Mass-spectrometric exploration of proteome structure and function

Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry

(2016) Yupeng Zheng et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Positional proteomics reveals differences in N-terminal proteoform stability

(2016) D. Gawron et al.   Molecular Systems Biology

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

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

(2016) Stefka Tyanova et al.   NATURE METHODS

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

(2016) Alexander Leitner et al.   TRENDS IN BIOCHEMICAL SCIENCES

A draft map of the mouse pluripotent stem cell spatial proteome

(2016) Andy Christoforou et al.   Nature Communications

Analytic framework for peptidomics applied to large-scale neuropeptide identification

(2016) Anna Secher et al.   Nature Communications

Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases

(2016) Martin Steger et al.   eLife

Global, quantitative and dynamic mapping of protein subcellular localization

(2016) Daniel N Itzhak et al.   eLife

Plasma Proteome Profiling to Assess Human Health and Disease

(2016) Philipp E. Geyer et al.   Cell Systems

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

Quantitative Proteomic Analysis of Histone Modifications

(2015) He Huang et al.   CHEMICAL REVIEWS

The Nuclear Proteome of a Vertebrate

(2015) Martin Wühr et al.   CURRENT BIOLOGY

Proteome sequencing goes deep

(2015) Alicia L Richards et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry

(2015) Fan Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Prediction of colorectal cancer diagnosis based on circulating plasma proteins

(2015) S. Surinova et al.   EMBO Molecular Medicine

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

(2015) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

(2015) Florian Meier et al.   JOURNAL OF PROTEOME RESEARCH

Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification

(2015) Matthew M. Makowski et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

(2015) Etienne Caron et al.   MOLECULAR & CELLULAR PROTEOMICS

Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair

(2015) H. B. Schiller et al.   Molecular Systems Biology

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

(2015) Thomas Walzthoeni et al.   NATURE METHODS

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

(2015) Fan Liu et al.   NATURE METHODS

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

Multidimensional proteomics for cell biology

(2015) Mark Larance et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural characterization of the interaction of Ubp6 with the 26S proteasome

(2015) Antje Aufderheide et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

(2015) M. Raschle et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry

(2015) Arti T. Navare et al.   STRUCTURE

Mass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications

(2014) Sophia Doll et al.   ACS Chemical Biology

Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

(2014) Yibo Wu et al.   CELL

The Structural Basis of Substrate Recognition by the Eukaryotic Chaperonin TRiC/CCT

(2014) Lukasz A. Joachimiak et al.   CELL

Cell-Type-Resolved Quantitative Proteomics of Murine Liver

(2014) S. Babak Azimifar et al.   Cell Metabolism

Analyzing the First Drafts of the Human Proteome

(2014) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards

(2014) Jacek R. Wiśniewski et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach

(2014) Steven A. Carr et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)

(2014) Eva C. Keilhauer et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Global analysis of protein structural changes in complex proteomes

(2014) Yuehan Feng et al.   NATURE BIOTECHNOLOGY

A mass spectrometry–based hybrid method for structural modeling of protein complexes

(2014) Argyris Politis et al.   NATURE METHODS

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

The growing landscape of lysine acetylation links metabolism and cell signalling

(2014) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Uncovering global SUMOylation signaling networks in a site-specific manner

(2014) Ivo A Hendriks et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

Orbitrap Mass Spectrometry

(2013) Roman A. Zubarev et al.   ANALYTICAL CHEMISTRY

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

(2013) Ron Milo   BIOESSAYS

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

(2013) John D. Chapman et al.   MASS SPECTROMETRY REVIEWS

The One Hour Yeast Proteome

(2013) Alexander S. Hebert 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

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

(2013) Paola Picotti et al.   NATURE

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

Direct Proteomic Quantification of the Secretome of Activated Immune Cells

(2013) F. Meissner et al.   SCIENCE

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

Twenty Years of Gas Phase Structural Biology

(2013) Julien Marcoux et al.   STRUCTURE

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Systems Genetics of Metabolism: The Use of the BXD Murine Reference Panel for Multiscalar Integration of Traits

(2012) Pénélope A. Andreux et al.   CELL

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat 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

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Direct identification of ligand-receptor interactions on living cells and tissues

(2012) Andreas P Frei et al.   NATURE BIOTECHNOLOGY

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

(2012) Anders R Kristensen et al.   NATURE METHODS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

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

(2012) Wade H. Dunham et al.   PROTEOMICS

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting

(2011) Liwen Wang et al.   ANALYTICAL CHEMISTRY

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry

(2011) Christina Ludwig et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep proteome and transcriptome mapping of a human cancer cell line

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

The quantitative proteome of a human cell line

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

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

(2011) John C. Tran et al.   NATURE

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

(2011) Oded Kleifeld et al.   Nature Protocols

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

(2011) P. P. Hsu et al.   SCIENCE

Mass Spectrometry of Intact V-Type ATPases Reveals Bound Lipids and the Effects of Nucleotide Binding

(2011) M. Zhou et al.   SCIENCE

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange MS

(2009) John R. Engen   ANALYTICAL CHEMISTRY

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

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

(2009) Johan Malmström et al.   NATURE

Target profiling of small molecules by chemical proteomics

(2009) Uwe Rix et al.   Nature Chemical Biology

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

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

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY