The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

(2013) Markku Varjosalo et al.   NATURE METHODS

Viral immune modulators perturb the human molecular network by common and unique strategies

(2012) Andreas Pichlmair et al.   NATURE

A method to resolve the composition of heterogeneous affinity-purified protein complexes assembled around a common protein by chemical cross-linking, gel electrophoresis and mass spectrometry

(2012) Elena L Rudashevskaya et al.   Nature Protocols

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

(2012) Laura Trinkle-Mulcahy   PROTEOMICS

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

(2012) Alexey I. Nesvizhskii   PROTEOMICS

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

(2012) Wade H. Dunham et al.   PROTEOMICS

Coupled Activation and Degradation of eEF2K Regulates Protein Synthesis in Response to Genotoxic Stress

(2012) F. Kruiswijk et al.   Science Signaling

Structure-Function Analysis of Core STRIPAK Proteins

(2011) Michelle J. Kean et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Examining the Complexity of Human RNA Polymerase Complexes using HaloTag Technology Coupled to Label Free Quantitative Proteomics

(2011) Danette L. Daniels et al.   JOURNAL OF PROTEOME RESEARCH

Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling

(2011) Wim de Lau et al.   NATURE

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Wade H. Dunham et al.   PROTEOMICS

BioMart: driving a paradigm change in biological data management

(2011) A. Kasprzyk   Database-The Journal of Biological Databases and Curation

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

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

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

A WD-Repeat Protein Stabilizes ORC Binding to Chromatin

(2010) Zhen Shen et al.   MOLECULAR CELL

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

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

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

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