Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications

Roles of the Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR pathways in controlling growth and sensitivity to therapy-implications for cancer and aging

(2016) Linda S. Steelman et al.   Aging-US

Phosphoproteomics in drug discovery

(2013) Melody K. Morris et al.   DRUG DISCOVERY TODAY

Mass spectrometric protein maps for biomarker discovery and clinical research

(2013) Yansheng Liu et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Syk Inhibits the Activity of Protein Kinase A by Phosphorylating Tyrosine 330 of the Catalytic Subunit

(2013) Shuai Yu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enrichment specificity of micro and nano-sized titanium and zirconium dioxides particles in phosphopeptide mapping

(2013) Annalisa Vilasi et al.   JOURNAL OF MASS SPECTROMETRY

Rapid Combinatorial ERLIC–SCX Solid-Phase Extraction for In-Depth Phosphoproteome Analysis

(2013) Mostafa Zarei et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors

(2013) Devin K. Schweppe et al.   Journal of Proteomics

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

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

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

(2013) Philippe P. Roux et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Measurement of Phosphoproteome Response to Osmotic Stress inArabidopsisBased on Library-Assisted eXtracted Ion Chromatogram (LAXIC)

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

Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action

(2013) P. Wang 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

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

(2013) Sara Zanivan et al.   Cell Reports

Advances in phosphopeptide enrichment techniques for phosphoproteomics

(2012) Luisa Beltran et al.   AMINO ACIDS

Is phosphoproteomics ready for clinical research?

(2012) Anton B. Iliuk et al.   CLINICA CHIMICA ACTA

Searching for reliable premortem protein biomarkers for prion diseases: progress and challenges to date

(2012) Di Ma et al.   Expert Review of Proteomics

Comparison of IMAC and MOAC for phosphopeptide enrichment by column chromatography

(2012) Luc Negroni et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

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

Comparison of 4-plex to 8-plex iTRAQ Quantitative Measurements of Proteins in Human Plasma Samples

(2012) Gwenael Pottiez et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteomic Analysis of Leukemia Cells under Basal and Drug-treated Conditions Identifies Markers of Kinase Pathway Activation and Mechanisms of Resistance

(2012) Maria P. Alcolea et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

(2012) L. Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complementary Fe3+- and Ti4+-immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptides

(2012) Alan Chuan-Ying Lai et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Analytical strategies for shotgun phosphoproteomics: Status and prospects

(2012) Haruna Imamura et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Sample preparation and analytical strategies for large-scale phosphoproteomics experiments

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

The use of selected reaction monitoring in quantitative proteomics

(2012) Stephen W Holman et al.   Bioanalysis

Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: A review

(2011) Alexander Leitner et al.   ANALYTICA CHIMICA ACTA

Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC and ZIC-cHILIC) Provide High Resolution Separation and Increase Sensitivity in Proteome Analysis

(2011) Serena Di Palma et al.   ANALYTICAL CHEMISTRY

Overview

(2011) Jennifer E. Van Eyk   CIRCULATION RESEARCH

Novel Prognostic Markers in the Serum of Patients With Castration-Resistant Prostate Cancer Derived From Quantitative Analysis of the Pten Conditional Knockout Mouse Proteome

(2011) Martin Kälin et al.   EUROPEAN UROLOGY

Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches

(2011) Ronald J Hause et al.   Expert Review of Proteomics

Mechanical Regulation of Glycogen Synthase Kinase 3β (GSK3β) in Mesenchymal Stem Cells Is Dependent on Akt Protein Serine 473 Phosphorylation via mTORC2 Protein

(2011) Natasha Case et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine

(2011) Q. Tian et al.   JOURNAL OF INTERNAL MEDICINE

Comparison of ERLIC–TiO2, HILIC–TiO2, and SCX–TiO2for Global Phosphoproteomics Approaches

(2011) Mostafa Zarei et al.   JOURNAL OF PROTEOME RESEARCH

Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma

(2011) Eric Kuhn et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Houjiang Zhou et al.   MOLECULAR & CELLULAR PROTEOMICS

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer

(2011) I. Cima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Phosphoproteomics Reveals Crosstalk Between Bcr-Abl and Negative Feedback Mechanisms Controlling Src Signaling

(2011) L. Rubbi et al.   Science Signaling

Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells

(2011) A. N. Kettenbach et al.   Science Signaling

Probing the Phosphoproteome of HeLa Cells Using Nanocast Metal Oxide Microspheres for Phosphopeptide Enrichment

(2010) Alexander Leitner et al.   ANALYTICAL CHEMISTRY

Peptide Labeling with Isobaric Tags Yields Higher Identification Rates Using iTRAQ 4-Plex Compared to TMT 6-Plex and iTRAQ 8-Plex on LTQ Orbitrap

(2010) Peter Pichler et al.   ANALYTICAL CHEMISTRY

Protein Kinase Substrate Profiling with a High-Density Peptide Microarray

(2010) Xiaoming Han et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

A comparative phosphoproteomic analysis of a human tumor metastasis model using a label-free quantitative approach

(2010) Xiaolei Xie et al.   ELECTROPHORESIS

Deciphering signaling pathways in clinical tissues for personalized medicine using protein microarrays

(2010) K. Malinowsky et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling in Diabetes Prone and Resistant Mice

(2010) Leo K. Iwai et al.   JOURNAL OF PROTEOME RESEARCH

On the Development of Plasma Protein Biomarkers

(2010) Silvia Surinova 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

Addressing Accuracy and Precision Issues in iTRAQ Quantitation

(2010) Natasha A. Karp et al.   MOLECULAR & CELLULAR PROTEOMICS

Phosphoproteomics in cancer

(2010) H.C. Harsha et al.   Molecular Oncology

Reverse phase protein microarrays advance to use in clinical trials

(2010) Claudius Mueller et al.   Molecular Oncology

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

Personalized medicine in oncology: the future is now

(2010) Richard L. Schilsky   NATURE REVIEWS DRUG DISCOVERY

Protein Microarrays: Novel Developments and Applications

(2010) Luis Berrade et al.   PHARMACEUTICAL RESEARCH

Optimizing the performance of tin dioxide microspheres for phosphopeptide enrichment

(2009) Alexander Leitner et al.   ANALYTICA CHIMICA ACTA

The Clinical Plasma Proteome: A Survey of Clinical Assays for Proteins in Plasma and Serum

(2009) N. L. Anderson   CLINICAL CHEMISTRY

Approaching clinical proteomics: current state and future fields of application in fluid proteomics

(2009) Rolf Apweiler et al.   CLINICAL CHEMISTRY AND LABORATORY MEDICINE

Tyrosine phosphorylation: thirty years and counting

(2009) Tony Hunter   CURRENT OPINION IN CELL BIOLOGY

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma

(2009) Michael A. Kuzyk 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

An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers

(2009) Jeffrey R. Whiteaker et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Targeting innate immunity protein kinase signalling in inflammation

(2009) Matthias Gaestel et al.   NATURE REVIEWS DRUG DISCOVERY

Evidence for phosphorylation of serine 753 in CFTR using a novel metal-ion affinity resin and matrix-assisted laser desorption mass spectrometry

(2009) David C. A. Neville et al.   PROTEIN SCIENCE

Enrichment and analysis of phosphopeptides under different experimental conditions using titanium dioxide affinity chromatography and mass spectrometry

(2009) Uma K. Aryal et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases

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

Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling Reveals System-Wide Modulation of Protein-Protein Interactions

(2009) V. Mayya et al.   Science Signaling

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

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

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

(2008) Boris Macek et al.   Annual Review of Pharmacology and Toxicology

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

Immobilized Metal Affinity Chromatography Revisited: pH/Acid Control toward High Selectivity in Phosphoproteomics

(2008) Chia-Feng Tsai et al.   JOURNAL OF PROTEOME RESEARCH

Identification of c-Src Tyrosine Kinase Substrates Using Mass Spectrometry and Peptide Microarrays

(2008) Ramars Amanchy et al.   JOURNAL OF PROTEOME RESEARCH

Online Automatedin VivoZebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo

(2008) Simone Lemeer et al.   JOURNAL OF PROTEOME RESEARCH

Solid Tumor Proteome and Phosphoproteome Analysis by High Resolution Mass Spectrometry

(2008) Sara Zanivan et al.   JOURNAL OF PROTEOME RESEARCH

Multiplexed Cell Signaling Analysis of Human Breast Cancer Applications for Personalized Therapy

(2008) Julia D. Wulfkuhle et al.   JOURNAL OF PROTEOME RESEARCH

Fully Automatic Separation and Identification of Phosphopeptides by Continuous pH-Gradient Anion Exchange Online Coupled with Reversed-Phase Liquid Chromatography Mass Spectrometry

(2008) Jie Dai et al.   JOURNAL OF PROTEOME RESEARCH

Contributions of the Raf/MEK/ERK, PI3K/PTEN/Akt/mTOR and Jak/STAT pathways to leukemia

(2008) L S Steelman et al.   LEUKEMIA

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

Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions

(2008) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Clinical Quantitation of Prostate-specific Antigen Biomarker in the Low Nanogram/Milliliter Range by Conventional Bore Liquid Chromatography-Tandem Mass Spectrometry (Multiple Reaction Monitoring) Coupling and Correlation with ELISA Tests

(2008) Tanguy Fortin et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2008) Henrik Daub et al.   MOLECULAR CELL

Signaling networks assembled by oncogenic EGFR and c-Met

(2008) A. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Covalent capture of kinase-specific phosphopeptides reveals Cdk1-cyclin B substrates

(2008) J. D. Blethrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A quantitative atlas of mitotic phosphorylation

(2008) N. Dephoure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography

(2008) Guanghui Han et al.   PROTEOMICS

Quantitative phosphoproteomics by mass spectrometry: Past, present, and future

(2008) Aleksandra Nita-Lazar et al.   PROTEOMICS

Electrostatic Repulsion Hydrophilic Interaction Chromatography for Isocratic Separation of Charged Solutes and Selective Isolation of Phosphopeptides

(2007) Andrew J. Alpert   ANALYTICAL CHEMISTRY