Applications of stable isotope dimethyl labeling in quantitative proteomics

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

(2011) Alexander Leitner et al.   ANALYTICA CHIMICA ACTA

Evaluation of the Deuterium Isotope Effect in Zwitterionic Hydrophilic Interaction Liquid Chromatography Separations for Implementation in a Quantitative Proteomic Approach

(2011) Serena Di Palma et al.   ANALYTICAL CHEMISTRY

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

Contribution of cathepsin L to secretome composition and cleavage pattern of mouse embryonic fibroblasts

(2011) Stefan Tholen et al.   BIOLOGICAL CHEMISTRY

A Quantitative Proteomic Approach to Prion Disease Biomarker Research: Delving into the Glycoproteome

(2011) Xin Wei et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Phosphoproteomics Studies Using Stable Isotope Dimethyl Labeling Coupled with IMAC-HILIC-nanoLC−MS/MS for Estrogen-Induced Transcriptional Regulation

(2011) Chin-Jen Wu et al.   JOURNAL OF PROTEOME RESEARCH

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope–labeled peptides

(2011) Salvatore Cappadona et al.   Journal of Proteomics

Protein signatures associated with tumor cell dissemination in head and neck cancer

(2011) Onno B. Bleijerveld et al.   Journal of Proteomics

Quantitative shot-gun proteomics and MS-based activity assay for revealing gender differences in enzyme contents for rat liver microsome

(2011) Hung-Jen Huang et al.   Journal of Proteomics

Filter-aided sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins

(2011) Jing Lu et al.   Journal of Proteomics

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

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

Proteome-wide systems analysis of a cellulosic biofuel-producing microbe

(2011) A. C. Tolonen et al.   Molecular Systems Biology

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

(2011) Oded Kleifeld et al.   Nature Protocols

N- and C-terminal degradomics: new approaches to reveal biological roles for plant proteases from substrate identification

(2011) Pitter F. Huesgen et al.   PHYSIOLOGIA PLANTARUM

Tyrosine Phosphorylation Profiling in FGF-2 Stimulated Human Embryonic Stem Cells

(2011) Vanessa M. Y. Ding et al.   PLoS One

The Worker Honeybee Fat Body Proteome Is Extensively Remodeled Preceding a Major Life-History Transition

(2011) Queenie W. T. Chan et al.   PLoS One

An entirely specific type I A-kinase anchoring protein that can sequester two molecules of protein kinase A at mitochondria

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

Investigating the role of FGF-2 in stem cell maintenance by global phosphoproteomics profiling

(2011) Adja D. Zoumaro-Djayoon et al.   PROTEOMICS

Urinary CD14 as a potential biomarker for benign prostatic hyperplasia - discovery by combining MALDI-TOF-based biostatistics and ESI-MS/MS-based stable-isotope labeling

(2011) Hong-Lin Cheng et al.   Proteomics Clinical Applications

Phosphoproteomics for the Masses

(2010) Paul A. Grimsrud et al.   ACS Chemical Biology

A Fully Automated System with Online Sample Loading, Isotope Dimethyl Labeling and Multidimensional Separation for High-Throughput Quantitative Proteome Analysis

(2010) Fangjun Wang et al.   ANALYTICAL CHEMISTRY

High-resolution mapping of prostaglandin E2-dependent signaling networks identifies a constitutively active PKA signaling node in CD8+CD45RO+ T cells

(2010) N. G. Oberprieler et al.   BLOOD

Sphingosine Kinase Interacting Protein is an A-Kinase Anchoring Protein Specific for Type I cAMP-Dependent Protein Kinase

(2010) Duangnapa Kovanich  et al.   CHEMBIOCHEM

Target Profiling of a Small Library of Phosphodiesterase 5 (PDE5) Inhibitors using Chemical Proteomics

(2010) Reinout Raijmakers et al.   ChemMedChem

Autophosphorylation and ATM Activation

(2010) Sergei V. Kozlov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evaluation of Metalloendopeptidase Lys-N Protease Performance under Different Sample Handling Conditions

(2010) Nadia Taouatas et al.   JOURNAL OF PROTEOME RESEARCH

Mapping the Protein Interaction Network in Methicillin-ResistantStaphylococcus aureus

(2010) Artem Cherkasov et al.   JOURNAL OF PROTEOME RESEARCH

Probing the Proteome Response to Toluene Exposure in the Solvent TolerantPseudomonas putidaS12

(2010) Dorien Wijte et al.   JOURNAL OF PROTEOME RESEARCH

Dimethyl Isotope Labeling Assisted De Novo Peptide Sequencing

(2010) Marco L. Hennrich et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Proteome-wide analysis of protein carboxy termini: C terminomics

(2010) Oliver Schilling et al.   NATURE METHODS

Ecological Adaptation of Diverse Honey Bee (Apis mellifera) Populations

(2010) Robert Parker et al.   PLoS One

Relative quantitative proteomic analysis reveals wound response proteins correlated with after-cooking darkening

(2010) J. Patrick Murphy et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry

(2009) Bas van Breukelen et al.   BIOINFORMATICS

Whole proteome analysis of osteoprogenitor differentiation induced by disordered nanotopography and mediated by ERK signalling

(2009) Fahsai Kantawong et al.   BIOMATERIALS

The phosphoproteomics data explosion

(2009) Simone Lemeer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Revealing promiscuous drug–target interactions by chemical proteomics

(2009) Marcus Bantscheff et al.   DRUG DISCOVERY TODAY

MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics

(2009) Peter Mortensen et al.   JOURNAL OF PROTEOME RESEARCH

Selectivity in Enrichment of cAMP-dependent Protein Kinase Regulatory Subunits Type I and Type II and Their Interactors Using Modified cAMP Affinity Resins

(2009) Thin Thin Aye et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Nanoproteomics for Protein Complexes (QNanoPX) Related to Estrogen Transcriptional Action

(2009) Pai-Chiao Cheng et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Proteomics by Metabolic Labeling of Model Organisms

(2009) Joost W. Gouw 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

Assessing biological variation and protein processing in primary human leukocytes by automated multiplex stable isotope labeling coupled to 2 dimensional peptide separation

(2009) Reinout Raijmakers et al.   Molecular BioSystems

A chemical proteomics based enrichment technique targeting the interactome of the PDE5 inhibitor PF-4540124

(2009) Poupak Dadvar et al.   Molecular BioSystems

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Protein quantification across hundreds of experimental conditions

(2009) Z. Khan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana

(2009) Jue-Liang Hsu et al.   Proteome Science

Nucleophosmin in the pathogenesis of arsenic-related bladder carcinogenesis revealed by quantitative proteomics

(2009) Shu-Hui Chen et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

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

A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases:In vivo characterization and structure/function relationships

(2008) Arjen Scholten et al.   MASS SPECTROMETRY REVIEWS

Automated Online Sequential Isotope Labeling for Protein Quantitation Applied to Proteasome Tissue-specific Diversity

(2008) Reinout Raijmakers et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics of Photoreceptor Outer Segments Identifies a Subset of SNARE and Rab Proteins Implicated in Membrane Vesicle Trafficking and Fusion

(2008) Michael C. M. Kwok et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Phosphoproteomics of Zebrafish Fyn/Yes Morpholino Knockdown Embryos

(2008) Simone Lemeer et al.   MOLECULAR & CELLULAR PROTEOMICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

Targeted Disruption of the PME-1 Gene Causes Loss of Demethylated PP2A and Perinatal Lethality in Mice

(2008) Silvia Ortega-Gutiérrez et al.   PLoS One

Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates

(2008) Paul J. Boersema et al.   PROTEOMICS