A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis von Rudolph, Jan Daniel, Cox, Jürgen

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The Perseus computational platform for comprehensive analysis of (prote)omics data von Tyanova, Stefka, Temu, Tikira, Sinitcyn, Pavel, Carlson, Arthur, Hein, Marco Y, Geiger, Tamar, Mann, Matthias, Cox, Jürgen

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Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ von Cox, Jürgen, Hein, Marco Y., Luber, Christian A., Paron, Igor, Nagaraj, Nagarjuna, Mann, Matthias

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Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification von Yu, Sung-Huan, Kyriakidou, Pelagia, Cox, Jürgen

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Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment von Cox, Jürgen, Neuhauser, Nadin, Michalski, Annette, Scheltema, Richard A, Olsen, Jesper V, Mann, Matthias

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The PRIDE database and related tools and resources in 2019: improving support for quantification data von Perez-Riverol, Yasset, Csordas, Attila, Bai, Jingwen, Bernal-Llinares, Manuel, Hewapathirana, Suresh, Kundu, Deepti J, Inuganti, Avinash, Griss, Johannes, Mayer, Gerhard, Eisenacher, Martin, Pérez, Enrique, Uszkoreit, Julian, Pfeuffer, Julianus, Sachsenberg, Timo, Yılmaz, Şule, Tiwary, Shivani, Cox, Jürgen, Audain, Enrique, Walzer, Mathias, Jarnuczak, Andrew F, Ternent, Tobias, Brazma, Alvis, Vizcaíno, Juan Antonio

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A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards von Wiśniewski, Jacek R., Hein, Marco Y., Cox, Jürgen, Mann, Matthias

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Global, quantitative and dynamic mapping of protein subcellular localization von Itzhak, Daniel N, Tyanova, Stefka, Cox, Jürgen, Borner, Georg Hh

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Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors[S] von Deshmukh, Atul S., Murgia, Marta, Nagaraj, Nagarjuna, Treebak, Jonas T., Cox, Jürgen, Mann, Matthias

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Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells von Stingele, Silvia, Stoehr, Gabriele, Peplowska, Karolina, Cox, Jürgen, Mann, Matthias, Storchova, Zuzana

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A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances von Hein, Marco Y., Hubner, Nina C., Poser, Ina, Cox, Jürgen, Nagaraj, Nagarjuna, Toyoda, Yusuke, Gak, Igor A., Weisswange, Ina, Mansfeld, Jörg, Buchholz, Frank, Hyman, Anthony A., Mann, Matthias

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Sleep-wake cycles drive daily dynamics of synaptic phosphorylation von Brüning, Franziska, Noya, Sara B, Bange, Tanja, Koutsouli, Stella, Rudolph, Jan D, Tyagarajan, Shiva K, Cox, Jürgen, Mann, Matthias, Brown, Steven A, Robles, Maria S

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The Coming Age of Complete, Accurate, and Ubiquitous Proteomes von Mann, Matthias, Kulak, Nils A., Nagaraj, Nagarjuna, Cox, Jürgen

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Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling von Sharma, Kirti, D’Souza, Rochelle C.J., Tyanova, Stefka, Schaab, Christoph, Wiśniewski, Jacek R., Cox, Jürgen, Mann, Matthias

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Acetylation site specificities of lysine deacetylase inhibitors in human cells von Schölz, Christian, Weinert, Brian T, Wagner, Sebastian A, Beli, Petra, Miyake, Yasuyuki, Qi, Jun, Jensen, Lars J, Streicher, Werner, McCarthy, Anna R, Westwood, Nicholas J, Lain, Sonia, Cox, Jürgen, Matthias, Patrick, Mann, Matthias, Bradner, James E, Choudhary, Chunaram

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Global detection of human variants and isoforms by deep proteome sequencing von Sinitcyn, Pavel, Richards, Alicia L., Weatheritt, Robert J., Brademan, Dain R., Marx, Harald, Shishkova, Evgenia, Meyer, Jesse G., Hebert, Alexander S., Westphall, Michael S., Blencowe, Benjamin J., Cox, Jürgen, Coon, Joshua J.

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A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles von Wagner, Sebastian A., Beli, Petra, Weinert, Brian T., Nielsen, Michael L., Cox, Jürgen, Mann, Matthias, Choudhary, Chunaram

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A Systematic Investigation into the Nature of Tryptic HCD Spectra von Michalski, Annette, Neuhauser, Nadin, Cox, Jürgen, Mann, Matthias

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Defining the Adult Neural Stem Cell Niche Proteome Identifies Key Regulators of Adult Neurogenesis von Kjell, Jacob, Fischer-Sternjak, Judith, Thompson, Amelia J., Friess, Christian, Sticco, Matthew J., Salinas, Favio, Cox, Jürgen, Martinelli, David C., Ninkovic, Jovica, Franze, Kristian, Schiller, Herbert B., Götz, Magdalena

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Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis von Krahmer, Natalie, Najafi, Bahar, Schueder, Florian, Quagliarini, Fabiana, Steger, Martin, Seitz, Susanne, Kasper, Robert, Salinas, Favio, Cox, Jürgen, Uhlenhaut, Nina Henriette, Walther, Tobias Christian, Jungmann, Ralf, Zeigerer, Anja, Borner, Georg Heinz Helmut, Mann, Matthias

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