Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic (Q38217990)

31 August 2017

Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic (English)

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31 August 2017

2

Ruedi Aebersold

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31 August 2017

Martin A Jünger

1

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PubMed ID

24902836

31 August 2017

language of work or name

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2 July 2013

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Wiley interdisciplinary reviews. Developmental biology

31 August 2017

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31 August 2017

3

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31 August 2017

1

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31 August 2017

83-112

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The origins of protein phosphorylation

31 August 2017

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Transforming gene product of Rous sarcoma virus phosphorylates tyrosine

21 January 2018

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Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

21 January 2018

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Large-scale phosphorylation analysis of mouse liver

21 January 2018

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Stepchild phosphohistidine: acid-labile phosphorylation becomes accessible by functional proteomics

21 January 2018

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The regulation of protein function by multisite phosphorylation--a 25 year update

21 January 2018

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Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution

21 January 2018

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Impact of phosphoproteomics on studies of bacterial physiology

21 January 2018

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The phosphoproteomics data explosion.

21 January 2018

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Mechanisms of specificity in protein phosphorylation

21 January 2018

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Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information

21 January 2018

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A mechanism for the evolution of phosphorylation sites

21 January 2018

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Tyrosine phosphorylation: thirty years and counting

21 January 2018

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Positive selection of tyrosine loss in metazoan evolution.

21 January 2018

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Two-component signaling circuit structure and properties

21 January 2018

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Protein kinase A-alpha directly phosphorylates FoxO1 in vascular endothelial cells to regulate expression of vascular cellular adhesion molecule-1 mRNA.

21 January 2018

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Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

21 January 2018

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Combining chemical genetics and proteomics to identify protein kinase substrates

21 January 2018

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Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets

21 January 2018

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The age of crosstalk: phosphorylation, ubiquitination, and beyond

21 January 2018

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Dynamic interplay between O-glycosylation and O-phosphorylation of nucleocytoplasmic proteins: a new paradigm for metabolic control of signal transduction and transcription

21 January 2018

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Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins

21 January 2018

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O-GlcNAc modification: why so intimately associated with phosphorylation?

21 January 2018

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Kinase consensus sequences: a breeding ground for crosstalk

21 January 2018

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Arginine methylation of FOXO transcription factors inhibits their phosphorylation by Akt.

21 January 2018

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The C-terminal domain of RNA polymerase II is modified by site-specific methylation

21 January 2018

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Using protein microarrays to study phosphorylation-mediated signal transduction

21 January 2018

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Single-cell pharmacodynamic monitoring of S6 ribosomal protein phosphorylation in AML blasts during a clinical trial combining the mTOR inhibitor sirolimus and intensive chemotherapy

21 January 2018

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Highly multiparametric analysis by mass cytometry

21 January 2018

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Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum

21 January 2018

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Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation

21 January 2018

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Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

21 January 2018

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Targeted proteome investigation via selected reaction monitoring mass spectrometry

21 January 2018

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Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer.

21 January 2018

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Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics

21 January 2018

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Subcellular phosphoproteomics

21 January 2018

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An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells

21 January 2018

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Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

21 January 2018

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Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation

21 January 2018

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Dissection of the insulin signaling pathway via quantitative phosphoproteomics

21 January 2018

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In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling

21 January 2018

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The human plasma proteome: history, character, and diagnostic prospects

21 January 2018

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Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

21 January 2018

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Optimization of mass spectrometry-compatible surfactants for shotgun proteomics

21 January 2018

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Shotgun identification of protein modifications from protein complexes and lens tissue

21 January 2018

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Large-scale characterization of HeLa cell nuclear phosphoproteins

21 January 2018

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

21 January 2018

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Separation of multiphosphorylated peptide isomers by hydrophilic interaction chromatography on an aminopropyl phase

21 January 2018

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Simultaneous analysis of proteome, phospho- and glycoproteome of rat kidney tissue with electrostatic repulsion hydrophilic interaction chromatography

21 January 2018

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Advances in quantitative phosphoproteomics

21 January 2018

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Optimized IMAC-IMAC protocol for phosphopeptide recovery from complex biological samples

21 January 2018

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SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides

21 January 2018

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Chemical tagging strategies for mass spectrometry-based phospho-proteomics

21 January 2018

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Improved beta-elimination-based affinity purification strategy for enrichment of phosphopeptides

21 January 2018

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Phosphopeptide modification and enrichment by oxidation-reduction condensation

21 January 2018

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Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments

21 January 2018

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Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues

21 January 2018

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Improvement of phosphoproteome analyses using FAIMS and decision tree fragmentation. application to the insulin signaling pathway in Drosophila melanogaster S2 cells

21 January 2018

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Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes

21 January 2018

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Optimization and use of peptide mass measurement accuracy in shotgun proteomics.

21 January 2018

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Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation

21 January 2018

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A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry

21 January 2018

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The ABC's (and XYZ's) of peptide sequencing

21 January 2018

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Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation.

21 January 2018

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Optimized Orbitrap HCD for quantitative analysis of phosphopeptides.

21 January 2018

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Precision proteomics: the case for high resolution and high mass accuracy

21 January 2018

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Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-Orbitrap instrument

21 January 2018

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Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment

21 January 2018

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Tandem mass spectrometry strategies for phosphoproteome analysis.

21 January 2018

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Decision tree-driven tandem mass spectrometry for shotgun proteomics

21 January 2018

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Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

21 January 2018

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Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

21 January 2018

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A novel strategy for quantitative proteomics using isotope-coded protein labels

21 January 2018

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Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues

21 January 2018

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Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

21 January 2018

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Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

21 January 2018

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Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

21 January 2018

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iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics

21 January 2018

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Use of selected reaction monitoring data for label-free quantification of protein modification stoichiometry

21 January 2018

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Measurement of protein phosphorylation stoichiometry by selected reaction monitoring mass spectrometry

21 January 2018

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A large-scale method to measure absolute protein phosphorylation stoichiometries

21 January 2018

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A quantitative results-driven approach to analyzing multisite protein phosphorylation: the phosphate-dependent phosphorylation profile of the transcription factor Pho4.

21 January 2018

1 reference

Differential multisite phosphorylation of the trehalose-6-phosphate synthase gene family in Arabidopsis thaliana: a mass spectrometry-based process for multiparallel peptide library phosphorylation analysis

21 January 2018

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Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches.

21 January 2018

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Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks

21 January 2018

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Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides

21 January 2018

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A probability-based approach for high-throughput protein phosphorylation analysis and site localization

21 January 2018

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SLoMo: automated site localization of modifications from ETD/ECD mass spectra.

21 January 2018

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Confident phosphorylation site localization using the Mascot Delta Score

21 January 2018

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PhosphoScore: an open-source phosphorylation site assignment tool for MSn data

21 January 2018

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Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis

21 January 2018

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Comprehensive phosphorylation site analysis of individual phosphoproteins applying scoring schemes for MS/MS data.

21 January 2018

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Phosphoproteome resource for systems biology research.

21 January 2018

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PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

21 January 2018

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

21 January 2018

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PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database.

21 January 2018

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PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

21 January 2018

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P3DB: a plant protein phosphorylation database

21 January 2018

1 reference

SysPTM: a systematic resource for proteomic research on post-translational modifications

21 January 2018

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Human Protein Reference Database--2009 update

21 January 2018

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

21 January 2018

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An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets

21 January 2018

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Predicting protein post-translational modifications using meta-analysis of proteome scale data sets

21 January 2018

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A curated compendium of phosphorylation motifs

21 January 2018

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Discovery of phosphorylation motif mixtures in phosphoproteomics data

21 January 2018

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Defining the specificity space of the human SRC homology 2 domain

21 January 2018

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Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach

21 January 2018

1 reference

Linear Motif Atlas for Phosphorylation-Dependent Signaling

21 January 2018

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Systematic Discovery of In Vivo Phosphorylation Networks

21 January 2018

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Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

21 January 2018

1 reference

Predicting protein kinase specificity: Predikin update and performance in the DREAM4 challenge

21 January 2018

1 reference

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

21 January 2018

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GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy

21 January 2018

1 reference

Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences

21 January 2018

1 reference

KEA: kinase enrichment analysis

21 January 2018

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Cytoscape 2.8: new features for data integration and network visualization

21 January 2018

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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

21 January 2018

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The BioGRID Interaction Database: 2011 update

21 January 2018

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MINT, the molecular interaction database: 2012 update

21 January 2018

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The IntAct molecular interaction database in 2012

21 January 2018

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PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

21 January 2018

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PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation

21 January 2018

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PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.

21 January 2018

1 reference

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

21 January 2018

1 reference

Computational analysis of phosphoproteomics: progresses and perspectives.

21 January 2018

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A face in the crowd: recognizing peptides through database search

21 January 2018

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Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites

21 January 2018

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Modeling signaling networks using high-throughput phospho-proteomics

21 January 2018

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Integrative features of the yeast phosphoproteome and protein-protein interaction map

21 January 2018

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Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis

21 January 2018

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Magic bullets for protein kinases

21 January 2018

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Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor

21 January 2018

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Tsc2 is not a critical target of Akt during normal Drosophila development

21 January 2018

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Akt phosphorylates both Tsc1 and Tsc2 in Drosophila, but neither phosphorylation is required for normal animal growth

21 January 2018

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Regulation of yeast central metabolism by enzyme phosphorylation

21 January 2018

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Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins.

21 January 2018

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PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

21 January 2018

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Phosphoproteome analysis of Drosophila melanogaster embryos

21 January 2018

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Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors

21 January 2018

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Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells

21 January 2018

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Toward a comprehensive characterization of a human cancer cell phosphoproteome.

21 January 2018

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Reproducible isolation of distinct, overlapping segments of the phosphoproteome

21 January 2018

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Multiple Reaction Monitoring to Identify Sites of Protein Phosphorylation with High Sensitivity

21 January 2018

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OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/WDEV.121

1 reference

release_ubqwcytgzbdglollzkwflgj5uu

31 August 2017

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Fatcat

https://api.fatcat.wiki/v0/release/ubqwcytgzbdglollzkwflgj5uu

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24 November 2022

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PubMed ID

24902836

1 reference

PubMed ID

24902836