Search Results - "Cox, Jürgen"

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

“…Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We…”
Get full text

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

“…Perseus is a comprehensive, user-friendly software platform for the biological analysis of quantitative proteomics data. It is intended to help biologists with…”
Get full text

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

“…Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide…”
Get full text

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

“…Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value…”
Get full text

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

“…A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe…”
Get full text

The PRIDE database and related tools and resources in 2019: improving support for quantification data by 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

“…Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based…”
Get full text

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

“…Absolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies…”
Get full text

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

“…Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and…”
Get full text

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

“…Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is…”
Get full text

Acetylation site specificities of lysine deacetylase inhibitors in human cells by 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

“…Comprehensive analysis of changes in protein acetylation in response to lysine deacetylase inhibitors uncovers inhibitor specificities. Lysine deacetylases…”
Get full text

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

“…Extra chromosome copies markedly alter the physiology of eukaryotic cells, but the underlying reasons are not well understood. We created human trisomic and…”
Get full text

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances by 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

“…The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the…”
Get full text

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation by 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

“…The circadian clock drives daily changes of physiology, including sleep-wake cycles, through regulation of transcription, protein abundance, and function…”
Get full text

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

“…High-resolution mass spectrometry (MS)-based proteomics has progressed tremendously over the years. For model organisms like yeast, we can now quantify…”
Get full text

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

“…Regulatory protein phosphorylation controls normal and pathophysiological signaling in eukaryotic cells. Despite great advances in mass-spectrometry-based…”
Get full text

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

“…Post-translational modification of proteins by ubiquitin is a fundamentally important regulatory mechanism. However, proteome-wide analysis of endogenous…”
Get full text

Global detection of human variants and isoforms by deep proteome sequencing by 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.

“…An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically…”
Get full text

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

“…Modern mass spectrometry-based proteomics can produce millions of peptide fragmentation spectra, which are automatically identified in databases using…”
Get full text

Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis by 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

“…Lipid metabolism is highly compartmentalized between cellular organelles that dynamically adapt their compositions and interactions in response to metabolic…”
Get full text

Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity by Mordret, Ernest, Dahan, Orna, Asraf, Omer, Rak, Roni, Yehonadav, Avia, Barnabas, Georgina D., Cox, Jürgen, Geiger, Tamar, Lindner, Ariel B., Pilpel, Yitzhak

“…The translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless, translation errors are frequent, and…”
Get full text