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

SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments

(2012) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

(2011) T. Glatter et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda 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

Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis

(2011) Damian Fermin et al.   PROTEOMICS

Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline

(2011) David C. Trudgian et al.   PROTEOMICS

Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins

(2010) Ying Zhang et al.   ANALYTICAL CHEMISTRY

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

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

The Bait Compatibility Index: Computational Bait Selection for Interaction Proteomics Experiments

(2010) Sudipto Saha et al.   JOURNAL OF PROTEOME RESEARCH

Modeling Contaminants in AP-MS/MS Experiments

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

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

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

(2010) Nina C. Hubner et al.   METHODS

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes

(2010) Amber L. Mosley et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

(2010) Hyungwon Choi et al.   Molecular Systems Biology

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

ProHits: integrated software for mass spectrometry–based interaction proteomics

(2010) Guomin Liu et al.   NATURE BIOTECHNOLOGY

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Streamlined analysis schema for high-throughput identification of endogenous protein complexes

(2010) A. Malovannaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Evaluation of Clustering Algorithms for Protein Complex and Protein Interaction Network Assembly

(2009) Mihaela E. Sardiu et al.   JOURNAL OF PROTEOME RESEARCH

High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes

(2009) Philippe Cloutier et al.   METHODS

IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient Peptide Alignment Approach and Spectral Data Validation

(2009) Chih-Chiang Tsou et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics

(2009) Mihaela E. Sardiu et al.   PLoS One

Empirical Bayes Analysis of Quantitative Proteomics Experiments

(2009) Adam A. Margolin et al.   PLoS One

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

From pull-down data to protein interaction networks and complexes with biological relevance

(2008) B. Zhang et al.   BIOINFORMATICS

Mapping the human protein interactome

(2008) Daniel Figeys   CELL RESEARCH

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

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

Spectral Index for Assessment of Differential Protein Expression in Shotgun Proteomics

(2008) Xiaoyun Fu et al.   JOURNAL OF PROTEOME RESEARCH

Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose RepressionSaccharomyces cerevisiaeStrains: The Comparison of Two Quantitative Methods

(2008) Renata Usaite et al.   JOURNAL OF PROTEOME RESEARCH

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

(2008) Hyungwon Choi et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

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

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

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

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

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

Predicting Co-Complexed Protein Pairs from Heterogeneous Data

(2008) Jian Qiu et al.   PLoS Computational Biology