Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation

(2016) Christopher J. Tape et al.   CELL

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Characterizing Protein–Protein Interactions Using Mass Spectrometry: Challenges and Opportunities

(2016) Arne H. Smits et al.   TRENDS IN BIOTECHNOLOGY

A draft map of the mouse pluripotent stem cell spatial proteome

(2016) Andy Christoforou et al.   Nature Communications

Global, quantitative and dynamic mapping of protein subcellular localization

(2016) Daniel N Itzhak et al.   eLife

Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer

(2015) Brian K. Erickson et al.   ANALYTICAL CHEMISTRY

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions

(2015) Faraz K. Mardakheh et al.   DEVELOPMENTAL CELL

Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments

(2015) Nichollas E. Scott et al.   Journal of Proteomics

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Single-cell and multivariate approaches in genetic perturbation screens

(2014) Prisca Liberali et al.   NATURE REVIEWS GENETICS

iFASP: Combining Isobaric Mass Tagging with Filter-Aided Sample Preparation

(2013) Gary S. McDowell et al.   JOURNAL OF PROTEOME RESEARCH

Predicting functional gene interactions with the hierarchical interaction score

(2013) Berend Snijder et al.   NATURE METHODS

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method

(2010) Jacek R. Wiśniewski et al.   ANALYTICAL BIOCHEMISTRY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions

(2010) Matthew W. B. Trotter et al.   PROTEOMICS

A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage

(2009) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE