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Hübers, Corinne and Abdul Pari, Ashik Ahmed and Grieshober, Denise and Petkov, Martin and Schmidt, Alexander and Messmer, Tatjana and Heyer, Christian Moritz and Schölch, Sebastian and Kapel, Stephanie S. and Gengenbacher, Nicolas and Singhal, Mahak and Schieb, Benjamin and Fricke, Claudine and Will, Rainer and Remans, Kim and Utikal, Jochen Sven and Reissfelder, Christoph and Schlesner, Matthias and Hodivala-Dilke, Kairbaan M. and Kersten, Sander and Goerdt, Sergij and Augustin, Hellmut G. and Felcht, Moritz. (2023) Primary tumor-derived systemic nANGPTL4 inhibits metastasis. Journal of Experimental Medicine, 220 (1). pp. 1-18.

Lambert, Elisabeth and Mehdipour, Ahmad Reza and Schmidt, Alex and Hummer, Gerhard and Perez, Camilo. (2022) Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications, 13. 1022 .

Ghosh, Souvik and Ataman, Meric and Bak, Maciej and Börsch, Anastasiya and Schmidt, Alexander and Buczak, Katarzyna and Martin, Georges and Dimitriades, Beatrice and Herrmann, Christina J. and Kanitz, Alexander and Zavolan, Mihaela. (2022) CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Research, 50 (6). pp. 3096-3114.

Hauser, David and Behr, Katharina and Konno, Kohtarou and Schreiner, Dietmar and Schmidt, Alexander and Watanabe, Masahiko and Bischofberger, Josef and Scheiffele, Peter. (2022) Targeted proteoform mapping uncovers specific Neurexin-3 variants required for dendritic inhibition. Neuron, 110 (13). pp. 2094-2109.

Ng, Charlotte K. Y. and Dazert, Eva and Boldanova, Tuyana and Coto-Llerena, Mairene and Nuciforo, Sandro and Ercan, Caner and Suslov, Aleksei and Meier, Marie-Anne and Bock, Thomas and Schmidt, Alexander and Ketterer, Sylvia and Wang, Xueya and Wieland, Stefan and Matter, Matthias S. and Colombi, Marco and Piscuoglio, Salvatore and Terracciano, Luigi M. and Hall, Michael N. and Heim, Markus H.. (2022) Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. Nature Communications, 13. p. 2436.

Adaixo, Ricardo and Steiner, Eva M. and Righetto, Ricardo D. and Schmidt, Alexander and Stahlberg, Henning and Taylor, Nicholas M. I.. (2022) Cryo-EM structure of native human thyroglobulin. Nature communications, 13 (1). p. 61.

Fröhlich, Klemens and Brombacher, Eva and Fahrner, Matthias and Vogele, Daniel and Kook, Lucas and Pinter, Niko and Bronsert, Peter and Timme-Bronsert, Sylvia and Schmidt, Alexander and Bärenfaller, Katja and Kreutz, Clemens and Schilling, Oliver. (2022) Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nature Communications, 13 (1). p. 2622.

Varela, Minia Antelo and Schmidt, Alexander. (2022) The Emerging Potential of Advanced Targeted Mass Spectrometry to Become a Routine Tool for Protein Quantification in Biomedical Research. Chimia, 76 (1-2). pp. 81-89.

Mele, Valentina and Basso, Camilla and Governa, Valeria and Glaus Garzon, Jesus F. and Muraro, Manuele G. and Däster, Silvio and Nebiker, Christian A. and Mechera, Robert and Bolli, Martin and Schmidt, Alexander and Geiger, Roger and Spagnoli, Giulio C. and Christoforidis, Dimitri and Majno, Pietro E. and Borsig, Lubor and Iezzi, Giandomenica. (2022) Identification of TPM2 and CNN1 as Novel Prognostic Markers in Functionally Characterized Human Colon Cancer-Associated Stromal Cells. Cancers, 14 (8). pp. 1-12.

Litsios, Athanasios and Goswami, Pooja and Terpstra, Hanna M. and Coffin, Carleton and Vuillemenot, Luc-Alban and Rovetta, Mattia and Ghazal, Ghada and Guerra, Paolo and Buczak, Katarzyna and Schmidt, Alexander and Tollis, Sylvain and Tyers, Mike and Royer, Catherine A. and Milias-Argeitis, Andreas and Heinemann, Matthias. (2022) The timing of Start is determined primarily by increased synthesis of the Cln3 activator rather than dilution of the Whi5 inhibitor. Molecular Biology of the Cell, 33 (5). rp2.

Pérez-Schindler, Joaquín and Kohl, Bastian and Schneider-Heieck, Konstantin and Leuchtmann, Aurel B. and Henríquez-Olguín, Carlos and Adak, Volkan and Maier, Geraldine and Delezie, Julien and Sakoparnig, Thomas and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Hondele, Maria and Jensen, Thomas E. and Hiller, Sebastian and Handschin, Christoph. (2021) RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates. Proceedings of the National Academy of Sciences of the United States of America, 118 (36). e2105951118.

Striednig, Bianca and Lanner, Ulrike and Niggli, Selina and Katic, Ana and Vormittag, Simone and Brülisauer, Sabrina and Hochstrasser, Ramon and Kaech, Andres and Welin, Amanda and Flieger, Antje and Ziegler, Urs and Schmidt, Alexander and Hilbi, Hubert and Personnic, Nicolas. (2021) Quorum sensing governs a transmissive Legionella subpopulation at the pathogen vacuole periphery. EMBO reports, 22 (9). e52972.

Mori, Matteo and Zhang, Zhongge and Banaei-Esfahani, Amir and Lalanne, Jean-Benoît and Okano, Hiroyuki and Collins, Ben C. and Schmidt, Alexander and Schubert, Olga T. and Lee, Deok-Sun and Li, Gene-Wei and Aebersold, Ruedi and Hwa, Terence and Ludwig, Christina. (2021) From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Molecular systems biology, 17 (5). e9536.

Burigotto, Matteo and Mattivi, Alessia and Migliorati, Daniele and Magnani, Giovanni and Valentini, Chiara and Roccuzzo, Michela and Offterdinger, Martin and Pizzato, Massimo and Schmidt, Alexander and Villunger, Andreas and Maffini, Stefano and Fava, Luca L.. (2021) Centriolar distal appendages activate the centrosome-PIDDosome-p53 signalling axis via ANKRD26. The EMBO journal, 40 (4). e104844.

Correia, Ana Luísa and Guimaraes, Joao C. and Auf der Maur, Priska and De Silva, Duvini and Trefny, Marcel P. and Okamoto, Ryoko and Bruno, Sandro and Schmidt, Alexander and Mertz, Kirsten and Volkmann, Katrin and Terracciano, Luigi and Zippelius, Alfred and Vetter, Marcus and Kurzeder, Christian and Weber, Walter Paul and Bentires-Alj, Mohamed. (2021) Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy. Nature, 594 (7864). pp. 566-571.

Donato, Cinzia and Buczak, Katarzyna and Schmidt, Alexander and Aceto, Nicola. (2021) Mass spectrometry analysis of circulating breast cancer cells from a Xenograft mouse model. STAR Protocols, 2 (2). p. 100480.

Ham, Alexander S. and Chojnowska, Kathrin and Tintignac, Lionel A. and Lin, Shuo and Schmidt, Alexander and Ham, Daniel J. and Sinnreich, Michael and Rüegg, Markus A.. (2020) mTORC1 signalling is not essential for the maintenance of muscle mass and function in adult sedentary mice. Journal of Cachexia, Sarcopenia and Muscle, 11 (1). pp. 259-273.

Burmann, Björn M. and Gerez, Juan A. and Matečko-Burmann, Irena and Campioni, Silvia and Kumari, Pratibha and Ghosh, Dhiman and Mazur, Adam and Aspholm, Emelie E. and Šulskis, Darius and Wawrzyniuk, Magdalena and Bock, Thomas and Schmidt, Alexander and Rüdiger, Stefan G. D. and Riek, Roland and Hiller, Sebastian. (2020) Regulation of α-synuclein by chaperones in mammalian cells. Nature, 577. pp. 127-132.

Fabrice, Tohnyui Ndinyanka and Fiedler, Thomas and Studer, Vera and Vinet, Adrien and Brogna, Francesco and Schmidt, Alexander and Pieters, Jean. (2020) Interactome and F-Actin Interaction Analysis of Dictyostelium discoideum Coronin A. International journal of molecular sciences, 21 (4). p. 1469.

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

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

Kohl, Bastian and Brüderlin, Mitchell and Ritz, Danilo and Schmidt, Alexander and Hiller, Sebastian. (2020) Protocol for High-Yield Production of Photo-Leucine-Labeled Proteins in Escherichia coli. Journal of Proteome Research, 19 (8). pp. 3100-3108.

Schmidt, Alexander and Farine, Hervé and Keller, Marcel P. and Sebastian, Agata and Kozera, Lukasz and Welford, Richard W. D. and Strasser, Daniel S.. (2020) Immunoaffinity Targeted Mass Spectrometry Analysis of Human Plasma Samples Reveals an Imbalance of Active and Inactive CXCL10 in Primary Sjögren's Syndrome Disease Patients. Journal of proteome research, 19 (10). pp. 4196-4209.

Prautsch, Katharina M. and Schmidt, Alexander and Paradiso, Viola and Schaefer, Dirk J. and Guzman, Raphael and Kalbermatten, Daniel F. and Madduri, Srinivas. (2020) Modulation of Human Adipose Stem Cells' Neurotrophic Capacity Using a Variety of Growth Factors for Neural Tissue Engineering Applications: Axonal Growth, Transcriptional, and Phosphoproteomic Analyses In Vitro. Cells, 9 (9). pp. 1-21.

Opitz, Christian and Ahrné, Erik and Goldie, Kenneth N. and Schmidt, Alexander and Grzesiek, Stephan. (2019) Deuterium induces a distinctive Escherichia coli proteome that correlates with the reduction in growth rate. Journal of Biological Chemistry, 294 (7). pp. 2279-2292.

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

Lin, Lin and Lezan, Emmanuelle and Schmidt, Alexander and Basler, Marek. (2019) Abundance of bacterial Type VI secretion system components measured by targeted proteomics. Nature Communications, 10 (1). p. 2584.

Jourdan, Joëlle and Walz, Annabelle and Matile, Hugues and Schmidt, Alexander and Wu, Jianbo and Wang, Xiaofang and Dong, Yuxiang and Vennerstrom, Jonathan L. and Schmidt, Remo S. and Wittlin, Sergio and Mäser, Pascal. (2019) Stochastic protein alkylation by antimalarial peroxides. ACS Infectious Diseases, 5 (12). pp. 2067-2075.

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

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

Litsios, Athanasios and Huberts, Daphne H. E. W. and Terpstra, Hanna M. and Guerra, Paolo and Schmidt, Alexander and Buczak, Katarzyna and Papagiannakis, Alexandros and Rovetta, Mattia and Hekelaar, Johan and Hubmann, Georg and Exterkate, Marten and Milias-Argeitis, Andreas and 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). pp. 1382-1392.

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

Arquint, Christian and Cubizolles, Fabien and Morand, Agathe and Schmidt, Alexander and 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). p. 16.

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

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

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

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

Gasser, Véronique and Baco, Etienne and Cunrath, Olivier and Saint August, Pamela and Perraud, Quentin and Zill, Nicolas and Schleberger, Christian and Schmidt, Alexander and Paulen, Aurélie and Bumann, Dirk and Mislin, Gaëtan L. A. and 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). pp. 819-832.

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

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

Ahrné, Erik and Glatter, Timo and Viganò, Cristina and Schubert, Conrad von and Nigg, Erich A. and Schmidt, Alexander. (2016) Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments. Journal of Proteome Research, 15 (8). pp. 2537-2547.

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

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

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

Ittig, Simon Josef and Schmutz, Christoph and Kasper, Christoph Alexander and Amstutz, Marlise and Schmidt, Alexander and Sauteur, Loïc and Vigano, M. Alessandra and Low, Shyan Huey and Affolter, Markus and Cornelis, Guy R. and Nigg, Erich A. and Arrieumerlou, Cécile. (2015) A bacterial type III secretion-based protein delivery tool for broad applications in cell biology. The Journal of cell biology, 211 (4). pp. 913-931.

Glatter, Timo and Ahrné, Erik and 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). pp. 4472-4485.

Ahrné, Erik and Martinez-Segura, Amalia and Syed, Afzal Pasha and Vina-Vilaseca, Arnau and Gruber, Andreas J. and Marguerat, Samuel and Schmidt, Alexander. (2015) Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry. Methods, 85. pp. 100-107.

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

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

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

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

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

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

Bauer, Manuel and Ahrné, Erik and Baron, Anna P. and Glatter, Timo and Fava, Luca L. and Santamaria, Anna and Nigg, Erich A. and Schmidt, Alexander. (2014) Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites. Journal of proteome research, Vol. 13, H. 12. pp. 5973-5988.

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

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

Gruber, Andreas R. and Martin, Georges and Müller, Philipp and Schmidt, Alexander and Gruber, Andreas J. and Gumienny, Rafal and Mittal, Nitish and Jayachandran, Rajesh and Pieters, Jean and Keller, Walter and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature Communications, 5 (5465). pp. 1-10.

von Meyenn, Ferdinand and Porstmann, Thomas and Gasser, Emanuel and Selevsek, Nathalie and Schmidt, Alexander and Aebersold, Ruedi and Stoffel, Markus. (2013) Glucagon-Induced Acetylation of Foxa2 Regulates Hepatic Lipid Metabolism. Cell metabolism, Vol. 17, H. 3. pp. 436-447.

Picotti, Paola and Clément-Ziza, Mathieu and Lam, Henry and Campbell, David S. and Schmidt, Alexander and Deutsch, Eric W. and Röst, Hannes and Sun, Zhi and Rinner, Oliver and Reiter, Lukas and Shen, Qin and Michaelson, Jacob J. and Frei, Andreas and Alberti, Simon and Kusebauch, Ulrike and Wollscheid, Bernd and Moritz, Robert L. and Beyer, Andreas and Aebersold, Ruedi. (2013) A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature, Vol. 494, H. 7436. pp. 266-270.

Wong, Catherine C. L. and Cociorva, Daniel and Miller, Christine A. and Schmidt, Alexander and Monell, Craig and Aebersold, Ruedi and Yates, John R.. (2013) Proteomics of Pyrococcus furiosus (Pfu) : Identification of Extracted Proteins by Three Independent Methods. Journal of Proteome Research, Vol. 12, H. 2. pp. 763-770.

Kochanowski, Karl and Volkmer, Benjamin and Gerosa, Luca and Haverkorn van Rijsewijk, Bart R. and Schmidt, Alexander and 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, Vol. 110, H. 3. pp. 1130-1135.

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

Stützer, Ina and Selevsek, Nathalie and Esterhazy, Daria and Schmidt, Alexander and Aebersold, Ruedi and 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, Vol. 288, H. 15. pp. 10536-10547.

Schmutz, Christoph and Ahrne, Erik Lennart and Kasper, Christoph Alexander and Tschon, Therese and Sorg, Isabel and Dreier, Roland Felix and Schmidt, Alexander and Arrieumerlou, Cecile. (2013) Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Molecular & cellular proteomics, Vol. 12, H. 10. pp. 2952-2968.

Lehtinen, Sonja and Marsellach, Francesc Xavier and Codlin, Sandra and Schmidt, Alexander and Clément-Ziza, Mathieu and Beyer, Andreas and Bähler, Jürg and Orengo, Christine and Pancaldi, Vera. (2013) Stress induces remodelling of yeast interaction and co-expression networks. Molecular biosystems, Vol. 9, H. 7. pp. 1697-1707.

Gunaratne, Jayantha and Schmidt, Alexander and Quandt, Andreas and Neo, Suat Peng and Saraç, Omer Sinan and Gracia, Tannia and Loguercio, Salvatore and Ahrné, Erik and Xia, Rachel Li Hai and Tan, Keng Hwa and Lössner, Christopher and Bähler, Jürg and Beyer, Andreas and Blackstock, Walter and Aebersold, Ruedi. (2013) Extensive mass spectrometry-based analysis of the fission yeast proteome : the Schizosaccharomyces pombe Peptide Atlas. Molecular & cellular proteomics, Vol. 12, H. 6. pp. 1741-1751.

Ahrné, Erik and Molzahn, Lars and Glatter, Timo and Schmidt, Alexander. (2013) Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics, Vol. 13, H. 17. pp. 2567-2578.

Québatte, Maxime and Dick, Mathias S. and Kaever, Volkhard and Schmidt, Alexander and 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 (4). pp. 756-775.

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

Engel, Philipp and Goepfert, Arnaud and Stanger, Frédéric V. and Harms, Alexander and Schmidt, Alexander and Schirmer, Tilman and Dehio, Christoph. (2012) Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Nature, 482 (7383). pp. 107-110.

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

Glatter, Timo and Ludwig, Christina and Ahrné, Erik and Aebersold, Ruedi and Heck, Albert J. R. and 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, Vol. 11, H. 11. pp. 5145-5156.

Marguerat, Samuel and Schmidt, Alexander and Codlin, Sandra and Chen, Wei and Aebersold, Ruedi and Bähler, Jürg. (2012) Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell, Vol. 151, H. 3. pp. 671-683.

Danzer, Carsten and Eckhardt, Katrin and Schmidt, Alexander and Fankhauser, Niklaus and Ribrioux, Sebastien and Wollscheid, Bernd and Müller, Lukas and Schiess, Ralph and Züllig, Richard and Lehmann, Roger and Spinas, Giatgen and Aebersold, Rudolf and Krek, Wilhelm. (2012) Comprehensive description of the N-glycoproteome of mouse pancreatic ?-cells and human islets. Journal of Proteome Research, 11 (3). pp. 1598-1608.

Ludwig, Christina and Claassen, Manfred and Schmidt, Alexander and 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.

Santamaria, A. and Wang, B. and Elowe, S. and Malik, R. and Zhang, F. and Bauer, M. and Schmidt, A. and Sillje, H. H. and Koerner, R. and Nigg, E. A.. (2011) The Plk1-dependent phosphoproteome of the early mitotic spindle. Molecular & cellular proteomics, Vol. 10, H. 1 , M110.004457.

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

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

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

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

Strübbe, Gero and Popp, Christian and Schmidt, Alexander and Pauli, Andrea and Ringrose, Leonie and Beisel, Christian and 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). pp. 5572-5577.

Esterházy, Daria and Stützer, Ina and Wang, Haiyan and Rechsteiner, Markus P. and Beauchamp, Jeremy and Döbeli, Heinz and Hilpert, Hans and Matile, Hugues and Prummer, Michael and Schmidt, Alexander and Lieske, Nora and Boehm, Bernhard and Marselli, Lorella and Bosco, Domenico and Kerr-Conte, Julie and Aebersold, Ruedi and Spinas, Giatgen Andreia and Moch, Holger and Migliorini, Cristiano and Stoffel, Markus. (2011) Bace2 Is a Beta-Cell-Enriched Protease that Regulates Pancreatic Beta-Cell Function and Mass. Cell Metabolism, 14 (3). pp. 365-377.

Higdon, Roger and Reiter, Lukas and Hather, Gregory and Haynes, Winston and Kolker, Natali and Stewart, Elizabeth and Bauman, Andrew T. and Picotti, Paola and Schmidt, Alexander and van Belle, Gerald and Aebersold, Ruedi and Kolker, Eugene. (2011) IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics. Journal of Proteomics , 75 (1). pp. 116-121.

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

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

Tebbe, Andreas and Schmidt, Alexander and Konstantinidis, Kosta and Falb, Michaela and Bisle, Birgit and Klein, Christian and Aivaliotis, Michalis and Kellermann, Josef and Siedler, Frank and Pfeiffer, Friedhelm and Lottspeich, Friedrich and Oesterhelt, Dieter . (2009) Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics, 9 (15). pp. 3843-3855.

Kühner, Sebastian and van Noort, Vera and Betts, Matthew J. and Leo-Macias, Alejandra and Batisse, Claire and Rode, Michaela and Yamada, Takuji and Maier, Tobias and Bader, Samuel and Beltran-Alvarez, Pedro and Castaño-Diez, Daniel and Chen, Wei-Hua and Devos, Damien and Güell, Marc and Norambuena, Tomas and Racke, Ines and Rybin, Vladimir and Schmidt, Alexander and Yus, Eva and Aebersold, Ruedi and Herrmann, Richard and Böttcher, Bettina and Frangakis, Achilleas S. and Russell, Robert B. and Serrano, Luis and Bork, Peer and Gavin, Anne-Claude. (2009) Proteome organization in a genome-reduced bacterium. Science, 326 (5957). pp. 1235-1240.

Beck, Martin and Malmström, Johan A. and Lange, Vinzenz and Schmidt, Alexander and Deutsch, Eric W. and Aebersold, Ruedi . (2009) Visual proteomics of the human pathogen Leptospira interrogans. Nature Methods, 6 (11). pp. 817-823.

Schiess, Ralph and Mueller, Lukas N. and Schmidt, Alexander and Mueller, Markus and Wollscheid, Bernd and Aebersold, Ruedi . (2009) Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Molecular and Cellular Proteomics, 8 (4). pp. 624-638.

Schmidt, Alexander and Claassen, Manfred and Aebersold, Ruedi. (2009) Directed mass spectrometry: towards hypothesis-driven proteomics. Current Opinion in Chemical Biology, 13 (5-6). pp. 510-517.

Reiter, Lukas and Claassen, Manfred and Schrimpf, Sabine P. and Jovanovic, Marko and Schmidt, Alexander and Buhmann, Joachim M. and Hengartner, Michael O. and 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). pp. 2405-2417.

Leidel, Sebastian and Pedrioli, Patrick G. A. and Bucher, Tamara and Brost, Renée and Costanzo, Michael and Schmidt, Alexander and Aebersold, Ruedi and Boone, Charles and Hofmann, Kay and Peter, Matthias . (2009) Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature, 458 (7235). pp. 228-232.

Malmström, Johan and Beck, Martin and Schmidt, Alexander and Lange, Vinzenz and Deutsch, Eric W. and Aebersold, Ruedi . (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature, 460 (7256). pp. 762-765.

Wepf, Alexander and Glatter, Timo and Schmidt, Alexander and Aebersold, Ruedi and Gstaiger, Matthias . (2009) Quantitative interaction proteomics using mass spectrometry. Nature Methods, 6 (3). pp. 203-205.

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

Letarte, Simon and Brusniak, Mi-Youn and Campbell, David and Eddes, James and Kemp, Christopher J. and Lau, Hollis and Mueller, Lukas and Schmidt, Alexander and Shannon, Paul and Kelly-Spratt, Karen S. and Vitek, Olga and Zhang, Hui and Aebersold, Ruedi and 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). p. 105.

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

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

Rinner, Oliver and Seebacher, Jan and Walzthoeni, Thomas and Mueller, Lukas N. and Beck, Martin and Schmidt, Alexander and Mueller, Markus and Aebersold, Ruedi. (2008) Identification of cross-linked peptides from large sequence databases. Nature methods, 5 (4). pp. 315-318.

Meltretter, Jasmin and Schmidt, Alexander and Humeny, Andreas and Becker, Cord-Michael and 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). pp. 2899-2906.

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

Djouder, Nabil and Christian Metzler, Stefan and Schmidt, Alexander and Wirbelauer, Christiane and Gstaiger, Matthias and Aebersold, Ruedi and Hess, Daniel and 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). pp. 28-40.

Mueller, Lukas N. and Rinner, Oliver and Schmidt, Alexander and Letarte, Simon and Bodenmiller, Bernd and Brusniak, Mi-Youn and Vitek, Olga and Aebersold, Ruedi and Müller, Markus . (2007) SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics, 7 (19). pp. 3470-3480.

Sarioglu, Hakan and Brandner, Stefanie and Jacobsen, Carola and Meindl, Thomas and Schmidt, Alexander and Kellermann, Josef and Lottspeich, Friedrich and 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). pp. 2407-2421.

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

Bisle, Birgit and Schmidt, Alexander and Scheibe, Burghardt and Klein, Christian and Tebbe, Andreas and Kellermann, Joseph and Siedler, Frank and Pfeiffer, Friedhelm and Lottspeich, Friedrich and Oesterhelt, Dieter . (2006) Quantitative profiling of the membrane proteome in a halophilic archaeon. Molecular and Cellular Proteomics, 5 (9). pp. 1543-1558.

Hochleitner, Elisabeth O. and Kastner, Berthold and Fröhlich, Thomas and Schmidt, Alexander and Lührmann, Reinhard and Arnold, Georg and 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). pp. 2536-2542.

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

Book Section

Manfredi, Pablo and Santi, Isabella and Maffei, Enea and Lezan, Emmanuelle and Schmidt, Alexander and Jenal, Urs. (2021) Defining Proteomic Signatures to Predict Multidrug Persistence in Pseudomonas aeruginosa. In: Bacterial Persistence: Methods and Protocols. New York, NY, pp. 161-175.

Preprint

Eckhardt, Jan and Ruiz, Alexis and Koenig, Stéphane and Frieden, Maiud and Schmidt, Alexander and Treves, Susan and Zorzato, Francesco. (2022) Quantitative proteomic analysis of skeletal muscles from wild type and transgenic mice carrying recessive Ryr1 mutations linked to congenital myopathies. bioRxiv.