The emergence of proteome-wide technologies: systematic analysis of proteins comes of age

Analyzing protein–protein interactions in the post-interactomic era. Are we ready for the endgame?

(2014) Nils Johnsson   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease

(2014) Puneet Talwar et al.   BMC GENOMICS

Discovering the Hippo pathway protein-protein interactome

(2014) Iván M Moya et al.   CELL RESEARCH

RNA- and Antibody-Based Profiling of the Human Proteome with Focus on Chromosome 19

(2014) Charlotte Stadler et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture

(2014) John D. Bagert et al.   MOLECULAR & CELLULAR PROTEOMICS

The binary protein-protein interaction landscape of Escherichia coli

(2014) Seesandra V Rajagopala et al.   NATURE BIOTECHNOLOGY

Analysis of the Robustness of Network-Based Disease-Gene Prioritization Methods Reveals Redundancy in the Human Interactome and Functional Diversity of Disease-Genes

(2014) Emre Guney et al.   PLoS One

SILAC-based proteomic quantification of chemoattractant-induced cytoskeleton dynamics on a second to minute timescale

(2014) Grzegorz J. Sobczyk et al.   Nature Communications

Plant Protein Interactomes

(2013) Pascal Braun et al.   Annual Review of Plant Biology

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

An introduction to mass cytometry: fundamentals and applications

(2013) Scott D. Tanner et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Profiling of Ubiquitin-like Modifications Reveals Features of Mitotic Control

(2013) Yifat Merbl et al.   CELL

Protein–protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches

(2013) Armand G. Ngounou Wetie et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Single-cell imaging mass spectrometry

(2013) Melissa K Passarelli et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Mass spectrometry supported determination of protein complex structure

(2013) Thomas Walzthoeni et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The proteomics and interactomics of human erythrocytes

(2013) Steven R Goodman et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Towards Lipidomics of Low-Abundant Species for Exploring Tumor Heterogeneity Guided by High-Resolution Mass Spectrometry Imaging

(2013) Jonathan Cimino et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Formation and dissociation of proteasome storage granules are regulated by cytosolic pH

(2013) Lee Zeev Peters et al.   JOURNAL OF CELL BIOLOGY

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

(2013) Michal Breker et al.   JOURNAL OF CELL BIOLOGY

Life in the balance – a mechanistic view of the crosstalk between autophagy and apoptosis

(2013) Assaf D. Rubinstein et al.   JOURNAL OF CELL SCIENCE

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

(2013) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

The Human Proteome Organization Chromosome 6 Consortium: Integrating chromosome-centric and biology/disease driven strategies

(2013) C.H. Borchers et al.   Journal of Proteomics

Exploring mitochondrial system properties of neurodegenerative diseases through interactome mapping

(2013) James Vlasblom et al.   Journal of Proteomics

Quantitative Phosphoproteomics Reveals the Role of Protein Arginine Phosphorylation in the Bacterial Stress Response

(2013) Andreas Schmidt et al.   MOLECULAR & CELLULAR PROTEOMICS

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Analysis of Condition-specific Subcellular Protein Distribution and Abundance

(2013) Sunhee Jung et al.   MOLECULAR & CELLULAR PROTEOMICS

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Initial Quantitative Proteomic Map of 28 Mouse Tissues Using the SILAC Mouse

(2013) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

The Translational Landscape of the Mammalian Cell Cycle

(2013) Craig R. Stumpf et al.   MOLECULAR CELL

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Construction of human activity-based phosphorylation networks

(2013) R. H. Newman et al.   Molecular Systems Biology

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

NetGestalt: integrating multidimensional omics data over biological networks

(2013) Zhiao Shi et al.   NATURE METHODS

QuaNCAT: quantitating proteome dynamics in primary cells

(2013) Andrew J M Howden et al.   NATURE METHODS

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Integration of miRNA and Protein Profiling Reveals Coordinated Neuroadaptations in the Alcohol-Dependent Mouse Brain

(2013) Giorgio Gorini et al.   PLoS One

A chemostat array enables the spatio-temporal analysis of the yeast proteome

(2013) N. Denervaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass spectrometry-based metabolomics of single yeast cells

(2013) A. J. Ibanez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Expression Under Pressure

(2013) C. Vogel   SCIENCE

Direct Proteomic Quantification of the Secretome of Activated Immune Cells

(2013) F. Meissner et al.   SCIENCE

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis

(2013) A. M. Robitaille et al.   SCIENCE

Single-Cell Metabolomics: Analytical and Biological Perspectives

(2013) R. Zenobi   SCIENCE

Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

(2013) Teck Yew Low et al.   Cell Reports

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

(2013) Louis-François Handfield et al.   PLoS Computational Biology

Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

(2013) Yan Zhang et al.   PLoS Computational Biology

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Adaptation to stress in yeast: to translate or not?: Figure 1

(2012) Clare E. Simpson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Progress toward single cell metabolomics

(2012) Stanislav S Rubakhin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Proteome Dynamics: Revisiting Turnover with a Global Perspective

(2012) Amy J. Claydon et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Tandem fluorescent protein timers for in vivo analysis of protein dynamics

(2012) Anton Khmelinskii et al.   NATURE BIOTECHNOLOGY

Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress

(2012) Johnny M. Tkach et al.   NATURE CELL BIOLOGY

Using bleach-chase to measure protein half-lives in living cells

(2012) Naama Geva-Zatorsky et al.   Nature Protocols

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT)

(2012) Jennifer J. L. Hodas et al.   PROTEOMICS

Protein turnover: Measurement of proteome dynamics by whole animal metabolic labelling with stable isotope labelled amino acids

(2012) Amy J. Claydon et al.   PROTEOMICS

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Mass spectrometry-based proteomics for systems biology

(2011) Eduard Sabidó et al.   CURRENT OPINION IN BIOTECHNOLOGY

Getting the whole picture: combining throughput with content in microscopy

(2011) N. Rimon et al.   JOURNAL OF CELL SCIENCE

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic Analysis of Protein Pools, Isoforms, and Modifications Affecting Turnover and Subcellular Localization

(2011) Yasmeen Ahmad et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

Deep proteome and transcriptome mapping of a human cancer cell line

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

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

Quantification of mRNA and protein and integration with protein turnover in a bacterium

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

Absolute quantification of microbial proteomes at different states by directed mass spectrometry

(2011) A. Schmidt et al.   Molecular Systems Biology

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Profiling metabolites and peptides in single cells

(2011) Stanislav S Rubakhin et al.   NATURE METHODS

Investigating the role of FGF-2 in stem cell maintenance by global phosphoproteomics profiling

(2011) Adja D. Zoumaro-Djayoon et al.   PROTEOMICS

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Proteome Half-Life Dynamics in Living Human Cells

(2011) E. Eden et al.   SCIENCE

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses

(2010) Naama Geva-Zatorsky et al.   CELL

Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection

(2010) Lanying Zeng et al.   CELL

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

(2010) Dorota F. Zielinska et al.   CELL

Next generation microfluidic platforms for high-throughput protein biochemistry

(2010) Sebastian J Maerkl   CURRENT OPINION IN BIOTECHNOLOGY

High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection

(2010) S. J. Cooper et al.   GENOME RESEARCH

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease

(2010) M. Soler-Lopez et al.   GENOME RESEARCH

In vivo quantification of protein–protein interactions in Saccharomyces cerevisiae using bimolecular fluorescence complementation assay

(2010) Min-Kyung Sung et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Multitagging Proteomic Strategy to Estimate Protein Turnover Rates in Dynamic Systems

(2010) Karthik P. Jayapal et al.   JOURNAL OF PROTEOME RESEARCH

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Protein abundances are more conserved than mRNA abundances across diverse taxa

(2010) Jon M. Laurent et al.   PROTEOMICS

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Global analysis of the yeast osmotic stress response by quantitative proteomics

(2009) Boumediene Soufi et al.   Molecular BioSystems

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells

(2009) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays

(2009) Yifat Merbl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE

Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging

(2009) Jennifer Lippincott-Schwartz et al.   TRENDS IN CELL BIOLOGY

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

(2008) S. C. Popescu et al.   GENES & DEVELOPMENT

Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC

(2008) Mary K. Doherty et al.   JOURNAL OF PROTEOME RESEARCH

Monitoring Protein-Protein Interactions between the Mammalian Integral Membrane Transporters and PDZ-interacting Partners Using a Modified Split-ubiquitin Membrane Yeast Two-hybrid System

(2008) Serge M. Gisler et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Translational control of localized mRNAs: restricting protein synthesis in space and time

(2008) Florence Besse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Diversity of degradation signals in the ubiquitin–proteasome system

(2008) Tommer Ravid et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biochemical approaches for discovering protein-protein interactions

(2008) Jan A. Miernyk et al.   PLANT JOURNAL

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

(2008) M. E. Hillenmeyer et al.   SCIENCE

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE