The Coming of Age of Phosphoproteomics—from Large Data Sets to Inference of Protein Functions

Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions

(2013) M. Courcelles et al.   Molecular Systems Biology

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

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

(2013) Danielle L Swaney et al.   NATURE METHODS

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

Technologies and challenges in large-scale phosphoproteomics

(2013) Kasper Engholm-Keller et al.   PROTEOMICS

Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis

(2013) A. M. Robitaille et al.   SCIENCE

Advances in phosphopeptide enrichment techniques for phosphoproteomics

(2012) Luisa Beltran et al.   AMINO ACIDS

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

(2012) Jacek R. Wiśniewski et al.   ANALYTICAL CHEMISTRY

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses

(2012) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Functional Interplay between Caspase Cleavage and Phosphorylation Sculpts the Apoptotic Proteome

(2012) Melissa M. Dix et al.   CELL

Occurrence and Detection of Phosphopeptide Isomers in Large-Scale Phosphoproteomics Experiments

(2012) Mathieu Courcelles et al.   JOURNAL OF PROTEOME RESEARCH

Improve the Coverage for the Analysis of Phosphoproteome of HeLa Cells by a Tandem Digestion Approach

(2012) Yangyang Bian et al.   JOURNAL OF PROTEOME RESEARCH

TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics

(2012) Jun Zhong et al.   MOLECULAR & CELLULAR PROTEOMICS

Sequential Posttranslational Modifications Program FEN1 Degradation during Cell-Cycle Progression

(2012) Zhigang Guo et al.   MOLECULAR CELL

Phosphorylation sites of higher stoichiometry are more conserved

(2012) Chris Soon Heng Tan et al.   NATURE METHODS

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Sample preparation and analytical strategies for large-scale phosphoproteomics experiments

(2012) Evgeny Kanshin et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Advances in Quantitative Phosphoproteomics

(2011) Carol L. Nilsson   ANALYTICAL CHEMISTRY

Universal and Confident Phosphorylation Site Localization Using phosphoRS

(2011) Thomas Taus et al.   JOURNAL OF PROTEOME RESEARCH

Activation and Function of the MAPKs and Their Substrates, the MAPK-Activated Protein Kinases

(2011) M. Cargnello et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis

(2011) Scott B. Ficarro et al.   MOLECULAR & CELLULAR PROTEOMICS

Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes

(2011) Ronghu Wu et al.   MOLECULAR & CELLULAR PROTEOMICS

Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics

(2011) Mark P. Jedrychowski et al.   MOLECULAR & CELLULAR PROTEOMICS

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Processive phosphorylation of ERK MAP kinase in mammalian cells

(2011) K. Aoki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Phos-tag SDS-PAGE systems for phosphorylation profiling of proteins with a wide range of molecular masses under neutral pH conditions

(2011) Eiji Kinoshita et al.   PROTEOMICS

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

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

(2011) P. P. Hsu et al.   SCIENCE

Protein kinase signaling networks in cancer

(2010) John Brognard et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Phosphorylation-Dependent Interaction of SATB1 and PIAS1 Directs SUMO-Regulated Caspase Cleavage of SATB1

(2010) Joseph-Anthony T. Tan et al.   MOLECULAR AND CELLULAR BIOLOGY

Akt-RSK-S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases

(2010) A. Moritz et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

Regulation of cell proliferation and survival: Convergence of protein kinases and caspases

(2009) James S. Duncan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Caspases and Kinases in a Death Grip

(2009) Manabu Kurokawa et al.   CELL

The RASopathies: developmental syndromes of Ras/MAPK pathway dysregulation

(2009) William E Tidyman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

SLoMo: Automated Site Localization of Modifications from ETD/ECD Mass Spectra

(2009) Christopher M. Bailey et al.   JOURNAL OF PROTEOME RESEARCH

Stoichiometric Quantification of Akt Phosphorylation Using LC-MS/MS

(2009) Abdelmadjid Atrih et al.   JOURNAL OF PROTEOME RESEARCH

A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation

(2009) Vinh Nguyen et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

(2009) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Functional Proteomics Identifies Targets of Phosphorylation by B-Raf Signaling in Melanoma

(2009) William M. Old et al.   MOLECULAR CELL

ELM: the status of the 2010 eukaryotic linear motif resource

(2009) Cathryn M. Gould et al.   NUCLEIC ACIDS RESEARCH

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry

(2009) D. L. Swaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell-Specific Information Processing in Segregating Populations of Eph Receptor Ephrin-Expressing Cells

(2009) C. Jorgensen et al.   SCIENCE

Niobium(V) Oxide (Nb2O5): Application to Phosphoproteomics

(2008) Scott B. Ficarro et al.   ANALYTICAL CHEMISTRY

Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

(2008) Neil FW Saunders et al.   BMC BIOINFORMATICS

A Comparative Study of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) versus SCX-IMAC-Based Methods for Phosphopeptide Isolation/Enrichment

(2008) Chee Sian Gan et al.   JOURNAL OF PROTEOME RESEARCH

TiO2-Based Phosphoproteomic Analysis of the Plasma Membrane and the Effects of Phosphatase Inhibitor Treatment

(2008) Tine E. Thingholm et al.   JOURNAL OF PROTEOME RESEARCH

PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSnData

(2008) Brian E. Ruttenberg et al.   JOURNAL OF PROTEOME RESEARCH

PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information

(2008) Yunhu Wan et al.   JOURNAL OF PROTEOME RESEARCH

Hydrophilic Interaction Chromatography Reduces the Complexity of the Phosphoproteome and Improves Global Phosphopeptide Isolation and Detection

(2008) Dean E. McNulty et al.   MOLECULAR & CELLULAR PROTEOMICS

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

(2008) Judit Villén et al.   Nature Protocols

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH