Mass Spectrometry–Based Proteomics and Network Biology

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Biological signalling activity measurements using mass spectrometry

(2011) Pedro R. Cutillas et al.   BIOCHEMICAL JOURNAL

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

(2011) Mi-Youn K Brusniak et al.   BMC BIOINFORMATICS

Network News: Innovations in 21st Century Systems Biology

(2011) Adam P. Arkin et al.   CELL

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)

(2011) Joanna Amberger et al.   HUMAN MUTATION

Selected reaction monitoring applied to proteomics

(2011) Sebastien Gallien et al.   JOURNAL OF MASS SPECTROMETRY

Reorganized PKA-AKAP associations in the failing human heart

(2011) Thin-Thin Aye et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Ubiquitinated Proteome: Ready for Global?

(2011) Yi Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

(2011) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

(2011) J. Munoz et al.   Molecular Systems Biology

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

(2011) R. Costenoble et al.   Molecular Systems Biology

Deep proteome and transcriptome mapping of a human cancer cell line

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

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

(2011) K. K. Lee et al.   Molecular Systems Biology

Proteomic snapshot of the EGF-induced ubiquitin network

(2011) E. Argenzio 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

The quantitative proteome of a human cell line

(2011) M. Beck 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

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

A Genome-Wide RNAi Screen Identifies Core Components of the G2-M DNA Damage Checkpoint

(2011) S. Kondo et al.   Science Signaling

The Potential Cost of High-Throughput Proteomics

(2011) F. M. White   Science Signaling

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Recent advances in clustering methods for protein interaction networks

(2010) Jianxin Wang et al.   BMC GENOMICS

Dynamics of Cullin-RING Ubiquitin Ligase Network Revealed by Systematic Quantitative Proteomics

(2010) Eric J. Bennett et al.   CELL

Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers

(2010) Michiel Vermeulen et al.   CELL

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

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

(2010) Dorota F. Zielinska et al.   CELL

Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry

(2010) Lisa M. Wodicka et al.   CHEMISTRY & BIOLOGY

Strategies for the identification of kinase substrates using analog-sensitive kinases

(2010) André Koch et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Global Analysis of Cdc14 Phosphatase Reveals Diverse Roles in Mitotic Processes

(2010) Joanna Bloom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

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

General lessons from large-scale studies to identify human cancer predisposition genes.J Pathol2010; 220: 255-262

(2010) Jean-Baptiste Cazier et al.   JOURNAL OF PATHOLOGY

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

(2010) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Profiling ofN-Acetylated Protein Termini Provides In-depth Insights into the N-terminal Nature of the Proteome

(2010) Andreas O. Helbig et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation

(2010) Benjamin D. Cosgrove et al.   Molecular BioSystems

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

(2010) Hyungwon Choi et al.   Molecular Systems Biology

Dissecting spatio-temporal protein networks driving human heart development and related disorders

(2010) Kasper Lage et al.   Molecular Systems Biology

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

(2010) J. Mok et al.   Science Signaling

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

(2010) A. Bensimon et al.   Science Signaling

Akt-RSK-S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases

(2010) A. Moritz et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

The next-generation sequencing technology and application

(2010) Xiaoguang Zhou et al.   Protein & Cell

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

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 Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

(2009) Eric E. Zhang et al.   CELL

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

Phosphorylation Dynamics during Early Differentiation of Human Embryonic Stem Cells

(2009) Dennis Van Hoof et al.   Cell Stem Cell

Directed mass spectrometry: towards hypothesis-driven proteomics

(2009) Alexander Schmidt et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The phosphoproteomics data explosion

(2009) Simone Lemeer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Revealing promiscuous drug–target interactions by chemical proteomics

(2009) Marcus Bantscheff et al.   DRUG DISCOVERY TODAY

Systems biology: experimental design

(2009) Clemens Kreutz et al.   FEBS Journal

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg 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

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS

A Genomic Strategy to Elucidate Modules of Oncogenic Pathway Signaling Networks

(2009) Jeffrey T. Chang et al.   MOLECULAR CELL

Quantitative Proteomics Reveals a Dynamic Interactome and Phase-Specific Phosphorylation in the Neurospora Circadian Clock

(2009) Christopher L. Baker et al.   MOLECULAR CELL

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

(2009) Timo Glatter et al.   Molecular Systems Biology

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

(2009) Johan Malmström et al.   NATURE

Sensitive multiplexed analysis of kinase activities and activity-based kinase identification

(2009) Kazuishi Kubota et al.   NATURE BIOTECHNOLOGY

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Cell fate decisions are specified by the dynamic ERK interactome

(2009) Alex von Kriegsheim et al.   NATURE CELL BIOLOGY

Target profiling of small molecules by chemical proteomics

(2009) Uwe Rix et al.   Nature Chemical Biology

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

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

(2009) Paola Picotti et al.   NATURE METHODS

Global identification of protein kinase substrates by protein microarray analysis

(2009) Janine Mok et al.   Nature Protocols

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

(2009) Da Wei Huang et al.   Nature Protocols

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Unbiased RNA-protein interaction screen by quantitative proteomics

(2009) F. Butter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental and computational tools useful for (re)construction of dynamic kinase–substrate networks

(2009) Chris Soon Heng Tan et al.   PROTEOMICS

Analytical strategies for phosphoproteomics

(2009) Tine E. Thingholm et al.   PROTEOMICS

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS

(2009) Scott J. Geromanos et al.   PROTEOMICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Cell-Specific Information Processing in Segregating Populations of Eph Receptor Ephrin-Expressing Cells

(2009) C. Jorgensen et al.   SCIENCE

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(2009) C. Choudhary et al.   SCIENCE

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

Neurotransmitters Drive Combinatorial Multistate Postsynaptic Density Networks

(2009) M. P. Coba et al.   Science Signaling

Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling Reveals System-Wide Modulation of Protein-Protein Interactions

(2009) V. Mayya et al.   Science Signaling

Zinc finger nuclease technology heralds a new era in mammalian transgenesis

(2009) Fabienne Le Provost et al.   TRENDS IN BIOTECHNOLOGY

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

(2009) Alexander Mitsos et al.   PLoS Computational Biology

Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini

(2008) Sami Mahrus et al.   CELL

Two-hybrid technologies in proteomics research

(2008) Bernhard Suter et al.   CURRENT OPINION IN BIOTECHNOLOGY

Network integration and graph analysis in mammalian molecular systems biology

(2008) A. Ma'ayan   IET Systems Biology

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

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

Accurate Inclusion Mass Screening

(2008) Jacob D. Jaffe et al.   MOLECULAR & CELLULAR PROTEOMICS

Kinase-Selective Enrichment Enables Quantitative Phosphoproteomics of the Kinome across the Cell Cycle

(2008) Henrik Daub et al.   MOLECULAR CELL

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

(2008) Kartik M Mani et al.   Molecular Systems Biology

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

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

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

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY

Native mass spectrometry: a bridge between interactomics and structural biology

(2008) Albert J R Heck   NATURE METHODS

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Covalent capture of kinase-specific phosphopeptides reveals Cdk1-cyclin B substrates

(2008) J. D. Blethrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) H. Yu et al.   SCIENCE