Affinity-purification coupled to mass spectrometry: Basic principles and strategies

Computational structural analysis of protein interactions and networks

(2012) Yogesh Hooda et al.   PROTEOMICS

Molecular interaction databases

(2012) Sandra Orchard   PROTEOMICS

Two steps forward-one step back: Advances in affinity purification mass spectrometry of macromolecular complexes

(2012) Marlene Oeffinger   PROTEOMICS

Mapping physical interactions within chromatin by proteomic approaches

(2012) Jean-Philippe Lambert et al.   PROTEOMICS

Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry

(2012) Laura Trinkle-Mulcahy   PROTEOMICS

Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays

(2012) Pascal Braun   PROTEOMICS

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

(2012) Alexey I. Nesvizhskii   PROTEOMICS

Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

(2011) Jeroen Kool et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

Drug target deconvolution by chemical proteomics

(2011) Manfred Raida   CURRENT OPINION IN CHEMICAL BIOLOGY

Mass Spectrometric Strategies and Their Applications for Molecular Mass Determination of Recombinant Therapeutic Proteins

(2011) Marina Carini et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

High-sensitive protein analysis by FESI-CE-MALDI-MS

(2011) Mohammad Reza Pourhaghighi et al.   ELECTROPHORESIS

Identification of a host cell target for the thiazolide class of broad-spectrum anti-parasitic drugs

(2011) Joachim Müller et al.   EXPERIMENTAL PARASITOLOGY

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

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

Proteomic Studies of Syk-Interacting Proteins Using a Novel Amine-Specific Isotope Tag and GFP Nanotrap

(2011) Jacob A. Galan et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis

(2011) Helmut Hofemeister et al.   METHODS

High throughput gene trapping and postinsertional modifications of gene trap alleles

(2011) Frank Schnütgen et al.   METHODS

Systematic exploration of essential yeast gene function with temperature-sensitive mutants

(2011) Zhijian Li et al.   NATURE BIOTECHNOLOGY

A century of mass spectrometry: from atoms to proteomes

(2011) John R Yates III   NATURE METHODS

A roadmap to generate renewable protein binders to the human proteome

(2011) Karen Colwill et al.   NATURE METHODS

Subunit Stoichiometry, Evolution, and Functional Implications of an Asymmetric Plant Plastid ClpP/R Protease Complex inArabidopsis

(2011) Paul Dominic B. Olinares et al.   PLANT CELL

Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough

(2011) Swapnil R. Chhabra et al.   PLoS One

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

(2011) Dana V. Skarra et al.   PROTEOMICS

A cost-benefit analysis of multidimensional fractionation of affinity purification-mass spectrometry samples

(2011) Wade H. Dunham et al.   PROTEOMICS

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Modeling Contaminants in AP-MS/MS Experiments

(2010) Mathieu Lavallée-Adam et al.   JOURNAL OF PROTEOME RESEARCH

Recombineering BAC transgenes for protein tagging

(2010) Giovanni Ciotta et al.   METHODS

Extracting gene function from protein–protein interactions using Quantitative BAC InteraCtomics (QUBIC)

(2010) Nina C. Hubner et al.   METHODS

A Lentiviral Functional Proteomics Approach Identifies Chromatin Remodeling Complexes Important for the Induction of Pluripotency

(2010) Anthony B. Mak et al.   MOLECULAR & CELLULAR PROTEOMICS

The Protein Interaction Network of the Human Transcription Machinery Reveals a Role for the Conserved GTPase RPAP4/GPN1 and Microtubule Assembly in Nuclear Import and Biogenesis of RNA Polymerase II

(2010) Diane Forget et al.   MOLECULAR & CELLULAR PROTEOMICS

Defining the budding yeast chromatin-associated interactome

(2010) Jean-Philippe Lambert et al.   Molecular Systems Biology

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

(2010) J. R. A. Hutchins et al.   SCIENCE

Affinity Purification of an Archaeal DNA Replication Protein Network

(2010) Z. Li et al.   mBio

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases

(2009) M. H. Olma et al.   JOURNAL OF CELL SCIENCE

From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part II 1985-2000

(2009) Emilio Gelpí   JOURNAL OF MASS SPECTROMETRY

Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

(2009) Esperanza Fernández et al.   Molecular Systems Biology

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

(2009) Timo Glatter et al.   Molecular Systems Biology

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

Trim24 targets endogenous p53 for degradation

(2009) Kendra Allton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput generation of tagged stable cell lines for proteomic analysis

(2009) Jorge Z. Torres et al.   PROTEOMICS

Epitope tagging

(2008) Bill Brizzard   BIOTECHNIQUES

High confidence determination of specific protein–protein interactions using quantitative mass spectrometry

(2008) Michiel Vermeulen et al.   CURRENT OPINION IN BIOTECHNOLOGY

The interaction network of the chaperonin CCT

(2008) Carien Dekker et al.   EMBO JOURNAL

PP4R4/KIAA1622 Forms a Novel Stable Cytosolic Complex with Phosphoprotein Phosphatase 4

(2008) Ginny I. Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2008) Laura Trinkle-Mulcahy et al.   JOURNAL OF CELL BIOLOGY

From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part I 1965-1984

(2008) Emilio Gelpí   JOURNAL OF MASS SPECTROMETRY

A Targeted Proteomic Analysis of the Ubiquitin-Like Modifier Nedd8 and Associated Proteins

(2008) Jeffrey Jones et al.   JOURNAL OF PROTEOME RESEARCH

A PP2A Phosphatase High Density Interaction Network Identifies a Novel Striatin-interacting Phosphatase and Kinase Complex Linked to the Cerebral Cavernous Malformation 3 (CCM3) Protein

(2008) Marilyn Goudreault et al.   MOLECULAR & CELLULAR PROTEOMICS

Combined Use of RNAi and Quantitative Proteomics to Study Gene Function in Drosophila

(2008) Tiziana Bonaldi et al.   MOLECULAR CELL

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

(2008) Ina Poser et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

(2008) M. E. Sardiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA