Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs by Clough Timothy, Thaminy Safia, Ragg Susanne, Aebersold Ruedi, Vitek Olga

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The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation by King Nichole L, Brunner Erich, Loevenich Sandra N, Deutsch Eric W, Stein Stephen E, Aebersold Ruedi, Hafen Ernst

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M. tuberculosis relies on trace oxygen to maintain energy homeostasis and survive in hypoxic environments by Kalia, Nitin Pal, Singh, Samsher, Hards, Kiel, Cheung, Chen-Yi, Sviriaeva, Ekaterina, Banaei-Esfahani, Amir, Aebersold, Ruedi, Berney, Michael, Cook, Gregory M., Pethe, Kevin

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ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry by Ramos Hector, Kusebauch Ulrike, Picotti Paola, Reiter Lukas, Campbell David, Christiansen Mark, Kwok Sung-Tat, Brusniak Mi-Youn K, Deutsch Eric W, Chen Jingchun, Moritz Robert L, Aebersold Ruedi

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openBIS: a flexible framework for managing and analyzing complex data in biology research by Bauch Angela, Adamczyk Izabela, Buczek Piotr, Elmer Franz-Josef, Enimanev Kaloyan, Glyzewski Pawel, Kohler Manuel, Pylak Tomasz, Quandt Andreas, Ramakrishnan Chandrasekhar, Beisel Christian, Malmström Lars, Aebersold Ruedi, Rinn Bernd

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Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics by Mueller Lukas N, Letarte Simon, Lau Hollis, Garbutt Andrew, Eddes James, Cooke Kelly, Campbell David, Bodenmiller Bernd, Brusniak Mi-Youn, Sharma Vagisha, Vitek Olga, Zhang Ning, Aebersold Ruedi, Watts Julian D

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From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions by Mori, Matteo, Zhang, Zhongge, Banaei‐Esfahani, Amir, Lalanne, Jean‐Benoît, Okano, Hiroyuki, Collins, Ben C, Schmidt, Alexander, Schubert, Olga T, Lee, Deok‐Sun, Li, Gene‐Wei, Aebersold, Ruedi, Hwa, Terence, Ludwig, Christina

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Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition by Lambert, Jean-Philippe, Ivosev, Gordana, Couzens, Amber L, Larsen, Brett, Taipale, Mikko, Lin, Zhen-Yuan, Zhong, Quan, Lindquist, Susan, Vidal, Marc, Aebersold, Ruedi, Pawson, Tony, Bonner, Ron, Tate, Stephen, Gingras, Anne-Claude

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Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome by Jevtov, Irena, Glatter, Timo, Schittenhelm, Ralf B., Rinner, Oliver, Roguska, Katarzyna, Wepf, Alexander, Junger, Martin A., Kohler, Katja, Choi, Hyungwon, Schmidt, Alexander, Nesvizhskii, Alexey I., Stocker, Hugo, Hafen, Ernst, Aebersold, Ruedi, Gstaiger, Matthias

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A mouse plasma peptide atlas as a resource for disease proteomics by Zhang, Qing, Menon, Rajasree, Wang, Hong, Bardeesy, Nabeel, Dinulescu, Daniela M., Kucherlapati, Raju, Politi, Katerina, Aebersold, Ruedi, Deutsch, Eric W., Pitteri, Sharon J., Faca, Vitor M., Newcomb, Lisa F., DePinho, Ronald A., Hung, Kenneth E., Omenn, Gilbert S., States, David J., Hanash, Samir M., Jacks, Tyler E

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How many human proteoforms are there? by Aebersold, Ruedi, Agar, Jeffrey N, Amster, I Jonathan, Baker, Mark S, Bertozzi, Carolyn R, Boja, Emily S, Costello, Catherine E, Cravatt, Benjamin F, Fenselau, Catherine, Garcia, Benjamin A, Ge, Ying, Gunawardena, Jeremy, Hendrickson, Ronald C, Hergenrother, Paul J, Huber, Christian G, Ivanov, Alexander R, Jensen, Ole N, Jewett, Michael C, Kelleher, Neil L, Krogan, Nevan J, Larsen, Martin R, Loo, Joseph A, Ogorzalek Loo, Rachel R, Lundberg, Emma, MacCoss, Michael J, Mallick, Parag, Mootha, Vamsi K, Mrksich, Milan, Muir, Tom W, Patrie, Steven M, Pesavento, James J, Pitteri, Sharon J, Rodriguez, Henry, Saghatelian, Alan, Sandoval, Wendy, Schlüter, Hartmut, Sechi, Salvatore, Slavoff, Sarah A, Smith, Lloyd M, Snyder, Michael P, Thomas, Paul M, Uhlén, Mathias, Van Eyk, Jennifer E, Vidal, Marc, Walt, David R, White, Forest M, Williams, Evan R, Wohlschlager, Therese, Wysocki, Vicki H, Yates, Nathan A, Young, Nicolas L, Zhang, Bing, Kiessling, Laura L

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