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Ghosh, Souvik; Guimaraes, Joao C.; Lanzafame, Manuela; Schmidt, Alexander; Syed, Afzal Pasha; Dimitriades, Beatrice; Börsch, Anastasiya; Ghosh, Shreemoyee; Mittal, Nitish; Montavon, Thomas; Correia, Ana Luisa; Danner, Johannes; Meister, Gunter; Terracciano, Luigi M.; Pfeffer, Sébastien; Piscuoglio, Salvatore; Zavolan, Mihaela (2020). Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. The EMBO Journal, 39 (18), e103922.

Guimaraes, Joao C; Mittal, Nitish; Gnann, Alexandra; Jedlinski, Dominik; Riba, Andrea; Buczak, Katarzyna; Schmidt, Alexander; Zavolan, Mihaela (2020). A rare codon-based translational program of cell proliferation. Genome biology, 21 (1), 44.


Monteiro, Francisca; Hubmann, Georg; Takhaveev, Vakil; Vedelaar, Silke R.; Norder, Justin; Hekelaar, Johan; Saldida, Joana; Litsios, Athanasios; Wijma, Hein J.; Schmidt, Alexander; Heinemann, Matthias (2019). Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor. Molecular systems biology, 15 (12), e9071.

Personnic, Nicolas; Striednig, Bianca; Lezan, Emmanuelle; Manske, Christian; Welin, Amanda; Schmidt, Alexander; Hilbi, Hubert (2019). Quorum sensing modulates the formation of virulent Legionella persisters within infected cells. Nature communications, 10 (1), 5216.

Litsios, Athanasios; Huberts, Daphne H. E. W.; Terpstra, Hanna M.; Guerra, Paolo; Schmidt, Alexander; Buczak, Katarzyna; Papagiannakis, Alexandros; Rovetta, Mattia; Hekelaar, Johan; Hubmann, Georg; Exterkate, Marten; Milias-Argeitis, Andreas; Heinemann, Matthias (2019). Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast. Nature cell biology, 21 (11), 1382-1392.

Jourdan, Joëlle; Walz, Annabelle; Matile, Hugues; Schmidt, Alexander; Wu, Jianbo; Wang, Xiaofang; Dong, Yuxiang; Vennerstrom, Jonathan L.; Schmidt, Remo S.; Wittlin, Sergio; Mäser, Pascal (2019). Stochastic Protein Alkylation by Antimalarial Peroxides. ACS infectious diseases, 5 (12), 2067-2075.

Dreier, Roland Felix; Ahrné, Erik; Broz, Petr; Schmidt, Alexander (2019). Global Ion Suppression Limits the Potential of Mass Spectrometry Based Phosphoproteomics. Journal of proteome research, 18 (1), 493-507.

Riba, Andrea; Di Nanni, Noemi; Mittal, Nitish; Arhné, Erik; Schmidt, Alexander; Zavolan, Mihaela (2019). Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proceedings of the National Academy of Sciences, 116 (30), 15023-15032.


Opitz, Christian; Ahrné, Erik; Goldie, Kenneth N.; Schmidt, Alexander; Grzesiek, Stephan (2018). Deuterium induces a distinctive Escherichia coli proteome that correlates with the reduction in growth rate. Journal of Biological Chemistry, 294 (7), 2279-2292.

Arquint, Christian; Cubizolles, Fabien; Morand, Agathe; Schmidt, Alexander; Nigg, Erich A. (2018). The SKP1-Cullin-F-box E3 ligase βTrCP and CDK2 cooperate to control STIL abundance and centriole number. Open biology, 8 (2), 16.


Mittal, Nitish; Guimaraes, Joao C.; Gross, Thomas; Schmidt, Alexander; Vina-Vilaseca, Arnau; Nedialkova, Danny D.; Aeschimann, Florian; Leidel, Sebastian A.; Spang, Anne; Zavolan, Mihaela (2017). The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nature Communications, 8 (457), 1-12.

Gencoglu, Mumun; Schmidt, Alexander; Becskei, Attila (2017). Measurement of in vivo protein binding affinities in a signaling network with mass spectrometry. ACS Synthetic Biology, 6 (7), 1305-1314.

Furrer, Regula; Eisele, Petra S.; Schmidt, Alexander; Beer, Markus; Handschin, Christoph (2017). Paracrine cross-talk between skeletal muscle and macrophages in exercise by PGC-1α-controlled BNP. Scientific Reports, 7, 40789.

Gumienny, Rafal; Jedlinski, Dominik J.; Schmidt, Alexander; Gypas, Foivos; Martin, Georges; Vina-Vilaseca, Arnau; Zavolan, Mihaela (2017). High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Research, 45 (5), 2341-2353.


Radzikowski, Jakub Leszek; Vedelaar, Silke; Siegel, David; Ortega, Álvaro Dario; Schmidt, Alexander; Heinemann, Matthias (2016). Bacterial persistence is an active σS stress response to metabolic flux limitation. Molecular Systems Biology, 12 (9), 882.

Bauer, Manuel; Cubizolles, Fabien; Schmidt, Alexander; Nigg, Erich A. (2016). Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging. The EMBO journal, 35 (19), 2152-2166.

Ahrné, Erik; Glatter, Timo; Viganò, Cristina; Schubert, Conrad von; Nigg, Erich A.; Schmidt, Alexander (2016). Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments. Journal of Proteome Research, 15 (8), 2537-47.

Gasser, Véronique; Baco, Etienne; Cunrath, Olivier; Saint August, Pamela; Perraud, Quentin; Zill, Nicolas; Schleberger, Christian; Schmidt, Alexander; Paulen, Aurélie; Bumann, Dirk; Mislin, Gaëtan L. A.; Schalk, Isabelle J. (2016). Catechol siderophores repress the pyochelin pathway and activate the enterobactin pathway in Pseudomonas aeruginosa: an opportunity for siderophore-antibiotic conjugates development. Environmental Microbiology, 18 (3), 819-32.

Schmidt, Alexander; Kochanowski, Karl; Vedelaar, Silke; Ahrne, Erik; Volkmer, Benjamin; Callipo, Luciano; Knoops, Kevin; Bauer, Manuel; Aebersold, Ruedi; Heinemann, Matthias (2016). The quantitative and condition-dependent Escherichia coli proteome. Nature biotechnology, 34 (1), 104-110.

Oettinghaus, B; Schulz, J M; Restelli, L M; Licci, M; Savoia, C; Schmidt, A; Schmitt, K; Grimm, A; Morè, L; Hench, J; Tolnay, M; Eckert, A; D'Adamo, P; Franken, P; Ishihara, N; Mihara, K; Bischofberger, J; Scorrano, L; Frank, S (2016). Synaptic dysfunction, memory deficits and hippocampal atrophy due to ablation of mitochondrial fission in adult forebrain neurons. Cell death and differentiation, 23 (1), 18-28.


Bauer, Manuel; Ahrné, Erik; Baron, Anna P; Glatter, Timo; Fava, Luca L; Santamaria, Anna; Nigg, Erich A; Schmidt, Alexander (2015). Assessment of current mass spectrometric workflows for the quantification of low abundant proteins and phosphorylation sites. Data in brief, 5, 297-304.

Janssens, Georges E; Meinema, Anne C; González, Javier; Wolters, Justina C; Schmidt, Alexander; Guryev, Victor; Bischoff, Rainer; Wit, Ernst C; Veenhoff, Liesbeth M; Heinemann, Matthias (2015). Protein biogenesis machinery is a driver of replicative aging in yeast. eLife, 4, e08527.

Glatter, Timo; Ahrné, Erik; Schmidt, Alexander (2015). Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. Journal of Proteome Research, 14 (11), 4472-85.

Ahrné, Erik; Martinez-Segura, Amalia; Syed, Afzal Pasha; Vina-Vilaseca, Arnau; Gruber, Andreas J; Marguerat, Samuel; Schmidt, Alexander (2015). Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry. Methods, 85, 100-7.

Sjostrom, Martin; Ossola, Reto; Breslin, Thomas; Rinner, Oliver; Malmstroem, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmstrom, Johan; Nimeus, Emma (2015). A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. Journal of Proteome Research, 14 (7), 2807-2818.

Laventie, Benoît-Joseph; Nesper, Jutta; Ahrné, Erik; Glatter, Timo; Schmidt, Alexander; Jenal, Urs (2015). Capture compound mass spectrometry - a powerful tool to identify novel c-di-GMP effector proteins. Journal of visualized experiments, 97 , e51404 (97), e51404.


Clément-Ziza, Mathieu; Marsellach, Francesc X; Codlin, Sandra; Papadakis, Manos A; Reinhardt, Susanne; Rodríguez-López, María; Martin, Stuart; Marguerat, Samuel; Schmidt, Alexander; Lee, Eunhye; Workman, Christopher T; Bähler, Jürg; Beyer, Andreas (2014). Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast. Molecular systems biology, 10 (11), 764.

Bauer, Manuel; Ahrné, Erik; Baron, Anna P; Glatter, Timo; Fava, Luca L; Santamaria, Anna; Nigg, Erich A; Schmidt, Alexander (2014). Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites. Journal of proteome research, 13 (12), 5973-88.

Claudi, Beatrice; Spröte, Petra; Chirkova, Anna; Personnic, Nicolas; Zankl, Janine; Schürmann, Nura; Schmidt, Alexander; Bumann, Dirk (2014). Phenotypic variation of salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell, 158 (4), 722-733.

Fengos, Georgios; Schmidt, Alexander; Martin, Katrin; Fluri, Erika; Aebersold, Ruedi; Iber, Dagmar; Pertz, Olivier (2014). Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome science, 12, 23.

Pieles, Kathrin; Glatter, Timo; Harms, Alexander; Schmidt, Alexander; Dehio, Christoph (2014). An experimental strategy for the identification of AMPylation targets from complex protein samples. Proteomics, 14 (9), 1048-1052.

Burton, Neil A.; Schürmann, Nura; Casse, Olivier; Steeb, Anne K.; Claudi, Beatrice; Zankl, Janine; Schmidt, Alexander; Bumann, Dirk (2014). Disparate Impact of Oxidative Host Defenses Determines the Fate of Salmonella during Systemic Infection in Mice. Cell Host & Microbe, 15 (1), 72-83.


Dehio, Christoph (2013). Dual input control : activation of the Bartonella henselae VirB/D4 type IV secretion system by the stringent sigma factor RpoH1 and the BatR/BatS two-component system. Molecular microbiology, 90, H. 4 (4), 756-775.

Schmutz, Christoph; Ahrné, Erik; Kasper, Christoph A; Tschon, Therese; Sorg, Isabel; Dreier, Roland F; Schmidt, Alexander; Arrieumerlou, Cécile (2013). Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Molecular & cellular proteomics, 12 (10), 2952-68.

Ahrné, Erik; Molzahn, Lars; Glatter, Timo; Schmidt, Alexander (2013). Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics, 13 (17), 2567-78.

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A.; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel exploitation of diverse host nutrients enhances salmonella virulence. PLoS Pathogens, 9 (4), e1003301.

Lehtinen, Sonja; Marsellach, Francesc Xavier; Codlin, Sandra; Schmidt, Alexander; Clément-Ziza, Mathieu; Beyer, Andreas; Bähler, Jürg; Orengo, Christine; Pancaldi, Vera (2013). Stress induces remodelling of yeast interaction and co-expression networks. Molecular biosystems, 9 (7), 1697-707.

Gunaratne, Jayantha; Schmidt, Alexander; Quandt, Andreas; Neo, Suat Peng; Saraç, Omer Sinan; Gracia, Tannia; Loguercio, Salvatore; Ahrné, Erik; Xia, Rachel Li Hai; Tan, Keng Hwa; Lössner, Christopher; Bähler, Jürg; Beyer, Andreas; Blackstock, Walter; Aebersold, Ruedi (2013). Extensive mass spectrometry-based analysis of the fission yeast proteome : the Schizosaccharomyces pombe Peptide Atlas. Molecular & cellular proteomics, 12 (6), 1741-51.

Stützer, Ina; Selevsek, Nathalie; Esterházy, Daria; Schmidt, Alexander; Aebersold, Ruedi; Stoffel, Markus (2013). Systematic proteomic analysis identifies beta-site amyloid precursor protein cleaving enzyme 2 and 1 (BACE2 and BACE1) substrates in pancreatic beta-cells. Journal of biological chemistry, 288 (15), 10536-47.

von Meyenn, Ferdinand; Porstmann, Thomas; Gasser, Emanuel; Selevsek, Nathalie; Schmidt, Alexander; Aebersold, Ruedi; Stoffel, Markus (2013). Glucagon-Induced Acetylation of Foxa2 Regulates Hepatic Lipid Metabolism. Cell metabolism, 17 (3), 436-47.

Picotti, Paola; Clément-Ziza, Mathieu; Lam, Henry; Campbell, David S; Schmidt, Alexander; Deutsch, Eric W; Röst, Hannes; Sun, Zhi; Rinner, Oliver; Reiter, Lukas; Shen, Qin; Michaelson, Jacob J; Frei, Andreas; Alberti, Simon; Kusebauch, Ulrike; Wollscheid, Bernd; Moritz, Robert L; Beyer, Andreas; Aebersold, Ruedi (2013). A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature, 494 (7436), 266-70.

Wong, Catherine C L; Cociorva, Daniel; Miller, Christine A; Schmidt, Alexander; Monell, Craig; Aebersold, Ruedi; Yates, John R (2013). Proteomics of Pyrococcus furiosus (Pfu) : Identification of Extracted Proteins by Three Independent Methods. Journal of Proteome Research, 12 (2), 763-70.

Kochanowski, Karl; Volkmer, Benjamin; Gerosa, Luca; Haverkorn van Rijsewijk, Bart R; Schmidt, Alexander; Heinemann, Matthias (2013). Functioning of a metabolic flux sensor in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 110 (3), 1130-5.


Marguerat, Samuel; Schmidt, Alexander; Codlin, Sandra; Chen, Wei; Aebersold, Ruedi; Bähler, Jürg (2012). Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell, 151 (3), 671-83.

Barat, Somedutta; Willer, Yvonne; Rizos, Konstantin; Claudi, Beatrice; Mazé, Alain; Schemmer, Anne K.; Kirchhoff, Dennis; Schmidt, Alexander; Burton, Neil; Bumann, Dirk (2012). Immunity to intracellular Salmonella depends on surface-associated antigens. PLoS Pathogens, 8 (10), e1002966.

Glatter, Timo; Ludwig, Christina; Ahrne, Erik; Aebersold, Ruedi; Heck, Albert J. R.; Schmidt, Alexander (2012). 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 (11), 5145-5156.

Nesper, J.; Reinders, A.; Glatter, T.; Schmidt, A.; Jenal, U. (2012). A novel capture compound for the identification and analysis of cyclic di-GMP binding proteins. Journal of Proteomics, 75 (15), 4874-4878.

Engel, Philipp; Goepfert, Arnaud; Stanger, Frédéric V.; Harms, Alexander; Schmidt, Alexander; Schirmer, Tilman; Dehio, Christoph (2012). Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Nature, 482 (7383), 107-10.

Danzer, Carsten; Eckhardt, Katrin; Schmidt, Alexander; Fankhauser, Niklaus; Ribrioux, Sebastien; Wollscheid, Bernd; Müller, Lukas; Schiess, Ralph; Züllig, Richard; Lehmann, Roger; Spinas, Giatgen; Aebersold, Rudolf; Krek, Wilhelm (2012). Comprehensive description of the N-glycoproteome of mouse pancreatic ?-cells and human islets. Journal of Proteome Research, 11 (3), 1598-608.

Ludwig, Christina; Claassen, Manfred; Schmidt, Alexander; Aebersold, Ruedi (2012). Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Molecular and Cellular Proteomics, 11 (3), M111.013987.


Glatter, Timo; Schittenhelm, Ralf B.; Rinner, Oliver; Roguska, Katarzyna; Wepf, Alexander; Juenger, Martin A.; Koehler, Katja; Jevtov, Irena; Choi, Hyungwon; Schmidt, Alexander; Nesvizhskii, Alexey I.; Stocker, Hugo; Hafen, Ernst; Aebersold, Ruedi; Gstaiger, Matthias (2011). Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology, 7, 547.

Beck, Martin; Schmidt, Alexander; Malmstroem, Johan; Claassen, Manfred; Ori, Alessandro; Szymborska, Anna; Herzog, Franz; Rinner, Oliver; Ellenberg, Jan; Aebersold, Ruedi (2011). The quantitative proteome of a human cell line. Molecular Systems Biology, 7, 549.

Esterházy, Daria; Stützer, Ina; Wang, Haiyan; Rechsteiner, Markus P.; Beauchamp, Jeremy; Döbeli, Heinz; Hilpert, Hans; Matile, Hugues; Prummer, Michael; Schmidt, Alexander; Lieske, Nora; Boehm, Bernhard; Marselli, Lorella; Bosco, Domenico; Kerr-Conte, Julie; Aebersold, Ruedi; Spinas, Giatgen Andreia; Moch, Holger; Migliorini, Cristiano; Stoffel, Markus (2011). Bace2 Is a Beta-Cell-Enriched Protease that Regulates Pancreatic Beta-Cell Function and Mass. Cell Metabolism, 14 (3), 365-77.

Higdon, Roger; Reiter, Lukas; Hather, Gregory; Haynes, Winston; Kolker, Natali; Stewart, Elizabeth; Bauman, Andrew T.; Picotti, Paola; Schmidt, Alexander; van Belle, Gerald; Aebersold, Ruedi; Kolker, Eugene (2011). IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics. Journal of Proteomics, 75 (1), 116-21.

Santamaria, Anna; Wang, Bin; Elowe, Sabine; Malik, Rainer; Zhang, Feng; Bauer, Manuel; Schmidt, Alexander; Silljé, Herman H W; Körner, Roman; Nigg, Erich A (2011). The Plk1-dependent phosphoproteome of the early mitotic spindle. Molecular & cellular proteomics, 10 (1), M110.004457.

Strübbe, Gero; Popp, Christian; Schmidt, Alexander; Pauli, Andrea; Ringrose, Leonie; Beisel, Christian; Paro, Renato (2011). Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proceedings of the National Academy of Sciences, 108 (14), 5572-7.

Schmidt, Alexander; Beck, Martin; Malmstroem, Johan; Lam, Henry; Claassen, Manfred; Campbell, David; Aebersold, Ruedi (2011). Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Molecular Systems Biology, 7, 510.

Maier, Tobias; Schmidt, Alexander; Güell, Marc; Kühner, Sebastian; Gavin, Anne-Claude; Aebersold, Ruedi; Serrano, Luis (2011). Quantification of mRNA and protein and integration with protein turnover in a bacterium. Molecular Systems Biology, 7, 511.


Bensimon, Ariel; Schmidt, Alexander; Ziv, Yael; Elkon, Ran; Wang, Shih-Ya; Chen, David J.; Aebersold, Ruedi; Shiloh, Yosef (2010). ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Science Signaling, 3 (151), rs3.

Hofmann, Andreas; Gerrits, Bertran; Schmidt, Alexander; Bock, Thomas; Bausch-Fluck, Damaris; Aebersold, Rudolf; Wollscheid, Bernd (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116 (13), e26-34.


Schmidt, Alexander; Bisle, Birgit; Kislinger, Thomas (2009). Quantitative peptide and protein profiling by mass spectrometry. Methods in Molecular Biology, 492, 21-38.

Wepf, Alexander; Glatter, Timo; Schmidt, Alexander; Aebersold, Ruedi; Gstaiger, Matthias (2009). Quantitative interaction proteomics using mass spectrometry. Nature Methods, 6 (3), 203-5.

Malmström, Johan; Beck, Martin; Schmidt, Alexander; Lange, Vinzenz; Deutsch, Eric W.; Aebersold, Ruedi (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature, 460 (7256), 762-5.

Leidel, Sebastian; Pedrioli, Patrick G. A.; Bucher, Tamara; Brost, Renée; Costanzo, Michael; Schmidt, Alexander; Aebersold, Ruedi; Boone, Charles; Hofmann, Kay; Peter, Matthias (2009). Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature, 458 (7235), 228-32.

Reiter, Lukas; Claassen, Manfred; Schrimpf, Sabine P.; Jovanovic, Marko; Schmidt, Alexander; Buhmann, Joachim M.; Hengartner, Michael O.; Aebersold, Ruedi (2009). Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular and Cellular Proteomics, 8 (11), 2405-17.

Schmidt, Alexander; Claassen, Manfred; Aebersold, Ruedi (2009). Directed mass spectrometry: towards hypothesis-driven proteomics. Current Opinion in Chemical Biology, 13 (5-6), 510-7.

Schiess, Ralph; Mueller, Lukas N.; Schmidt, Alexander; Mueller, Markus; Wollscheid, Bernd; Aebersold, Ruedi (2009). Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Molecular and Cellular Proteomics, 8 (4), 624-38.

Beck, Martin; Malmström, Johan A.; Lange, Vinzenz; Schmidt, Alexander; Deutsch, Eric W.; Aebersold, Ruedi (2009). Visual proteomics of the human pathogen Leptospira interrogans. Nature Methods, 6 (11), 817-23.

Kühner, Sebastian; van Noort, Vera; Betts, Matthew J.; Leo-Macias, Alejandra; Batisse, Claire; Rode, Michaela; Yamada, Takuji; Maier, Tobias; Bader, Samuel; Beltran-Alvarez, Pedro; Castaño-Diez, Daniel; Chen, Wei-Hua; Devos, Damien; Güell, Marc; Norambuena, Tomas; Racke, Ines; Rybin, Vladimir; Schmidt, Alexander; Yus, Eva; Aebersold, Ruedi; Herrmann, Richard; Böttcher, Bettina; Frangakis, Achilleas S.; Russell, Robert B.; Serrano, Luis; Bork, Peer; Gavin, Anne-Claude (2009). Proteome organization in a genome-reduced bacterium. Science, 326 (5957), 1235-40.

Tebbe, Andreas; Schmidt, Alexander; Konstantinidis, Kosta; Falb, Michaela; Bisle, Birgit; Klein, Christian; Aivaliotis, Michalis; Kellermann, Josef; Siedler, Frank; Pfeiffer, Friedhelm; Lottspeich, Friedrich; Oesterhelt, Dieter (2009). Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics, 9 (15), 3843-55.


Meltretter, Jasmin; Schmidt, Alexander; Humeny, Andreas; Becker, Cord-Michael; Pischetsrieder, Monika (2008). Analysis of the peptide profile of milk and its changes during thermal treatment and storage. Journal of Agricultural and Food Chemistry, 56 (9), 2899-906.

Rinner, Oliver; Seebacher, Jan; Walzthoeni, Thomas; Mueller, Lukas N; Beck, Martin; Schmidt, Alexander; Mueller, Markus; Aebersold, Ruedi (2008). Identification of cross-linked peptides from large sequence databases. Nature methods, 5 (4), 315-8.

Schmidt, Alexander; Gehlenborg, Nils; Bodenmiller, Bernd; Mueller, Lukas N.; Campbell, Dave; Mueller, Markus; Aebersold, Ruedi; Domon, Bruno (2008). An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Molecular and Cellular Proteomics, 7 (11), 2138-2150.

Klimek, John; Eddes, James S.; Hohmann, Laura; Jackson, Jennifer; Peterson, Amelia; Letarte, Simon; Gafken, Philip R.; Katz, Jonathan E.; Mallick, Parag; Lee, Hookeun; Schmidt, Alexander; Ossola, Reto; Eng, Jimmy K.; Aebersold, Ruedi; Martin, Daniel B. (2008). 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 (1), 96-103.

Letarte, Simon; Brusniak, Mi-Youn; Campbell, David; Eddes, James; Kemp, Christopher J.; Lau, Hollis; Mueller, Lukas; Schmidt, Alexander; Shannon, Paul; Kelly-Spratt, Karen S.; Vitek, Olga; Zhang, Hui; Aebersold, Ruedi; Watts, Julian D. (2008). Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clinical Proteomics, 4 (3-4), 105.


Mueller, Lukas N.; Rinner, Oliver; Schmidt, Alexander; Letarte, Simon; Bodenmiller, Bernd; Brusniak, Mi-Youn; Vitek, Olga; Aebersold, Ruedi; Müller, Markus (2007). SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics, 7 (19), 3470-80.

Djouder, Nabil; Christian Metzler, Stefan; Schmidt, Alexander; Wirbelauer, Christiane; Gstaiger, Matthias; Aebersold, Ruedi; Hess, Daniel; Krek, Wilhelm (2007). S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling. Molecular Cell, 28 (1), 28-40.

Bodenmiller, Bernd; Malmstrom, Johan; Gerrits, Bertran; Campbell, David; Lam, Henry; Schmidt, Alexander; Rinner, Oliver; N. Mueller, Lukas; T. Shannon, Paul; G. Pedrioli, Patrick; Panse, Christian; Lee, Hoo-Keun; Schlapbach, Ralph; Aebersold, Ruedi (2007). PhosphoPep-a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology, 3 (1), 139.


Bisle, Birgit; Schmidt, Alexander; Scheibe, Burghardt; Klein, Christian; Tebbe, Andreas; Kellermann, Joseph; Siedler, Frank; Pfeiffer, Friedhelm; Lottspeich, Friedrich; Oesterhelt, Dieter (2006). Quantitative profiling of the membrane proteome in a halophilic archaeon. Molecular and Cellular Proteomics, 5 (9), 1543-58.

Schmidt, Alexander; Aebersold, Ruedi (2006). High-accuracy proteome maps of human body fluids. Genome Biology, 7 (11), 242.

Sarioglu, Hakan; Brandner, Stefanie; Jacobsen, Carola; Meindl, Thomas; Schmidt, Alexander; Kellermann, Josef; Lottspeich, Friedrich; Andrae, Ulrich (2006). Quantitative analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels. Proteomics, 6 (8), 2407-2421.


Schmidt, Alexander; Kellermann, Josef; Lottspeich, Friedrich (2005). A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics, 5 (1), 4-15.

Hochleitner, Elisabeth O.; Kastner, Berthold; Fröhlich, Thomas; Schmidt, Alexander; Lührmann, Reinhard; Arnold, Georg; Lottspeich, Friedrich (2005). Protein stoichiometry of a multiprotein complex, the human spliceosomal U1 small nuclear ribonucleoprotein: absolute quantification using isotope-coded tags and mass spectrometry. Journal of Biological Chemistry, 280 (4), 2536-42.

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