Next-generation proteomics: towards an integrative view of proteome dynamics. (Q34315255)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

review article

1 reference

title

Next-generation proteomics: towards an integrative view of proteome dynamics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

Javier Munoz

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

Albert J.R. Heck

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

author name string

A F Maarten Altelaar

1

1 reference

1 August 2017

Albert J R Heck

3

1 reference

1 August 2017

4 December 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

published in

Nature Reviews Genetics

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

volume

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

page(s)

35-48

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/nrg3356

19 February 2020

exact match

0 references

cites work

Central Dogma of Molecular Biology

1 reference

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts

31 March 2020

1 reference

A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?

31 March 2020

1 reference

31 March 2020

1 reference

Mass spectrometry-based proteomics and network biology

31 March 2020

1 reference

Is proteomics the new genomics?

31 March 2020

1 reference

Quantitative, high-resolution proteomics for data-driven systems biology

31 March 2020

1 reference

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

31 March 2020

1 reference

The phosphoproteomics data explosion.

31 March 2020

1 reference

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

31 March 2020

1 reference

Deep proteome and transcriptome mapping of a human cancer cell line

31 March 2020

1 reference

The quantitative proteome of a human cell line.

31 March 2020

1 reference

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

31 March 2020

1 reference

Analysis and validation of proteomic data generated by tandem mass spectrometry

31 March 2020

1 reference

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

31 March 2020

1 reference

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

31 March 2020

1 reference

Database independent proteomics analysis of the ostrich and human proteome.

31 March 2020

1 reference

De novo sequencing and homology searching

31 March 2020

1 reference

Global quantification of mammalian gene expression control

31 March 2020

1 reference

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

31 March 2020

1 reference

Protease bias in absolute protein quantitation.

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Instant spectral assignment for advanced decision tree-driven mass spectrometry

31 March 2020

1 reference

Benchmarking stable isotope labeling based quantitative proteomics

31 March 2020

1 reference

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

31 March 2020

1 reference

SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function

31 March 2020

1 reference

aPKC phosphorylates NuMA-related LIN-5 to position the mitotic spindle during asymmetric division.

31 March 2020

1 reference

Super-SILAC mix for quantitative proteomics of human tumor tissue

31 March 2020

1 reference

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics.

31 March 2020

1 reference

Proteomic cornerstones of hematopoietic stem cell differentiation: distinct signatures of multipotent progenitors and myeloid committed cells

31 March 2020

1 reference

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

31 March 2020

1 reference

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

31 March 2020

1 reference

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

31 March 2020

1 reference

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap

31 March 2020

1 reference

Distinguishing protein-coding and noncoding genes in the human genome

31 March 2020

1 reference

Global transcription in pluripotent embryonic stem cells.

31 March 2020

1 reference

The reality of pervasive transcription

31 March 2020

1 reference

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

31 March 2020

1 reference

Widespread RNA and DNA sequence differences in the human transcriptome.

31 March 2020

1 reference

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"

31 March 2020

1 reference

Systems-level dynamic analyses of fate change in murine embryonic stem cells

31 March 2020

1 reference

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors

31 March 2020

1 reference

Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures

31 March 2020

1 reference

Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells

31 March 2020

1 reference

Lab-specific gene expression signatures in pluripotent stem cells

31 March 2020

1 reference

Proteomic and phosphoproteomic comparison of human ES and iPS cells

31 March 2020

1 reference

Role of mass spectrometry-based proteomics in the study of cellular reprogramming and induced pluripotent stem cells

31 March 2020

1 reference

Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides

31 March 2020

1 reference

The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics

31 March 2020

1 reference

Advancing cell biology through proteomics in space and time (PROSPECTS).

31 March 2020

1 reference

Immobilized gallium(III) affinity chromatography of phosphopeptides

31 March 2020

1 reference

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

31 March 2020

1 reference

Selective Isolation at the Femtomole Level of Phosphopeptides from Proteolytic Digests Using 2D-NanoLC-ESI-MS/MS and Titanium Oxide Precolumns

31 March 2020

1 reference

Immunoaffinity profiling of tyrosine phosphorylation in cancer cells

31 March 2020

1 reference

A tissue-specific atlas of mouse protein phosphorylation and expression

31 March 2020

1 reference

Systematic discovery of TLR signaling components delineates viral-sensing circuits

31 March 2020

1 reference

Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling

31 March 2020

1 reference

Phosphorylation dynamics during early differentiation of human embryonic stem cells.

31 March 2020

1 reference

Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment

31 March 2020

1 reference

Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases

31 March 2020

1 reference

Non-functional phosphorylations?

31 March 2020

1 reference

A large-scale method to measure absolute protein phosphorylation stoichiometries

31 March 2020

1 reference

Phosphorylation sites of higher stoichiometry are more conserved

31 March 2020

1 reference

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

31 March 2020

1 reference

A cell cycle phosphoproteome of the yeast centrosome

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates.

31 March 2020

1 reference

Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells

31 March 2020

1 reference

Lysine acetylation targets protein complexes and co-regulates major cellular functions

31 March 2020

1 reference

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

31 March 2020

1 reference

Proteomic snapshot of the EGF-induced ubiquitin network

31 March 2020

1 reference

A novel proteomics approach to identify SUMOylated proteins and their modification sites in human cells

31 March 2020

1 reference

Determination of site-specific glycan heterogeneity on glycoproteins.

31 March 2020

1 reference

Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints.

31 March 2020

1 reference

A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles

31 March 2020

1 reference

Control of Smad7 stability by competition between acetylation and ubiquitination

31 March 2020

1 reference

Inhibition of DNA binding of Sox2 by the SUMO conjugation

31 March 2020

1 reference

Reading protein modifications with interaction domains

31 March 2020

1 reference

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.

31 March 2020

1 reference

Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response

31 March 2020

1 reference

An empirical framework for binary interactome mapping

31 March 2020

1 reference

Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses

31 March 2020

1 reference

Mass spectrometry-based functional proteomics: from molecular machines to protein networks

31 March 2020

1 reference

Proteome survey reveals modularity of the yeast cell machinery

31 March 2020

1 reference

Analysis of protein complexes using mass spectrometry

31 March 2020

1 reference

Comparative assessment of large-scale data sets of protein-protein interactions

31 March 2020

1 reference

High-quality binary protein interaction map of the yeast interactome network

31 March 2020

1 reference

An experimentally derived confidence score for binary protein-protein interactions

31 March 2020

1 reference

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

31 March 2020

1 reference

A protein complex network of Drosophila melanogaster

31 March 2020

1 reference

Defining the human deubiquitinating enzyme interaction landscape

31 March 2020

1 reference

A global protein kinase and phosphatase interaction network in yeast.

31 March 2020

1 reference

Network organization of the human autophagy system

31 March 2020

1 reference

Global landscape of HIV-human protein complexes

31 March 2020

1 reference

Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection

31 March 2020

1 reference

Analysis of the human endogenous coregulator complexome.

31 March 2020

1 reference

A generic protein purification method for protein complex characterization and proteome exploration

31 March 2020

1 reference

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

31 March 2020

1 reference

Systematic analysis of human protein complexes identifies chromosome segregation proteins

31 March 2020

1 reference

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

31 March 2020

1 reference

A census of human soluble protein complexes

31 March 2020

1 reference

A high-throughput approach for measuring temporal changes in the interactome

31 March 2020

1 reference

Sororin mediates sister chromatid cohesion by antagonizing Wapl

31 March 2020

1 reference

Quantitative interaction proteomics using mass spectrometry

31 March 2020

1 reference

Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics

31 March 2020

1 reference

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

31 March 2020

1 reference

Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex

31 March 2020

1 reference

Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4

31 March 2020

1 reference

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

31 March 2020

1 reference

Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics

31 March 2020

1 reference

Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes

31 March 2020

1 reference

Native mass spectrometry: a bridge between interactomics and structural biology

31 March 2020

1 reference

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

31 March 2020

1 reference

Software for systems biology: from tools to integrated platforms

31 March 2020

1 reference

Differential network biology

31 March 2020

1 reference

Interactome networks and human disease

31 March 2020

1 reference

Exploring the genomes of cancer cells: progress and promise

31 March 2020

1 reference

Personal omics profiling reveals dynamic molecular and medical phenotypes

31 March 2020

1 reference

Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks.

31 March 2020

1 reference

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease.

31 March 2020

1 reference

A targeted proteomics-based pipeline for verification of biomarkers in plasma

31 March 2020

1 reference

31 March 2020

Bring on the biomarkers

1 reference

Cancer biomarkers: closer to delivering on their promise

31 March 2020

1 reference

Recommendations for biomarker identification and qualification in clinical proteomics

31 March 2020

1 reference

Elafin is a biomarker of graft-versus-host disease of the skin

31 March 2020

1 reference

Lung cancer signatures in plasma based on proteome profiling of mouse tumor models

31 March 2020

1 reference

Trends in ultrasensitive proteomics

31 March 2020

1 reference

High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers

31 March 2020

1 reference

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer

31 March 2020

1 reference

Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality

31 March 2020

1 reference

Harnessing the potential of induced pluripotent stem cells for regenerative medicine

31 March 2020

1 reference

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

31 March 2020

1 reference

Targeted proteomic strategy for clinical biomarker discovery

31 March 2020

1 reference

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

31 March 2020

1 reference

The cell in an era of systems biology

31 March 2020

1 reference

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

31 March 2020

1 reference

Evaluation and Optimization of ZIC-HILIC-RP as an Alternative MudPIT Strategy

31 March 2020

1 reference

Highly sensitive proteome analysis of FACS-sorted adult colon stem cells

31 March 2020

1 reference

Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600).

31 March 2020

1 reference

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

31 March 2020

1 reference

Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos.

31 March 2020

1 reference

Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry

31 March 2020

1 reference

Higher-energy C-trap dissociation for peptide modification analysis.

31 March 2020

1 reference

Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast

31 March 2020

1 reference

MDM2-HDAC1-mediated deacetylation of p53 is required for its degradation

31 March 2020

1 reference

Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin

31 March 2020

1 reference

Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23207911

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A combined approach for the localization and tandem affinity purification of protein complexes from metazoans.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23207911

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23207911

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3356

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

19 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23207911%20AND%20SRC:MED&resulttype=core&format=json