YearPaper
2007 Colinge J, Bennett KL. Introduction to computational proteomics. PLoS Comput Biol 2007, 3:e114. 
Abstract: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933459/
2008 Bürckstümmer T, Bennett KL. Analysis of cellular protein complexes by affinity purification and mass spectrometry. In Proteomics Methods Express 2008 (O’Connor CD and Hames BD, eds.), pp 119–134, Scion, Oxfordshire.
Abstract:
2008 Holzmann J, Frank P, Löffler E, Bennett KL, Gerner C and Rossmanith W. RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme. Cell 2008, Oct 31;135(3): 462–74.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/18984158
2008 Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, et al. Human Proteinpedia enables sharing of human protein data. Nature Biotech. 2008, 26, 164–167.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/18259167
2011 Bennett KL, Funk M, Tschernutter M, Breitwieser FP, Planyavsky M, Ubaida Mohien C, Muller A, Trajanoski Z, Colinge J, Superti-Furga G, Schmidt-Erfurth U. Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ(R)-labelled specimens. J Proteomics. 2011 Feb 1;74(2):151-66.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20940065
2011 Haura EB, Muller A, Breitwieser FP, Li J, Grebien F, Colinge J, Bennett KL. Using iTRAQ combined with tandem affinity purification to enhance low-abundance proteins associated with somatically mutated EGFR core complexes in lung cancer. J Proteome Res. 2011 Jan 7;10(1):182-90.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20945942
2012 Heo S, Yang JW, Huber ML, Planyavsky M, Bennett KL, Lubec G. Mass spectrometric characterization of recombinant rat 5-hydroxytryptamine receptor 1A (5-HT(1A) R) expressed in tsA201 human embryonic kidney cells. Proteomics. 2012 Nov;12(22):3338-42.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/22997067
2012 Maurer M, Müller AC, Wagner C, Huber ML, Rudashevskaya EL, Wagner SN, Bennett KL. Combining Filter-Aided Sample Preparation and Pseudoshotgun Technology To Profile the Proteome of a Low Number of Early Passage Human Melanoma Cells. J Proteome Res. 2012 Dec 24.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23214492
2012 Müller AC, Breitwieser FP, Fischer H, Schuster C, Brandt O, Colinge J, Superti-Furga G, Stingl G, Elbe-Buerger A, Bennett KL. A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ-labelling. J. Proteome Res. 2012 Jul 6;11(7):3715-27.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/22578099
2012 Pollreisz A, Funk M, Breitwieser FP, Parapatics K, Sacu S, Georgopoulos M, Dunavoelgyi R, Zlabinger GJ, Colinge J, Bennett KL, Schmidt-Erfurth U. Quantitative proteomics of aqueous and vitreous fluid from patients with idiopathic epiretinal membranes. Exp Eye Res. 2012 Nov 29;108C:48-58.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23201028
2012 Rudashevskaya EL, Sacco R, Kratochwill K, Huber ML, Gstaiger M, Superti-Furga G, Bennett KL. A method to resolve the composition of heterogeneous affinity-purified protein complexes assembled around a common protein by chemical cross-linking, gel electrophoresis and mass spectrometry. Nat Protoc. 2012 Dec 13;8(1):75-97.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23237831
2013 Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL. A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. J Proteome Res. 2013 Sep 6;12(9):4005-17.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23901793
2013 De Keersmaecker K, Porcu M, Cox L, Girardi T, Vandepoel R, Op de Beeck J, Gielen O, Mentens N, Bennett KL, Hantschel O. NUP214-ABL1 mediated cell proliferation in T-cell acute lymphoblastic leukemia is dependent on the LCK kinase and various interacting proteins. Haematologica. 2013 Jul 19. [Epub ahead of print].
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23872305
2013 Giambruno R, Grebien F, Stukalov A, Knoll C, Planyavsky M, Rudashevskaya EL, Colinge J, Superti-Furga G, Bennett KL. Affinity Purification Strategies for Proteomic Analysis of Transcription Factor Complexes. J Proteome Res. 2013 September 6; 12(9): 4018–4027.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23937658
2013 Herwig R, Knoll C, Planyavsky M, Pourbiabany A, Greilberger J, Bennett KL. Proteomic analysis of seminal plasma from infertile patients with oligoasthenoteratozoospermia due to oxidative stress and comparison with fertile volunteers. Fertil Steril. 2013 Aug; 100(2):355-66.e2.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23628110
2013 Mellacheruvu D, Wright Z, Couzens AL, Lambert J-P, St-Denis N, Li T, Mitev YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin Z-Y, Gonzalez Badillo B, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga S, Colinge J, Heck AJR, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras A-C, Nesvizhskii A. The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data. Nature Methods May; 24(Suppl): S50–S51.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23921808
2013 Rudashevskaya EL, Breitwieser FP, Huber ML, Colinge J, Müller AC, Bennett KL. Multiple and sequential data acquisition method: an improved method for fragmentation and detection of cross-linked peptides on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer. Anal Chem. 2013 Feb 5; 85(3):1454-61.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23301806
2013 Rudashevskaya EL, Sacco R, Kratochwill K, Huber ML, Gstaiger M, Superti-Furga G, Bennett KL. A method to resolve the composition of heterogeneous affinity-purified protein complexes assembled around a common protein by chemical cross-linking, gel electrophoresis and mass spectrometry. Nat Protoc. 2013 Jan;8(1):75-97.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23237831
2013 Fritzsche R, Karra D, Bennett KL, Ang FY, Heraud-Farlow JE, Tolino M, Doyle M, Bauer KE, Thomas S, Planyavsky M, Arn E, Bakosova A, Jungwirth K, Hörmann A, Palfi Z, Sandholzer J, Schwarz M, Macchi P, Colinge J, Superti-Furga G, Kiebler MA. Interactome of two diverse RNA granules links mRNA localization to translational repression in neurons. Cell Rep. 2013 Dec 26;5(6):1749-62. doi: 10.1016/j.celrep.2013.11.023. Epub 2013 Dec 19.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24360960
2013 Upadhyay AS, Vonderstein K, Pichlmair A, Stehling O, Bennett KL, Dobler G, Guo JT, Superti-Furga G, Lill R, Overby AK, Weber F. Viperin is an iron-sulfur protein that inhibits genome synthesis of tick-borne encephalitis virus via radical SAM domain activity. Cell Microbiol. 2013 Nov 19. doi: 10.1111/cmi.12241. [Epub ahead of print]
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24245804
2014 Huber ML, Sacco R, Parapatics K, Skucha A, Khamina K, Müller AC, Rudashevskaya EL, Bennett KL. abFASP-MS: Affinity-Based Filter-Aided Sample Preparation Mass Spectrometry for Quantitative Analysis of Chemically Labeled Protein Complexes. J Proteome Res. 2014 Feb 7;13(2):1147-55. doi: 10.1021/pr4009892. Epub 2014 Jan 17.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24400740
2014 Boucheron N, Tschismarov R, Goeschl L, Moser M, Lagger S, Sakaguchi S, Winter M, Lenz F, Vitko D, Breitwieser FP, Haust L, Hassan H, Bennett KL, Colinge J, Schreiner W, Egawa T, Taniuchi I, Matthias P, Seiser C, Ellmeier W. CD4 T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nat Immunol. 2014 May;15(5):439-48. doi: 10.1038/ni.2864. Epub 2014 Mar 30.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24681565
2014 Boucheron N, Tschismarov R, Goeschl L, A Moser M, Lagger S, Sakaguchi S, Winter M, Lenz F, Vitko D, Breitwieser FP, Müller L, Hassan H, Bennett KL, Colinge J, Schreiner W, Egawa T, Taniuchi I, Matthias P, Seiser C, Ellmeier W. Corrigendum: CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nat Immunol. 2014 Aug 19;15(9):894.doi:10.1038/ni0914-894e.
Abstract: http://www.nature.com/ni/journal/v15/n9/full/ni0914-894e.html
2014 Ghafari M, Whittle N, Miklósi AG, Kotlowski C, Schmuckermair C, Berger J, Bennett KL, Singewald N, Lubec G. Erratum to: Dietary magnesium restriction reduces amygdala-hypothalamic GluN1 receptor complex levels in mice. Brain Struct Funct. 2014 Jun 26. [Epub ahead of print]
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24965486
2014 Ghafari M, Whittle N, Miklósi AG, Kotlowsky C, Schmuckermair C, Berger J, Bennett KL, Singewald N, Lubec G. Dietary magnesium restriction reduces amygdala-hypothalamic GluN1 receptor complex levels in mice. Brain Struct Funct. 2014 May 8. [Epub ahead of print]
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24807818
2014 Giansanti P, Preisinger C, Huber KV, Gridling M, Superti-Furga G, Bennett KL, Heck AJ. Evaluating the promiscuous nature of tyrosine kinase inhibitors assessed in A431 epidermoid carcinoma cells by both chemical- and phosphoproteomics. ACS Chem Biol. 2014 Jul 18;9(7):1490-8. doi: 10.1021/cb500116c. Epub 2014 May 14.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24804581
2014 Gridling M, Ficarro S, Breitwieser FP, Song L, Parapatics K, Colinge J, Haura EB, Marto J, Superti-Furga G, Bennett KL, Rix U. Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics. Mol Cancer Ther. 2014 Sep 4. pii: molcanther.0152.2014. [Epub ahead of print]
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25189542
2014 Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN. Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma. J Proteome Res. 2014 Jun 6;13(6):2830-45. doi: 10.1021/pr401270y. Epub 2014 May 6.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24803318
2015 Ghafari M, Falsafi SK, Höger H, Bennett KL, Lubec G. Identification of new phosphorylation sites of AMPA receptors in the rat hippocampus-A ressource for neuroscience research. Proteomics Clin Appl. 2015 Feb 6. doi: 10.1002/prca.201400057.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25656447
2015 Hofer A, Cremosnik GS, Müller AC, Giambruno R, Trefzer C, Superti-Furga G, Bennett KL, Jessen HJ. A Modular Synthesis of Modified Phosphoanhydrides. Chemistry. 2015 Jun 1. doi: 10.1002/chem.201500838.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26033174
2015 Krishnaswamy JK, Singh A, Gowthaman U, Wu R, Gorrepati P, Sales Nascimento M, Gallman A, Liu D, Rhebergen AM, Calabro S, Xu L, Ranney P, Srivastava A, Ranson M, Gorham JD, McCaw Z, Kleeberger SR, Heinz LX, Müller AC, Bennett KL, Superti-Furga G, Henao-Mejia J, Sutterwala FS, Williams A, Flavell RA, Eisenbarth SC. Coincidental loss of DOCK8 function in NLRP10-deficient and C3H/HeJ mice results in defective dendritic cell migration. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3056-61. doi: 10.1073/pnas.1501554112. Epub 2015 Feb 23.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25713392
2015 Sase S, Sase A, Sialana F, Gröger M, Bennett KL, Stork O, Lubec G, Li L. Individual phases of contextual fear conditioning differentially modulate dorsal and ventral hippocampal GluA1-3, GluN1-containing receptor complexes and subunits. Hippocampus. 2015 Apr 25. doi: 10.1002/hipo.22470.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25914080
2015 Shanmugasundaram B, Sase A, Miklosi AG, Sialana FJ, Subramaniyan S, Aher YD, Gröger M, Höger H, Bennett KL, Lubec G. Frontal cortex and hippocampus neurotransmitter receptor complex level parallels spatial memory performance in the radial arm maze. Behav Brain Res. 2015 Aug 1;289:157-68. doi: 10.1016/j.bbr.2015.04.043. Epub 2015 Apr 28.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25930220
2015 Subramaniyan S, Hajali V, Scherf T, Sase SJ, Sialana FJ, Gröger M, Bennett KL, Pollak A, Li L, Korz V, Lubec G. Hippocampal receptor complexes paralleling LTP reinforcement in the spatial memory holeboard test in the rat. Behav Brain Res. 2015 Apr 15;283:162-74. doi: 10.1016/j.bbr.2015.01.036. Epub 2015 Jan 30.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25639541
2015 Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL. The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses. Mol Cell Proteomics. 2015 Dec;14(12):3299-309. doi: 10.1074/mcp.O115.051888. Epub 2015 Oct 4.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26435129
2015 Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Mueller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G. An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client. Mol Cell Proteomics. 2015 Dec 29. pii: mcp.O115.055350.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26714523
2015 Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, Sacco R, van Diemen FR, Olk N, Stukalov A, Marceau C, Janssen H, Carette JE, Bennett KL, Colinge J, Superti-Furga G, Brummelkamp TR. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015 Nov 27;350(6264):1092-6. doi: 10.1126/science.aac7557. Epub 2015 Oct 15.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26472760
2015 Harutyunyan AS, Giambruno R, Krendl C, Stukalov A, Klampfl T, Berg T, Chen D, Milosevic Feenstra JD, Jäger R, Gisslinger B, Gisslinger H, Rumi E, Passamonti F, Pietra D, Müller AC, Parapatics K, Breitwieser FP, Herrmann R, Colinge J, Bennett KL, Superti-Furga G, Cazzola M, Hammond E, Kralovics R. Germline RBBP6 mutations in familial myeloproliferative neoplasms. Blood. 2015 Nov 16. pii: blood-2015-09-668673.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26574608
2015 Hörmann K, Stukalov A, Müller AC, Heinz LX, Superti-Furga G, Colinge J, Bennett KL. A surface biotinylation strategy for reproducible plasma membrane protein purification and tracking of genetic and drug-induced alterations. J Proteome Res. 2015 Dec 24.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26699813
2015 Huber KV, Olek KM, Müller AC, Tan CS, Bennett KL, Colinge J, Superti-Furga G. Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling. Nat Methods. 2015 Nov;12(11):1055-7. doi: 10.1038/nmeth.3590. Epub 2015 Sep 21.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26389571
2015 Peter B, Winter GE, Blatt K, Bennett KL, Stefanzl G, Rix U, Eisenwort G, Hadzijusufovic E, Gridling M, Dutreix C, Hoermann G, Schwaab J, Radia D, Roesel J, Manley PW, Reiter A, Superti-Furga G, Valent P. Target interaction profiling of midostaurin and its metabolites in neoplastic mast cells predicts distinct effects on activation and growth. Leukemia. 2015 Sep 9. doi: 10.1038/leu.2015.242.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26349526
2015 Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One. 2015 Nov 5;10(11):e0142162. doi: 10.1371/journal.pone.0142162. eCollection 2015.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26539827
2016 Hörmann K, Stukalov A, Müller AC, Heinz LX, Superti-Furga G, Colinge J, Bennett KL. A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations. J Proteome Res. 2016 Feb 5;15(2):647-58. doi: 10.1021/acs.jproteome.5b01066. Epub 2016 Jan 12.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26699813
2016 Müller AC, Giambruno R, Weißer J, Májek P, Hofer A, Bigenzahn JW, Superti-Furga G, Jessen HJ, Bennett KL. Identifying Kinase Substrates via a Heavy ATP Kinase Assay and Quantitative Mass Spectrometry. Sci Rep. 2016 Jun 27;6:28107. doi: 10.1038/srep28107.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/27346722
2016 Sdelci S, Lardeau CH, Tallant C, Klepsch F, Klaiber B, Bennett J, Rathert P, Schuster M, Penz T, Fedorov O, Superti-Furga G, Bock C, Zuber J, Huber KV, Knapp S, Müller S, Kubicek S. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nat Chem Biol. 2016 May 9. doi: 10.1038/nchembio.2080.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/27159579
2016 Vitko D, Májek P, Schirghuber E, Kubicek S, Bennett KL. FASIL-MS: An Integrated Proteomic and Bioinformatic Workflow To Universally Quantitate In Vivo-Acetylated Positional Isomers. J Proteome Res. 2016 Aug 5;15(8):2579-94. doi: 10.1021/acs.jproteome.6b00130.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/27302567
2016 Peter B, Winter GE, Blatt K, Bennett KL, Stefanzl G, Rix U, Eisenwort G, Hadzijusufovic E, Gridling M, Dutreix C, Hoermann G, Schwaab J, Radia D, Roesel J, Manley PW, Reiter A, Superti-Furga G, Valent P. Target interaction profiling of midostaurin and its metabolites in neoplastic mast cells predicts distinct effects on activation and growth. Leukemia. 2016 Feb;30(2):464-72. doi: 10.1038/leu.2015.242.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26349526
2016 Sialana FJ, Gulyassy P, Májek P, Sjöstedt E, Kis V, Müller AC, Rudashevskaya EL, Mulder J, Bennett KL, Lubec G. Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels. Proteomics. 2016 Oct 19. doi: 10.1002/pmic.201600234.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/27759936
2016 Willmann KL, Sacco R, Martins R, Garncarz W, Krolo A, Knapp S, Bennett KL, Boztug K. Expanding the Interactome of the Noncanonical NF-_B Signaling Pathway. J Proteome Res. 2016 Sep 2;15(9):2900-9. doi: 10.1021/acs.jproteome.5b01004.
Abstract: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295629/
2016 Li J, Casteels T, Frogne T, Ingvorsen C, Honoré C, Courtney M, Huber KVM, Schmitner N, Kimmel RA, Romanov RA, Sturtzel C, Lardeau CH, Klughammer J, Farlik M, Sdelci S, Vieira A, Avolio F, Briand F, Baburin I, Májek P, Pauler FM, Penz T, Stukalov A, Gridling M, Parapatics K, Barbieux C, Berishvili E, Spittler A, Colinge J, Bennett KL, Hering S, Sulpice T, Bock C, Distel M, Harkany T, Meyer D, Superti-Furga G, Collombat P, Hecksher-Sørensen J, and Kubicek S. Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity, Cell 2017 Jan 12 (epub ahead of print 2016 Dec 1);168(1), 86-100. doi:10.1016/j.cell.2016.11.010.
Abstract: http://www.cell.com/cell/abstract/S0092-8674(16)31531-8
Abstract: