Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes (Q38010660)

26 August 2017

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Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes (English)

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26 August 2017

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Marlene Oeffinger

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26 August 2017

publication date

1 May 2012

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26 August 2017

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26 August 2017

volume

12

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26 August 2017

issue

10

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26 August 2017

page(s)

1591-1608

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Functional organization of the yeast proteome by systematic analysis of protein complexes

26 August 2017

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Dynamic modularity in protein interaction networks predicts breast cancer outcome

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The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information

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On the number of protein-protein interactions in the yeast proteome

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Conserved network motifs allow protein-protein interaction prediction.

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Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks

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Proteome survey reveals modularity of the yeast cell machinery

21 January 2018

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

21 January 2018

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Mlh1 is unique among mismatch repair proteins in its ability to promote crossing-over during meiosis

21 January 2018

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The protein kinases of Caenorhabditis elegans: a model for signal transduction in multicellular organisms

21 January 2018

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RA-GEF, a novel Rap1A guanine nucleotide exchange factor containing a Ras/Rap1A-associating domain, is conserved between nematode and humans

21 January 2018

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PDZ domain proteins: scaffolds for signaling complexes

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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https://api.crossref.org/works/10.1002%2FPMIC.201100509

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

Fluorescent proteins as proteomic probes.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

Chromatin assembly in a yeast whole-cell extract.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

A global protein kinase and phosphatase interaction network in yeast.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

Van der Waals interactions involving proteins

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Long-range and short-range mechanisms of hydrophobic attraction and hydrophilic repulsion in specific and aspecific interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

Targeted proteomic study of the cyclin-Cdk module.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100509

The molecular architecture of the nuclear pore complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Defining the budding yeast chromatin-associated interactome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

High-throughput mapping of a dynamic signaling network in mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Quantitative proteomics of the Cav2 channel nano-environments in the mammalian brain.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

The yeast nuclear pore complex: composition, architecture, and transport mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Toward a high-resolution view of nuclear dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Defining the human deubiquitinating enzyme interaction landscape

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Network organization of the human autophagy system

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Systematic analysis of human protein complexes identifies chromosome segregation proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Large-scale mapping of human protein-protein interactions by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Protein-protein interactions of tandem affinity purified protein kinases from rice

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Modulation of the Ras/Raf/MEK/ERK pathway by Ca(2+), and calmodulin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Highly efficient tandem affinity purification of trypanosome protein complexes based on a novel epitope combination

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A modified tandem affinity purification tag technique for the purification of protein complexes in mammalian cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

An efficient protein complex purification method for functional proteomics in higher eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-CDK complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Human rhinovirus 3C protease: cloning and expression of an active form in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin-RING ubiquitin-ligase complex SCF-Cdc34.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Affinity-purification mass spectrometry (AP-MS) of serine/threonine phosphatases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Unraveling the dynamics of protein interactions with quantitative mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Role of spectral counting in quantitative proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Analysis of protein complexes using mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Proteins connecting the nuclear pore complex with the nuclear interior

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Components of coated vesicles and nuclear pore complexes share a common molecular architecture

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

The FLAG peptide, a versatile fusion tag for the purification of recombinant proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Purification of telomerase from Euplotes aediculatus: requirement of a primer 3' overhang

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

StreptoTag: a novel method for the isolation of RNA-binding proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Capturing splicing complexes to study structure and mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Upf1 senses 3'UTR length to potentiate mRNA decay

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Dissecting the regulatory circuitry of a eukaryotic genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Single-RNA counting reveals alternative modes of gene expression in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Global analysis of protein expression in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Comprehensive analysis of diverse ribonucleoprotein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Dynamic Complex Formation During the Yeast Cell Cycle

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

The AAA-ATPase Rea1 drives removal of biogenesis factors during multiple stages of 60S ribosome assembly.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Quantitative proteomics by metabolic labeling of model organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Decoding signalling networks by mass spectrometry-based proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Nucleolar proteome dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Characterization of the human COP9 signalosome complex using affinity purification and mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

In-gel digestion for mass spectrometric characterization of RNA from fluorescently stained polyacrylamide gels.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A P4-ATPase protein interaction network reveals a link between aminophospholipid transport and phosphoinositide metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Proteome organization in a genome-reduced bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A roadmap to generate renewable protein binders to the human proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

Probing the structure and function of U2 snRNP with antisense oligonucleotides made of 2'-OMe RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

An affinity oligonucleotide displacement strategy to purify ribonucleoprotein complexes applied to human telomerase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

The ARiBo tag: a reliable tool for affinity purification of RNAs under native conditions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100509

21 January 2018

Identifiers

DOI

10.1002/PMIC.201100509

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26 August 2017

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