Search filters

List of works by Jürgen Cox

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data ⬇️

scientific article published on November 5, 2012

A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards.

scientific article published on 15 September 2014

A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

scientific article published on 10 April 2019

A Systematic Investigation into the Nature of Tryptic HCD Spectra ⬇️

scientific article published on October 10, 2012

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics

scientific article

A human interactome in three quantitative dimensions organized by stoichiometries and abundances

scientific article

A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics

scientific article

A novel chromatographic method allows on-line reanalysis of the proteome

scientific article published on 29 April 2008

A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles

scientific article (publication date: October 2011)

Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx

scientific article published on 11 January 2022

Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

scientific article

Acetylation site specificities of lysine deacetylase inhibitors in human cells

scientific article (publication date: 9 March 2015)

Analysis of the mouse liver proteome using advanced mass spectrometry.

scientific article published on 3 July 2007

Cell-type-resolved quantitative proteomics of murine liver

scientific article published on December 2014

Combined use of RNAi and quantitative proteomics to study gene function in Drosophila

scientific article published in September 2008

Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

scientific article published on 20 May 2009

DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

scientific article

Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation.

scientific article published on 17 May 2011

Deep proteome and transcriptome mapping of a human cancer cell line

scientific article

Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors

scientific article

Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates

scientific article published on 18 May 2022

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

scientific article published on 21 November 2016

EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification

scientific article published on 18 June 2018

Expert System for Computer-assisted Annotation of MS/MS Spectra ⬇️

scientific article published on August 10, 2012

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

scientific article published on 22 May 2019

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells.

scientific article published on January 2012

Glucose-regulated and drug-perturbed phosphoproteome reveals molecular mechanisms controlling insulin secretion

scientific article published on 14 November 2016

High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome

scientific article

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

scientific article published on 27 May 2019

Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry

scientific article published on 6 January 2016

How much peptide sequence information is contained in ion trap tandem mass spectra?

scientific article

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data

scientific article

In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis

scientific article published on 31 January 2013

In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism.

scientific article

Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry

scientific article published in June 2008

Is proteomics the new genomics?

scientific article

List of Contributors

Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles

scientific article

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

scientific article

MaxQuant for in-depth analysis of large SILAC datasets

scientific article published in January 2014

MaxQuant goes Linux

scientific article published on 01 June 2018

MaxQuant software for ion mobility enhanced shotgun proteomics

scientific article published on 10 March 2020

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides

article

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS ⬇️

scientific article published on February 28, 2011

N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes

scientific article

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

article

PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.

scientific article published on 23 May 2012

Predicting post-translational lysine acetylation using support vector machines.

scientific article published on 26 May 2010

Proceedings of the Frontiers of Retrovirology Conference 2016.

scientific article published on 26 September 2016

Proteomic Analysis of Cellular Systems

article

Proteomic maps of breast cancer subtypes

scientific article

Proteomic portrait of human breast cancer progression identifies novel prognostic markers

scientific article

Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation

scientific article published on 7 July 2010

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

scientific article

Quantitative proteomics reveals subset-specific viral recognition in dendritic cells.

scientific article published on 18 February 2010

Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response

scientific article

Quantitative, high-resolution proteomics for data-driven systems biology

scientific article

Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons

scientific article published on 02 July 2021

Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation

scientific article published on 11 February 2020

Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

scientific article (publication date: 6 November 2015)

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation

scientific article

Software lock mass by two-dimensional minimization of peptide mass errors

scientific article published on 22 April 2011

Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry

scientific article published on December 2008

Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function.

scientific article published in November 2017

Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins

scientific article published on 28 November 2007

Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles ⬇️

scientific article published on March 21, 2012

Super-SILAC mix for quantitative proteomics of human tumor tissue

scientific article published on 4 April 2010

System-wide changes to SUMO modifications in response to heat shock

scientific article

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap

scientific article published on 20 October 2011

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes ⬇️

scientific article published on February 21, 2013

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics.

scientific article

The Perseus computational platform for comprehensive analysis of (prote)omics data

scientific article

The Proteome of Primary Prostate Cancer

scientific article

The Proteome of Prostate Cancer Bone Metastasis Reveals Heterogeneity with Prognostic Implications

scientific article published on 24 July 2018

The dental proteome of Homo antecessor

scientific article published on 01 April 2020

The nucleolus functions as a phase-separated protein quality control compartment

scientific article

The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle

scientific article published on 18 June 2008

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes ⬇️

scientific article published on December 9, 2011

Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling

scientific article published on 21 August 2014

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

scientific article published on 01 February 2011

Paulina is supported by:

About Paulina

Help