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

Unraveling the dynamics of protein interactions with quantitative mass spectrometry

(2011) Sreenivasa R. Ramisetty et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

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

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

A roadmap to generate renewable protein binders to the human proteome

(2011) Karen Colwill et al.   NATURE METHODS

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

In-Gel Digestion for Mass Spectrometric Characterization of RNA from Fluorescently Stained Polyacrylamide Gels

(2010) Masato Taoka et al.   ANALYTICAL CHEMISTRY

Upf1 Senses 3′UTR Length to Potentiate mRNA Decay

(2010) J. Robert Hogg et al.   CELL

Role of spectral counting in quantitative proteomics

(2010) Deborah H Lundgren et al.   Expert Review of Proteomics

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

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

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

(2010) David J. Dilworth et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

(2010) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

The AAA-ATPase Rea1 Drives Removal of Biogenesis Factors during Multiple Stages of 60S Ribosome Assembly

(2010) Jochen Baßler et al.   MOLECULAR CELL

Defining the budding yeast chromatin-associated interactome

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

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

(2010) Jelle Van Leene 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

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2010) Geneviève Di Tomasso et al.   NUCLEIC ACIDS RESEARCH

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

(2010) M. E. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) C. S. Muller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) B. Slobodin et al.   RNA

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

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

A P4-ATPase Protein Interaction Network Reveals a Link between Aminophospholipid Transport and Phosphoinositide Metabolism

(2009) Catheleyne F. Puts et al.   JOURNAL OF PROTEOME RESEARCH

Establishment of a Protein Frequency Library and Its Application in the Reliable Identification of Specific Protein Interaction Partners

(2009) Séverine Boulon et al.   MOLECULAR & CELLULAR PROTEOMICS

A Targeted Spatial-Temporal Proteomics Approach Implicates Multiple Cellular Trafficking Pathways in Human Cytomegalovirus Virion Maturation

(2009) Nathaniel J. Moorman et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Proteomics by Metabolic Labeling of Model Organisms

(2009) Joost W. Gouw et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2009) Timo Glatter et al.   Molecular Systems Biology

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

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

(2009) Paola Picotti et al.   NATURE METHODS

Protein-Protein Interactions of Tandem Affinity Purified Protein Kinases from Rice

(2009) Jai S. Rohila et al.   PLoS One

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors

(2009) J. Schwenk et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

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

(2008) J. C. Marioni et al.   GENOME RESEARCH

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

(2008) G. Mittler et al.   GENOME RESEARCH

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

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

Characterization of the Human COP9 Signalosome Complex Using Affinity Purification and Mass Spectrometry

(2008) Lei Fang et al.   JOURNAL OF PROTEOME RESEARCH

Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry

(2008) Haizhen Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

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

(2008) Qun Pan et al.   NATURE GENETICS

Erratum: Corrigendum: Identification of cross-linked peptides from large sequence databases

(2008) Oliver Rinner et al.   NATURE METHODS

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

(2008) Ina Poser et al.   NATURE METHODS

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

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2008) Alice Lebreton et al.   NUCLEIC ACIDS RESEARCH

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

(2008) John M. Asara et al.   PROTEOMICS

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE