Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations (Q34097567)

31 July 2017

title

Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations (English)

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31 July 2017

Viveka Mayya

1

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31 July 2017

David K Han

series ordinal

2

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31 July 2017

publication date

1 December 2009

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Expert Review of Proteomics

31 July 2017

published in

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31 July 2017

volume

6

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31 July 2017

issue

6

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31 July 2017

page(s)

605-618

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describes a project that uses

31 July 2017

1 reference

Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Challenges and opportunities in defining the essential cancer kinome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

From promiscuity to precision: protein phosphatases get a makeover

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Tyrosine phosphorylation: thirty years and counting

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Analytical strategies for phosphoproteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Cancer driver mutations in protein kinase genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Dynamic proteomics of individual cancer cells in response to a drug.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Phosphoproteomics: unraveling the signaling web.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

The unfoldomics decade: an update on intrinsically disordered proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

A quantitative atlas of mitotic phosphorylation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Comparative conservation analysis of the human mitotic phosphoproteome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic Sequence Disorder

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Inhibition of ZAP-70 kinase activity via an analog-sensitive allele blocks T cell receptor and CD28 superagonist signaling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Signaling networks assembled by oncogenic EGFR and c-Met

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Profiling of UV-induced ATM/ATR signaling pathways.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Recognizing and exploiting differences between RNAi and small-molecule inhibitors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

PhosphoBlast, a computational tool for comparing phosphoprotein signatures among large datasets

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Mapping protein post-translational modifications with mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Chemical genetics reveals the requirement for Polo-like kinase 1 activity in positioning RhoA and triggering cytokinesis in human cells.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Cell-cycle-dependent phosphorylation of the nuclear pore Nup107-160 subcomplex

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Large-scale phosphorylation analysis of mouse liver

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Proteomic applications of protein quantification by isotope-dilution mass spectrometry.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Phosphoprotein analysis: from proteins to proteomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Reading protein modifications with interaction domains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Cell-signalling dynamics in time and space

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Combining chemical genetics and proteomics to identify protein kinase substrates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Kinomics: methods for deciphering the kinome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Multisite protein modification and intramolecular signaling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Analysis of protein phosphorylation by mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Mass spectrometric contributions to the practice of phosphorylation site mapping through 2003: a literature review

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

SKAR is a specific target of S6 kinase 1 in cell growth control

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Large-scale characterization of HeLa cell nuclear phosphoproteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Quantitative analysis of signaling networks.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Mutational analysis of the tyrosine phosphatome in colorectal cancers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Global analysis of protein expression in yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

N-Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Multisite phosphorylation provides sophisticated regulation of transcription factors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Protein kinases--the major drug targets of the twenty-first century?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

The origins of protein phosphorylation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Analysis of phosphorylated proteins and peptides by mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Functional modules in biological signalling networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Oncogenic kinase signalling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Signaling networks: the origins of cellular multitasking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Protein phosphorylation in signaling--50 years and counting

28 July 2018

1 reference

The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture.

21 January 2018

1 reference

Phosphoproteome analysis of Drosophila melanogaster embryos

21 January 2018

1 reference

Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo

21 January 2018

1 reference

Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.

21 January 2018

1 reference

Mechanisms of specificity in protein phosphorylation

21 January 2018

1 reference

Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach

21 January 2018

1 reference

In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution

21 January 2018

1 reference

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases

21 January 2018

1 reference

Cell biology. Evolving cell signals

21 January 2018

1 reference

Oncogenic re-wiring of cellular signaling pathways

21 January 2018

1 reference

ZIP codes for delivering SH2 domains

21 January 2018

1 reference

Physicochemical modelling of cell signalling pathways.

21 January 2018

1 reference

Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini

21 January 2018

1 reference

Protein tyrosine phosphatases in the human genome

21 January 2018

1 reference

Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance.

21 January 2018

1 reference

Highly selective enrichment of phosphorylated peptides using titanium dioxide

21 January 2018

1 reference

Reproducible isolation of distinct, overlapping segments of the phosphoproteome

21 January 2018

1 reference

Hitting the target: emerging technologies in the search for kinase substrates

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Tyrosine phosphorylation in cell signaling and disease

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2931417

Phosphoproteome Analysis of Fission Yeast

28 October 2018

1 reference

Phosphoprotein Isotope-Coded Affinity Tags: Application to the Enrichment and Identification of Low-Abundance Phosphoproteins

21 January 2018

1 reference

Measurement of stoichiometry of protein phosphorylation by biosynthetic labeling

21 January 2018

1 reference

12 December 2020

Meeting report: targeting the kinome--20 years of tyrosine kinase inhibitor research in Basel

1 reference

12 December 2020

Non-functional phosphorylations?

1 reference

12 December 2020

Phosphorylation of recombinant human ATP:citrate lyase by cAMP-dependent protein kinase abolishes homotropic allosteric regulation of the enzyme by citrate and increases the enzyme activity. Allosteric activation of ATP:citrate lyase by phosphorylat

1 reference

12 December 2020

Identifiers

DOI

10.1586/EPR.09.84

1 reference

31 July 2017

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31 July 2017

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