Recent findings and technological advances in phosphoproteomics for cells and tissues

Benchmarking Multiple Fragmentation Methods on an Orbitrap Fusion for Top-down Phospho-Proteoform Characterization

(2015) Andrea M. Brunner et al.   ANALYTICAL CHEMISTRY

Highly Sensitive Phosphoproteomics by Tailoring Solid-Phase Extraction to Electrostatic Repulsion-Hydrophilic Interaction Chromatography

(2015) Stefan Loroch et al.   ANALYTICAL CHEMISTRY

Advances in Phos-tag-based methodologies for separation and detection of the phosphoproteome

(2015) Eiji Kinoshita et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Phosphotyrosine Signaling Analysis in Human Tumors Is Confounded by Systemic Ischemia-Driven Artifacts and Intra-Specimen Heterogeneity

(2015) A. S. Gajadhar et al.   CANCER RESEARCH

A Single Kinase Generates the Majority of the Secreted Phosphoproteome

(2015) Vincent S. Tagliabracci et al.   CELL

Sample Collection Method Bias Effects in Quantitative Phosphoproteomics

(2015) Evgeny Kanshin et al.   JOURNAL OF PROTEOME RESEARCH

Why phosphoproteomics is still a challenge

(2015) Fiorella A. Solari et al.   Molecular BioSystems

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

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

Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation

(2015) K. B. Emdal et al.   Science Signaling

Enrichment of phosphorylated peptides and proteins by selective precipitation methods

(2015) Matthias Rainer et al.   Bioanalysis

MARQUIS: A multiplex method for absolute quantification of peptides and posttranslational modifications

(2015) Timothy G. Curran et al.   Nature Communications

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

(2015) Chia-Feng Tsai et al.   Nature Communications

A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation

(2015) Evgeny Kanshin et al.   Cell Reports

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas

(2015) Piero Giansanti et al.   Cell Reports

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

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

Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation

(2015) K. B. Emdal et al.   Science Signaling

Simultaneous Assessment of Kinetic, Site-Specific, and Structural Aspects of Enzymatic Protein Phosphorylation

(2014) Michiel van de Waterbeemd et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Tissue phosphoproteomics with PolyMAC identifies potential therapeutic targets in a transgenic mouse model of HER2 positive breast cancer

(2014) Adam C. Searleman et al.   ELECTROPHORESIS

Impact of Digestion Conditions on Phosphoproteomics

(2014) Clarissa Dickhut et al.   JOURNAL OF PROTEOME RESEARCH

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

(2014) Tanveer S. Batth et al.   JOURNAL OF PROTEOME RESEARCH

Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics

(2014) Dominic Helm et al.   MOLECULAR & CELLULAR PROTEOMICS

Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-treated Yeast Cells

(2014) Vytautas Iesmantavicius et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of Extracellular Signal-regulated Kinase 1 (ERK1) Direct Substrates using Stable Isotope Labeled Kinase Assay-Linked Phosphoproteomics

(2014) Liang Xue et al.   MOLECULAR & CELLULAR PROTEOMICS

Environmental Stress Affects the Activity of Metabolic and Growth Factor Signaling Networks and Induces Autophagy Markers in MCF7 Breast Cancer Cells

(2014) Pedro Casado et al.   MOLECULAR & CELLULAR PROTEOMICS

Alterations in the Cerebellar (Phospho)Proteome of a Cyclic Guanosine Monophosphate (cGMP)-dependent Protein Kinase Knockout Mouse

(2014) Eleonora Corradini et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution

(2014) Erik L. de Graaf et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive and Reproducible Phosphopeptide Enrichment Using Iron Immobilized Metal Ion Affinity Chromatography (Fe-IMAC) Columns

(2014) Benjamin Ruprecht et al.   MOLECULAR & CELLULAR PROTEOMICS

Ischemia in Tumors Induces Early and Sustained Phosphorylation Changes in Stress Kinase Pathways but Does Not Affect Global Protein Levels

(2014) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

(2014) S. Vaga et al.   Molecular Systems Biology

Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Phosphoproteomic analysis identifies the tumor suppressor PDCD4 as a RSK substrate negatively regulated by 14-3-3

(2014) J. A. Galan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Exploiting the Unique ATP-Binding Pocket of Toxoplasma Calcium-Dependent Protein Kinase 1 To Identify Its Substrates

(2013) Sebastian Lourido et al.   ACS Chemical Biology

Increasing Throughput in Targeted Proteomics Assays: 54-Plex Quantitation in a Single Mass Spectrometry Run

(2013) Robert A. Everley et al.   ANALYTICAL CHEMISTRY

Large-Scale Analysis of Peptide Sequence Variants: The Case for High-Field Asymmetric Waveform Ion Mobility Spectrometry

(2013) Andrew J. Creese et al.   ANALYTICAL CHEMISTRY

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

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

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

Phosphoproteome Analysis of Formalin-Fixed and Paraffin-Embedded Tissue Sections Mounted on Microscope Slides

(2013) Masaki Wakabayashi et al.   JOURNAL OF PROTEOME RESEARCH

Protein Digestion: An Overview of the Available Techniques and Recent Developments

(2013) Linda Switzar et al.   JOURNAL OF PROTEOME RESEARCH

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of Direct Tyrosine Kinase Substrates Based on Protein Kinase Assay-Linked Phosphoproteomics

(2013) Liang Xue et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Chiara Francavilla et al.   MOLECULAR CELL

Evolution and functional cross-talk of protein post-translational modifications

(2013) Pedro Beltrao et al.   Molecular Systems Biology

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

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

Robust phosphoproteome enrichment using monodisperse microsphere–based immobilized titanium (IV) ion affinity chromatography

(2013) Houjiang Zhou et al.   Nature Protocols

Technologies and challenges in large-scale phosphoproteomics

(2013) Kasper Engholm-Keller et al.   PROTEOMICS

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

(2013) A. Lundby et al.   Science Signaling

Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells

(2013) P. Casado et al.   Science Signaling

The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces

(2013) K. Van Roey et al.   Science Signaling

Molecular Mechanisms of SH2- and PTB-Domain-Containing Proteins in Receptor Tyrosine Kinase Signaling

(2013) M. J. Wagner et al.   Cold Spring Harbor Perspectives in Biology

Affinity Profiling of the Cellular Kinome for the Nucleotide Cofactors ATP, ADP, and GTP

(2012) Isabelle Becher et al.   ACS Chemical Biology

Advances in phosphopeptide enrichment techniques for phosphoproteomics

(2012) Luisa Beltran et al.   AMINO ACIDS

MMFPh: a maximal motif finder for phosphoproteomics datasets

(2012) Tuobin Wang et al.   BIOINFORMATICS

Global Quantitative Phosphoproteome Analysis of Human Tumor Xenografts Treated with a CD44 Antagonist

(2012) S. Weigand et al.   CANCER RESEARCH

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

Rapid Determination of Multiple Linear Kinase Substrate Motifs by Mass Spectrometry

(2012) Arminja N. Kettenbach et al.   CHEMISTRY & BIOLOGY

Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation

(2012) Boumediene Soufi et al.   CURRENT OPINION IN MICROBIOLOGY

Proteomics Pipeline for Biomarker Discovery of Laser Capture Microdissected Breast Cancer Tissue

(2012) Ning Qing Liu et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

A Strategy for Large-Scale Phosphoproteomics and SRM-Based Validation of Human Breast Cancer Tissue Samples

(2012) Ryohei Narumi et al.   JOURNAL OF PROTEOME RESEARCH

TiSH — a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC

(2012) Kasper Engholm-Keller et al.   Journal of Proteomics

Proteomic Investigations Reveal a Role for RNA Processing Factor THRAP3 in the DNA Damage Response

(2012) Petra Beli et al.   MOLECULAR CELL

Phosphorylation sites of higher stoichiometry are more conserved

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

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast

(2012) N. Dephoure et al.   Science Signaling

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

(2012) Alicia Lundby et al.   Nature Communications

Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

(2012) Alicia Lundby et al.   Cell Reports

Increasing phosphoproteomic coverage through sequential digestion by complementary proteases

(2011) Jason M. Gilmore et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Rapid and Reproducible Single-Stage Phosphopeptide Enrichment of Complex Peptide Mixtures: Application to General and Phosphotyrosine-Specific Phosphoproteomics Experiments

(2011) Arminja N. Kettenbach et al.   ANALYTICAL CHEMISTRY

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

(2011) Takeshi Masuda et al.   ANALYTICAL CHEMISTRY

Multidimensional Strategy for Sensitive Phosphoproteomics Incorporating Protein Prefractionation Combined with SIMAC, HILIC, and TiO2Chromatography Applied to Proximal EGF Signaling

(2011) Kasper Engholm-Keller et al.   JOURNAL OF PROTEOME RESEARCH

Improvement of Phosphoproteome Analyses Using FAIMS and Decision Tree Fragmentation. Application to the Insulin Signaling Pathway in Drosophila melanogaster S2 Cells

(2011) Gaëlle Bridon et al.   JOURNAL OF PROTEOME RESEARCH

Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment

(2011) Houjiang Zhou 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

iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics

(2011) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Phosphoproteome Profiling Reveals Unanticipated Networks Responsive to Cisplatin Treatment of Embryonic Stem Cells

(2011) A. Pines et al.   MOLECULAR AND CELLULAR BIOLOGY

Mapping intact protein isoforms in discovery mode using top-down proteomics

(2011) John C. Tran et al.   NATURE

Large-scale phosphosite quantification in tissues by a spike-in SILAC method

(2011) Mara Monetti et al.   NATURE METHODS

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

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

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

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

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

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

Identifying differentially regulated subnetworks from phosphoproteomic data

(2010) Martin Klammer et al.   BMC BIOINFORMATICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

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

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

In-depth Analyses of Kinase-dependent Tyrosine Phosphoproteomes Based on Metal Ion-functionalized Soluble Nanopolymers

(2010) Anton B. Iliuk et al.   MOLECULAR & CELLULAR PROTEOMICS

Site-specific Phosphorylation Dynamics of the Nuclear Proteome during the DNA Damage Response

(2010) Martin V. Bennetzen et al.   MOLECULAR & CELLULAR PROTEOMICS

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

(2010) A. Bensimon et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

Preparation of monodisperse immobilized Ti4+ affinity chromatography microspheres for specific enrichment of phosphopeptides

(2009) Zhiyuan Yu et al.   ANALYTICA CHIMICA ACTA

Enhanced Sensitivity in Proteomics Experiments Using FAIMS Coupled with a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer†

(2009) Julian Saba et al.   JOURNAL OF PROTEOME RESEARCH

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

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

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling

(2009) Paul J. Boersema et al.   MOLECULAR & CELLULAR PROTEOMICS

Sensitive multiplexed analysis of kinase activities and activity-based kinase identification

(2009) Kazuishi Kubota et al.   NATURE BIOTECHNOLOGY

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry

(2009) Yonghao Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species

(2009) Pedro Beltrao et al.   PLOS BIOLOGY

Specific Phosphopeptide Enrichment with Immobilized Titanium Ion Affinity Chromatography Adsorbent for Phosphoproteome Analysis

(2008) Houjiang Zhou et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteome Analysis ofDrosophila melanogasterEmbryos

(2008) Bo Zhai et al.   JOURNAL OF PROTEOME RESEARCH