anderson L, Caprioli R, Druker B, Hartwell L, Smith R. Perspective: A program to improve protein biomarker discovery for cancer Journal of Proteome Research. 4: 1104-1109. PMID 16083259 DOI: 10.1021/Pr050027N  0.355
2005 Martin DB, Eng JK, Nesvizhskii AI, Gemmill A, Aebersold R. Investigation of neutral loss during collision-induced dissociation of peptide ions. Analytical Chemistry. 77: 4870-82. PMID 16053300 DOI: 10.1021/Ac050701K  0.334
2005 Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R. Human Plasma PeptideAtlas. Proteomics. 5: 3497-500. PMID 16052627 DOI: 10.1002/Pmic.200500160  0.385
2005 Li XJ, Yi EC, Kemp CJ, Zhang H, Aebersold R. A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Molecular & Cellular Proteomics : McP. 4: 1328-40. PMID 16048906 DOI: 10.1074/Mcp.M500141-Mcp200  0.43
2005 Shih JL, Reck-Peterson SL, Newitt R, Mooseker MS, Aebersold R, Herskowitz I. Cell polarity protein Spa2P associates with proteins involved in actin function in Saccharomyces cerevisiae. Molecular Biology of the Cell. 16: 4595-608. PMID 16030260 DOI: 10.1091/Mbc.E05-02-0108  0.364
2005 Nesvizhskii AI, Aebersold R. Interpretation of shotgun proteomic data: the protein inference problem. Molecular & Cellular Proteomics : McP. 4: 1419-40. PMID 16009968 DOI: 10.1074/Mcp.R500012-Mcp200  0.481
2005 Schrimpf SP, Meskenaite V, Brunner E, Rutishauser D, Walther P, Eng J, Aebersold R, Sonderegger P. Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics. 5: 2531-41. PMID 15984043 DOI: 10.1002/Pmic.200401198  0.366
2005 Kuster B, Schirle M, Mallick P, Aebersold R. Scoring proteomes with proteotypic peptide probes. Nature Reviews. Molecular Cell Biology. 6: 577-83. PMID 15957003 DOI: 10.1038/Nrm1683  0.512
2005 Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q, Aebersold RH, Montine TJ. Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. Journal of Alzheimer's Disease : Jad. 7: 125-33; discussion 1. PMID 15851850 DOI: 10.3233/Jad-2005-7205  0.5
2005 Wright ME, Han DK, Aebersold R. Mass spectrometry-based expression profiling of clinical prostate cancer Molecular and Cellular Proteomics. 4: 545-554. PMID 15695425 DOI: 10.1074/Mcp.R500008-Mcp200  0.368
2005 Chen R, Pan S, Brentnall TA, Aebersold R. Proteomic profiling of pancreatic cancer for biomarker discovery. Molecular & Cellular Proteomics : McP. 4: 523-33. PMID 15684406 DOI: 10.1074/Mcp.R500004-Mcp200  0.356
2005 Yi EC, Li XJ, Cooke K, Lee H, Raught B, Page A, Aneliunas V, Hieter P, Goodlett DR, Aebersold R. Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics. 5: 380-7. PMID 15648049 DOI: 10.1002/Pmic.200400970  0.614
2005 Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, ... ... Aebersold R, et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biology. 6: R9. PMID 15642101 DOI: 10.1186/Gb-2004-6-1-R9  0.688
2005 Pan S, Zhang H, Rush J, Eng J, Zhang N, Patterson D, Comb MJ, Aebersold R. High throughput proteome screening for biomarker detection. Molecular & Cellular Proteomics : McP. 4: 182-90. PMID 15637048 DOI: 10.1074/Mcp.M400161-Mcp200  0.454
2005 Gingras AC, Aebersold R, Raught B. Advances in protein complex analysis using mass spectrometry. The Journal of Physiology. 563: 11-21. PMID 15611014 DOI: 10.1113/Jphysiol.2004.080440  0.635
2005 Zhang H, Yi EC, Li XJ, Mallick P, Kelly-Spratt KS, Masselon CD, Camp DG, Smith RD, Kemp CJ, Aebersold R. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Molecular & Cellular Proteomics : McP. 4: 144-55. PMID 15608340 DOI: 10.1074/Mcp.M400090-Mcp200  0.64
2005 Zhang J, Goodlett DR, Peskind ER, Quinn JF, Zhou Y, Wang Q, Pan C, Yi E, Eng J, Aebersold RH, Montine TJ. Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiology of Aging. 26: 207-27. PMID 15582749 DOI: 10.1016/J.Neurobiolaging.2004.03.012  0.537
2005 Wollscheid B, Watts JD, Aebersold R. Proteomics/genomics and signaling in lymphocytes. Current Opinion in Immunology. 16: 337-44. PMID 15134783 DOI: 10.1016/J.Coi.2004.03.016  0.327
2004 Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. The Journal of Cell Biology. 167: 1099-112. PMID 15596542 DOI: 10.1083/Jcb.200404119  0.609
2004 Flory MR, Carson AR, Muller EG, Aebersold R. An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome Molecular Cell. 16: 619-630. PMID 15546621 DOI: 10.1016/J.Molcel.2004.10.027  0.339
2004 Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, ... ... Aebersold R, et al. A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnology. 22: 1459-66. PMID 15529173 DOI: 10.1038/Nbt1031  0.376
2004 Tian Q, Feetham MC, Tao WA, He XC, Li L, Aebersold R, Hood L. Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proceedings of the National Academy of Sciences of the United States of America. 101: 15370-5. PMID 15492215 DOI: 10.1073/Pnas.0406499101  0.582
2004 Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Lipid raft proteins and their identification in T lymphocytes. Sub-Cellular Biochemistry. 37: 121-52. PMID 15376619 DOI: 10.1007/978-1-4757-5806-1_3  0.599
2004 Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG. System-based proteomic analysis of the interferon response in human liver cells. Genome Biology. 5: R54. PMID 15287976 DOI: 10.1186/Gb-2004-5-8-R54  0.528
2004 Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, Fausto N, Katze MG, Aebersold R. A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Molecular & Cellular Proteomics : McP. 3: 1039-41. PMID 15269248 DOI: 10.1074/Mcp.D400001-Mcp200  0.466
2004 Lu Y, Bottari P, Turecek F, Aebersold R, Gelb MH. Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Analytical Chemistry. 76: 4104-11. PMID 15253649 DOI: 10.1021/Ac049905B  0.487
2004 Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, ... Aebersold R, et al. Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Molecular & Cellular Proteomics : McP. 3: 960-9. PMID 15238602 DOI: 10.1074/Mcp.M400055-Mcp200  0.533
2004 Zhou Y, Gu G, Goodlett DR, Zhang T, Pan C, Montine TJ, Montine KS, Aebersold RH, Zhang J. Analysis of alpha-synuclein-associated proteins by quantitative proteomics. The Journal of Biological Chemistry. 279: 39155-64. PMID 15234983 DOI: 10.1074/Jbc.M405456200  0.53
2004 Li XJ, Pedrioli PG, Eng J, Martin D, Yi EC, Lee H, Aebersold R. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Analytical Chemistry. 76: 3856-60. PMID 15228367 DOI: 10.1021/Ac035375S  0.401
2004 Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Molecular & Cellular Proteomics : McP. 3: 531-3. PMID 15075378 DOI: 10.1074/Mcp.T400006-Mcp200  0.466
2004 Zhou H, Boyle R, Aebersold R. Quantitative protein analysis by solid phase isotope tagging and mass spectrometry. Methods in Molecular Biology (Clifton, N.J.). 261: 511-8. PMID 15064479 DOI: 10.1385/1-59259-762-9:511  0.458
2004 Shumaker-Parry JS, Aebersold R, Campbell CT. Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy. Analytical Chemistry. 76: 2071-82. PMID 15053673 DOI: 10.1021/Ac035159J  0.324
2004 Zhang H, Yan W, Aebersold R. Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Current Opinion in Chemical Biology. 8: 66-75. PMID 15036159 DOI: 10.1016/J.Cbpa.2003.12.001  0.475
2004 Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR. Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 803: 101-10. PMID 15026003 DOI: 10.1016/J.Jchromb.2003.09.005  0.627
2004 Bottari P, Aebersold R, Turecek F, Gelb MH. Design and Synthesis of Visible Isotope-Coded Affinity Tags for the Absolute Quantification of Specific Proteins in Complex Mixtures Bioconjugate Chemistry. 15: 380-388. PMID 15025535 DOI: 10.1021/Bc034174S  0.439
2004 Hardwidge PR, Rodriguez-Escudero I, Goode D, Donohoe S, Eng J, Goodlett DR, Aebersold R, Finlay BB. Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. The Journal of Biological Chemistry. 279: 20127-36. PMID 14988394 DOI: 10.1074/Jbc.M401228200  0.537
2004 Nesvizhskii AI, Aebersold R. Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discovery Today. 9: 173-81. PMID 14960397 DOI: 10.1016/S1359-6446(03)02978-7  0.426
2004 MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Molecular & Cellular Proteomics : McP. 3: 478-89. PMID 14766929 DOI: 10.1074/Mcp.M300129-Mcp200  0.591
2004 Mayer ML, Pot I, Chang M, Xu H, Aneliunas V, Kwok T, Newitt R, Aebersold R, Boone C, Brown GW, Hieter P. Identification of protein complexes required for efficient sister chromatid cohesion. Molecular Biology of the Cell. 15: 1736-45. PMID 14742714 DOI: 10.1091/Mbc.E03-08-0619  0.336
2004 Martin DB, Gifford DR, Wright ME, Keller A, Yi E, Goodlett DR, Aebersold R, Nelson PS. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Research. 64: 347-55. PMID 14729644 DOI: 10.1158/0008-5472.Can-03-2062  0.511
2004 Sozio MS, Mathis MA, Young JA, Wälchli S, Pitcher LA, Wrage PC, Bartók B, Campbell A, Watts JD, Aebersold R, Van Huijsduijnen RH, Van Oers NSC. PTPH1 Is a Predominant Protein-tyrosine Phosphatase Capable of Interacting with and Dephosphorylating the T Cell Receptor ζ Subunit Journal of Biological Chemistry. 279: 7760-7769. PMID 14672952 DOI: 10.1074/Jbc.M309994200  0.379
2004 Li XJ, Zhang H, Ranish JA, Aebersold R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Analytical Chemistry. 75: 6648-57. PMID 14640741 DOI: 10.1021/Ac034633I  0.486
2003 Camacho-Carvajal MM, Wollscheid B, Aebersold R, Steimle V, Schamel WW. Two-dimensional Blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates: a proteomics approach. Molecular & Cellular Proteomics : McP. 3: 176-82. PMID 14665681 DOI: 10.1074/Mcp.T300010-Mcp200  0.452
2003 Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry. 75: 4646-58. PMID 14632076 DOI: 10.1021/Ac0341261  0.484
2003 Hu S, Le Z, Newitt R, Aebersold R, Kraly JR, Jones M, Dovichi NJ. Identification of proteins in single-cell capillary electrophoresis fingerprints based on comigration with standard proteins. Analytical Chemistry. 75: 3502-5. PMID 14570203 DOI: 10.1021/Ac034154J  0.617
2003 Schmidt F, Donahoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SH, Aebersold R, Jungblut PR. Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Molecular & Cellular Proteomics : McP. 3: 24-42. PMID 14557599 DOI: 10.1074/Mcp.M300074-Mcp200  0.445
2003 Yi EC, Lee H, Aebersold R, Goodlett DR. A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Communications in Mass Spectrometry : Rcm. 17: 2093-8. PMID 12955739 DOI: 10.1002/Rcm.1150  0.597
2003 Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV. Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Molecular & Cellular Proteomics : McP. 2: 506-24. PMID 12872007 DOI: 10.1074/Mcp.M300044-Mcp200  0.757
2003 Guina T, Wu M, Miller SI, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Ernst RK, Lee KA. Proteomic analysis of Pseudomonas aeruginosa grown under magnesium limitation. Journal of the American Society For Mass Spectrometry. 14: 742-51. PMID 12837596 DOI: 10.1016/S1044-0305(03)00133-8  0.645
2003 Shiio Y, Eisenman RN, Yi EC, Donohoe S, Goodlett DR, Aebersold R. Quantitative proteomic analysis of chromatin-associated factors. Journal of the American Society For Mass Spectrometry. 14: 696-703. PMID 12837591 DOI: 10.1016/S1044-0305(03)00204-6  0.573
2003 Aebersold R. A mass spectrometric journey into protein and proteome research. Journal of the American Society For Mass Spectrometry. 14: 685-95. PMID 12837590 DOI: 10.1016/S1044-0305(03)00289-7  0.415
2003 von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. Molecular & Cellular Proteomics : McP. 2: 428-42. PMID 12832459 DOI: 10.1074/Mcp.M300041-Mcp200  0.658
2003 von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts. Molecular & Cellular Proteomics : McP. 2: 426-7. PMID 12832456 DOI: 10.1074/Mcp.D300002-Mcp200  0.633
2003 Aebersold R. Quantitative proteome analysis: methods and applications. The Journal of Infectious Diseases. S315-20. PMID 12792845 DOI: 10.1086/374756  0.314
2003 Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nature Biotechnology. 21: 660-6. PMID 12754519 DOI: 10.1038/Nbt827  0.481
2003 Ha SA, Torabinejad J, DeWald DB, Wenk MR, Lucast L, De Camilli P, Newitt RA, Aebersold R, Nothwehr SF. The synaptojanin-like protein Inp53/Sjl3 functions with clathrin in a yeast TGN-to-endosome pathway distinct from the GGA protein-dependent pathway. Molecular Biology of the Cell. 14: 1319-33. PMID 12686590 DOI: 10.1091/Mbc.E02-10-0686  0.35
2003 Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 422: 198-207. PMID 12634793 DOI: 10.1038/Nature01511  0.483
2003 Griffin TJ, Lock CM, Li XJ, Patel A, Chervetsova I, Lee H, Wright ME, Ranish JA, Chen SS, Aebersold R. Abundance ratio-dependent proteomic analysis by mass spectrometry. Analytical Chemistry. 75: 867-74. PMID 12622378 DOI: 10.1021/Ac026127J  0.746
2003 Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature Biotechnology. 21: 247-54. PMID 12610571 DOI: 10.1038/Nbt0303-247  0.333
2003 Guina T, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Miller SI. Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proceedings of the National Academy of Sciences of the United States of America. 100: 2771-6. PMID 12601166 DOI: 10.1073/Pnas.0435846100  0.509
2003 Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold R. The study of macromolecular complexes by quantitative proteomics. Nature Genetics. 33: 349-55. PMID 12590263 DOI: 10.1038/Ng1101  0.612
2003 Aebersold R, Cravatt BF. Proteomics--advances, applications and the challenges that remain. Trends in Biotechnology. 20: S1-2. PMID 12570151 DOI: 10.1016/S1471-1931(02)00206-9  0.469
2003 Tao WA, Aebersold R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Current Opinion in Biotechnology. 14: 110-8. PMID 12566010 DOI: 10.1016/S0958-1669(02)00018-6  0.622
2003 Aebersold R, Watts JD. The need for national centers for proteomics. Nature Biotechnology. 20: 651. PMID 12089539 DOI: 10.1038/Nbt0702-651  0.32
2002 Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. Journal of Proteome Research. 1: 47-54. PMID 12643526 DOI: 10.1021/Pr015509N  0.722
2002 Flory MR, Griffin TJ, Martin D, Aebersold R. Advances in quantitative proteomics using stable isotope tags. Trends in Biotechnology. 20: S23-9. PMID 12570156 DOI: 10.1016/S1471-1931(02)00203-3  0.627
2002 Zhang N, Aebersold R, Schwikowski B. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics. 2: 1406-12. PMID 12422357 DOI: 10.1002/1615-9861(200210)2:10<1406::Aid-Prot1406>3.0.Co;2-9  0.412
2002 Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proceedings of the National Academy of Sciences of the United States of America. 99: 14913-8. PMID 12403819 DOI: 10.1073/Pnas.192558999  0.595
2002 Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Analytical Chemistry. 74: 5383-92. PMID 12403597 DOI: 10.1021/Ac025747H  0.392
2002 Shiio Y, Donohoe S, Yi EC, Goodlett DR, Aebersold R, Eisenman RN. Quantitative proteomic analysis of Myc oncoprotein function. The Embo Journal. 21: 5088-96. PMID 12356725 DOI: 10.1093/Emboj/Cdf525  0.604
2002 Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR. Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis. 23: 3205-16. PMID 12298092 DOI: 10.1002/1522-2683(200209)23:18<3205::Aid-Elps3205>3.0.Co;2-Y  0.589
2002 Lee H, Griffin TJ, Gygi SP, Rist B, Aebersold R. Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. Analytical Chemistry. 74: 4353-60. PMID 12236342 DOI: 10.1021/Ac025757I  0.7
2002 Yang T, Espenshade PJ, Wright ME, Yabe D, Gong Y, Aebersold R, Goldstein JL, Brown MS. Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell. 110: 489-500. PMID 12202038 DOI: 10.1016/S0092-8674(02)00872-3  0.318
2002 Smolka M, Zhou H, Aebersold R. Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry Molecular & Cellular Proteomics : McP. 1: 19-29. PMID 12096137 DOI: 10.1074/Mcp.M100013-Mcp200  0.715
2002 Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 1: 323-33. PMID 12096114 DOI: 10.1074/Mcp.M200001-Mcp200  0.7
2002 James EA, Gygi SP, Adams ML, Pierce RH, Fausto N, Aebersold RH, Nelson SD, Bruschi SA. Mitochondrial aconitase modification, functional inhibition, and evidence for a supramolecular complex of the TCA cycle by the renal toxicant S-(1,1,2,2-tetrafluoroethyl)-L-cysteine. Biochemistry. 41: 6789-97. PMID 12022883 DOI: 10.1021/Bi020038J  0.39
2002 Zhou H, Ranish JA, Watts JD, Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nature Biotechnology. 20: 512-5. PMID 11981568 DOI: 10.1038/Nbt0502-512  0.405
2002 Marotti LA, Newitt R, Wang Y, Aebersold R, Dohlman HG. Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry. 41: 5067-74. PMID 11955054 DOI: 10.1021/Bi015940Q  0.361
2002 Hamerman JA, Hayashi F, Schroeder LA, Gygi SP, Haas AL, Hampson L, Coughlin P, Aebersold R, Aderem A. Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog. Journal of Immunology (Baltimore, Md. : 1950). 168: 2415-23. PMID 11859133 DOI: 10.4049/Jimmunol.168.5.2415  0.452
2002 Dramsi S, Scheid MP, Maiti A, Hojabrpour P, Chen X, Schubert K, Goodlett DR, Aebersold R, Duronio V. Identification of a novel phosphorylation site, Ser-170, as a regulator of bad pro-apoptotic activity. The Journal of Biological Chemistry. 277: 6399-405. PMID 11717309 DOI: 10.1074/Jbc.M109990200  0.471
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