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

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

The Coming of Age of Phosphoproteomics—from Large Data Sets to Inference of Protein Functions

(2013) Philippe P. Roux et al.   MOLECULAR & CELLULAR PROTEOMICS

Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics

(2013) Mohammad Pirmoradian et al.   MOLECULAR & CELLULAR PROTEOMICS

Functional Proteomics Defines the Molecular Switch Underlying FGF Receptor Trafficking and Cellular Outputs

(2013) Chiara Francavilla et al.   MOLECULAR CELL

Proteome-wide Identification of Poly(ADP-Ribosyl)ation Targets in Different Genotoxic Stress Responses

(2013) Stephanie Jungmichel et al.   MOLECULAR CELL

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

(2013) Brian T. Weinert et al.   MOLECULAR CELL

Genome-scale engineering for systems and synthetic biology

(2013) K. M. Esvelt et al.   Molecular Systems Biology

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome

(2013) Yajie Zhang et al.   NATURE METHODS

Functional Lysine Modification by an Intrinsically Reactive Primary Glycolytic Metabolite

(2013) R. E. Moellering et al.   SCIENCE

In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of  -Adrenergic Receptor Signaling

(2013) A. Lundby et al.   Science Signaling

In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis

(2013) Sara Zanivan et al.   Cell Reports

Quantitative mass spectrometry in proteomics

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine Tissues

(2012) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Refined Preparation and Use of Anti-diglycine Remnant (K-ε-GG) Antibody Enables Routine Quantification of 10,000s of Ubiquitination Sites in Single Proteomics Experiments

(2012) Namrata D. Udeshi et al.   MOLECULAR & CELLULAR PROTEOMICS

Regulation of yeast central metabolism by enzyme phosphorylation

(2012) Ana Paula Oliveira et al.   Molecular Systems Biology

Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients

(2012) Thomas Köcher et al.   Nature Protocols

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

(2012) Alicia Lundby et al.   Nature Communications

Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

(2012) Alicia Lundby et al.   Cell Reports

Increasing phosphoproteomic coverage through sequential digestion by complementary proteases

(2011) Jason M. Gilmore et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Combination of Chemical Genetics and Phosphoproteomics for Kinase Signaling Analysis Enables Confident Identification of Cellular Downstream Targets

(2011) Felix S. Oppermann et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment

(2011) Houjiang Zhou et al.   MOLECULAR & CELLULAR PROTEOMICS

iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics

(2011) Philipp Mertins 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

Mapping intact protein isoforms in discovery mode using top-down proteomics

(2011) John C. Tran et al.   NATURE

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

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Reactome pathway analysis to enrich biological discovery in proteomics data sets

(2011) Robin Haw et al.   PROTEOMICS

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

(2011) Y. Yu et al.   SCIENCE

The mTOR-Regulated Phosphoproteome Reveals a Mechanism of mTORC1-Mediated Inhibition of Growth Factor Signaling

(2011) P. P. Hsu et al.   SCIENCE

Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells

(2011) A. N. Kettenbach et al.   Science Signaling

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

Mitotic Substrates of the Kinase Aurora with Roles in Chromatin Regulation Identified Through Quantitative Phosphoproteomics of Fission Yeast

(2011) A. Koch et al.   Science Signaling

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

Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

(2010) Nagarjuna Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Identification of lysine succinylation as a new post-translational modification

(2010) Zhihong Zhang et al.   Nature Chemical Biology

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

(2010) B. Bodenmiller et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

Blinded by the Light: The Growing Complexity of p53

(2009) Karen H. Vousden et al.   CELL

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

(2009) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

A stress test for mass spectrometry–based proteomics

(2009) Ruedi Aebersold   NATURE METHODS

High-accuracy identification and bioinformatic analysis ofin vivoprotein phosphorylation sites in yeast

(2009) Florian Gnad et al.   PROTEOMICS

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis

(2008) Melissa M. Dix et al.   CELL

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

(2008) Henrik Daub et al.   MOLECULAR CELL

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Superoxide dismutase 1 regulates caspase-1 and endotoxic shock

(2008) Felix Meissner et al.   NATURE IMMUNOLOGY

Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

(2008) Nadia Taouatas et al.   NATURE METHODS

Precision proteomics: The case for high resolution and high mass accuracy

(2008) M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling