Illuminating the dark phosphoproteome

Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics

(2018) Clement M Potel et al.   NATURE METHODS

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells

(2018) Chris Soon Heng Tan et al.   SCIENCE

In vivo brain GPCR signaling elucidated by phosphoproteomics

(2018) Jeffrey J. Liu et al.   SCIENCE

Homing in: Mechanisms of Substrate Targeting by Protein Kinases

(2018) Chad J. Miller et al.   TRENDS IN BIOCHEMICAL SCIENCES

Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates

(2017) Evgeny Kanshin et al.   MOLECULAR & CELLULAR PROTEOMICS

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

Tumours with class 3 BRAF mutants are sensitive to the inhibition of activated RAS

(2017) Zhan Yao et al.   NATURE

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

(2017) George Rosenberger et al.   NATURE BIOTECHNOLOGY

Polypharmacology-based ceritinib repurposing using integrated functional proteomics

(2017) Brent M Kuenzi et al.   Nature Chemical Biology

Systems-level identification of PKA-dependent signaling in epithelial cells

(2017) Kiyoshi Isobe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest

(2017) Richard J. Mills et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The target landscape of clinical kinase drugs

(2017) Susan Klaeger et al.   SCIENCE

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

(2017) Pascal Leuenberger et al.   SCIENCE

Control of muscle formation by the fusogenic micropeptide myomixer

(2017) Pengpeng Bi et al.   SCIENCE

Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis

(2017) Martin Steger et al.   eLife

Small-molecule kinase inhibitors: an analysis of FDA-approved drugs

(2016) Peng Wu et al.   DRUG DISCOVERY TODAY

Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells

(2016) Heiner Koch et al.   JOURNAL OF PROTEOME RESEARCH

Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling

(2016) Emily S. Humphrey et al.   MOLECULAR & CELLULAR PROTEOMICS

Forward-genetics analysis of sleep in randomly mutagenized mice

(2016) Hiromasa Funato et al.   NATURE

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

LOVTRAP: an optogenetic system for photoinduced protein dissociation

(2016) Hui Wang et al.   NATURE METHODS

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

(2016) Francesca Sacco et al.   Nature Communications

Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases

(2016) Martin Steger et al.   eLife

Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

(2015) Nicholas M. Riley et al.   ANALYTICAL CHEMISTRY

Development of a new model system to dissect isoform specific Akt signalling in adipocytes

(2015) Esi Kajno et al.   BIOCHEMICAL JOURNAL

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data

(2015) Pengyi Yang et al.   BIOINFORMATICS

Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure

(2015) Kosaku Shinoda et al.   Cell Metabolism

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates

(2015) Nolan J. Hoffman et al.   Cell Metabolism

Identification of AMPK Phosphorylation Sites Reveals a Network of Proteins Involved in Cell Invasion and Facilitates Large-Scale Substrate Prediction

(2015) Bethany E. Schaffer et al.   Cell Metabolism

Proteome sequencing goes deep

(2015) Alicia L Richards et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Kinome Screen Identifies PFKFB3 and Glucose Metabolism as Important Regulators of the Insulin/Insulin-like Growth Factor (IGF)-1 Signaling Pathway

(2015) Sophie Trefely et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Genome-wide CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Screen Identifies NEK7 as an Essential Component of NLRP3 Inflammasome Activation

(2015) Jonathan L. Schmid-Burgk et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks

(2015) Linsey M. Raaijmakers et al.   JOURNAL OF PROTEOME RESEARCH

Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence

(2015) Erik L. de Graaf et al.   JOURNAL OF PROTEOME RESEARCH

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks

(2015) Omar Wagih et al.   MOLECULAR & CELLULAR PROTEOMICS

Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation

(2015) Matthew D. Hirschey et al.   MOLECULAR & CELLULAR PROTEOMICS

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

The promise and peril of chemical probes

(2015) Cheryl H Arrowsmith et al.   Nature Chemical Biology

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

(2015) Holger Franken et al.   Nature Protocols

The complex relationships between microglia, alpha-synuclein, and LRRK2 in Parkinson’s disease

(2015) J. Schapansky et al.   NEUROSCIENCE

Empirical inference of circuitry and plasticity in a kinase signaling network

(2015) Edmund H. Wilkes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Drosophila glucome screening identifies Ck1alpha as a regulator of mammalian glucose metabolism

(2015) Rupali Ugrankar et al.   Nature Communications

Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells

(2015) Chad M. Toledo et al.   Cell Reports

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Mass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications

(2014) Sophia Doll et al.   ACS Chemical Biology

Top Down proteomics: Facts and perspectives

(2014) Adam D. Catherman et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Recently targeted kinases and their inhibitors—the path to clinical trials

(2014) Stefan Knapp et al.   CURRENT OPINION IN PHARMACOLOGY

Structural Basis for Phosphorylation and Lysine Acetylation Cross-talk in a Kinase Motif Associated with Myocardial Ischemia and Cardioprotection

(2014) Benjamin L. Parker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human Proteins with Target Sites of Multiple Post-Translational Modification Types Are More Prone to Be Involved in Disease

(2014) Qianli Huang et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteomics Screen Reveals Akt Isoform-Specific Signals Linking RNA Processing to Lung Cancer

(2014) Ioannis Sanidas et al.   MOLECULAR CELL

Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

(2014) B. T. Weinert et al.   Molecular Systems Biology

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback

(2014) James E. Ferrell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies

(2014) Bhagwan Yadav et al.   Scientific Reports

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

Kinase Drug Discovery – What’s Next in the Field?

(2013) Philip Cohen et al.   ACS Chemical Biology

Mass Spectrometry Based Method to Increase Throughput for Kinome Analyses Using ATP Probes

(2013) F. E. McAllister et al.   ANALYTICAL CHEMISTRY

CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data

(2013) Gabriela Bindea et al.   BIOINFORMATICS

Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling

(2013) Frank Wippich et al.   CELL

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

(2013) Sean J. Humphrey et al.   Cell Metabolism

The Pseudokinase MLKL Mediates Necroptosis via a Molecular Switch Mechanism

(2013) James M. Murphy et al.   IMMUNITY

Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)

(2013) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

Comparing Immobilized Kinase Inhibitors and Covalent ATP Probes for Proteomic Profiling of Kinase Expression and Drug Selectivity

(2013) Simone Lemeer et al.   JOURNAL OF PROTEOME RESEARCH

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

(2013) John D. Chapman et al.   MASS SPECTROMETRY REVIEWS

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Phosphoproteomic Profiling Identifies Focal Adhesion Kinase as a Mediator of Docetaxel Resistance in Castrate-Resistant Prostate Cancer

(2013) B. Y. Lee et al.   MOLECULAR CANCER THERAPEUTICS

Functional Proteomics Defines the Molecular Switch Underlying FGF Receptor Trafficking and Cellular Outputs

(2013) Chiara Francavilla et al.   MOLECULAR CELL

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

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

(2013) Harald Marx et al.   NATURE BIOTECHNOLOGY

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation

(2013) Danielle L Swaney et al.   NATURE METHODS

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

(2013) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells

(2013) J.-Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay

(2013) D. M. Molina et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of  -Adrenergic Receptor Signaling

(2013) A. Lundby et al.   Science Signaling

Comparative Phosphoproteomic Analysis of Checkpoint Recovery Identifies New Regulators of the DNA Damage Response

(2013) V. A. Halim et al.   Science Signaling

In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis

(2013) Sara Zanivan et al.   Cell Reports

The human phosphatase interactome: An intricate family portrait

(2012) Francesca Sacco et al.   FEBS LETTERS

Muscle-specific Knock-out of NUAK Family SNF1-like Kinase 1 (NUAK1) Prevents High Fat Diet-induced Glucose Intolerance

(2012) Fumika Inazuka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A protease for 'middle-down' proteomics

(2012) Cong Wu et al.   NATURE METHODS

Microscale Phosphoproteome Analysis of 10 000 Cells from Human Cancer Cell Lines

(2011) Takeshi Masuda et al.   ANALYTICAL CHEMISTRY

Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease

(2011) Gerald W. Hart et al.   Annual Review of Biochemistry

Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

(2011) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

Phosphotyrosine mediated protein interactions of the discoidin domain receptor 1

(2011) Simone Lemeer et al.   Journal of Proteomics

Light-Activated Kinases Enable Temporal Dissection of Signaling Networks in Living Cells

(2011) Arnaud Gautier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

Rapid Phospho-Turnover by Receptor Tyrosine Kinases Impacts Downstream Signaling and Drug Binding

(2011) Laura B. Kleiman et al.   MOLECULAR CELL

Chemical Genetic Screen for AMPKα2 Substrates Uncovers a Network of Proteins Involved in Mitosis

(2011) Max R. Banko et al.   MOLECULAR CELL

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

(2011) J. Munoz et al.   Molecular Systems Biology

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The mTOR-Regulated Phosphoproteome Reveals a Mechanism of mTORC1-Mediated Inhibition of Growth Factor Signaling

(2011) P. P. Hsu et al.   SCIENCE

Proteome-Wide Mapping of the Drosophila Acetylome Demonstrates a High Degree of Conservation of Lysine Acetylation

(2011) B. T. Weinert et al.   Science Signaling

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

The Language of Histone Crosstalk

(2010) Jung-Shin Lee et al.   CELL

Probing the Probes: Fitness Factors For Small Molecule Tools

(2010) Paul Workman et al.   CHEMISTRY & BIOLOGY

Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

(2010) Nagarjuna Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

Evolutionary Constraints of Phosphorylation in Eukaryotes, Prokaryotes, and Mitochondria

(2010) Florian Gnad et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic genetic analysis of muscle morphogenesis and function in Drosophila

(2010) Frank Schnorrer et al.   NATURE

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

The Selectivity of Receptor Tyrosine Kinase Signaling Is Controlled by a Secondary SH2 Domain Binding Site

(2009) Jae Hyun Bae et al.   CELL

Proteomics strategy for quantitative protein interaction profiling in cell extracts

(2009) Kirti Sharma et al.   NATURE METHODS

Tuning the Activation Threshold of a Kinase Network by Nested Feedback Loops

(2009) Q. A. Justman et al.   SCIENCE

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases

(2009) C. S. H. Tan et al.   Science Signaling

Weak functional constraints on phosphoproteomes

(2009) Christian R. Landry et al.   TRENDS IN GENETICS

Kinase-Selective Enrichment Enables Quantitative Phosphoproteomics of the Kinome across the Cell Cycle

(2008) Henrik Daub et al.   MOLECULAR CELL

Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases

(2008) Beth Apsel et al.   Nature Chemical Biology

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Cross-talk between GlcNAcylation and phosphorylation: Site-specific phosphorylation dynamics in response to globally elevated O-GlcNAc

(2008) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling

Non-functional phosphorylations?

(2008) Gustav E. Lienhard   TRENDS IN BIOCHEMICAL SCIENCES