Mass-spectrometry-based draft of the human proteome

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Loss of Olfactory Receptor Function in Hominin Evolution

(2014) Graham M. Hughes et al.   PLoS One

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

State of the Human Proteome in 2013 as Viewed through PeptideAtlas: Comparing the Kidney, Urine, and Plasma Proteomes for the Biology- and Disease-Driven Human Proteome Project

(2013) Terry Farrah et al.   JOURNAL OF PROTEOME RESEARCH

Metrics for the Human Proteome Project 2013–2014 and Strategies for Finding Missing Proteins

(2013) Lydie Lane et al.   JOURNAL OF PROTEOME RESEARCH

Identification of Missing Proteins in the neXtProt Database and Unregistered Phosphopeptides in the PhosphoSitePlus Database As Part of the Chromosome-Centric Human Proteome Project

(2013) Takashi Shiromizu et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg 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

Reduced annexin A6 expression promotes the degradation of activated epidermal growth factor receptor and sensitizes invasive breast cancer cells to EGFR-targeted tyrosine kinase inhibitors

(2013) Rainelli B Koumangoye et al.   Molecular Cancer

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines

(2013) A. Ori et al.   Molecular Systems Biology

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

(2013) Harald Marx et al.   NATURE BIOTECHNOLOGY

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

Ribosomes, but no translation, for lincRNAs

(2013) Louisa Flintoft   NATURE REVIEWS GENETICS

Critical assessment of proteome-wide label-free absolute abundance estimation strategies

(2013) Erik Ahrné et al.   PROTEOMICS

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

(2013) Teck Yew Low et al.   Cell Reports

Global Proteome Analysis of the NCI-60 Cell Line Panel

(2013) Amin Moghaddas Gholami et al.   Cell Reports

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

(2012) Young-Ki Paik et al.   NATURE BIOTECHNOLOGY

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

Considerations on selected reaction monitoring experiments: Implications for the selectivity and accuracy of measurements

(2012) Bruno Domon   Proteomics Clinical Applications

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

(2011) Nicholas T. Ingolia et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics

(2011) Roger Higdon et al.   Journal of Proteomics

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Deep proteome and transcriptome mapping of a human cancer cell line

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

Proteomic snapshot of the EGF-induced ubiquitin network

(2011) E. Argenzio 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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Epidermal growth factor receptor ligands as new extracellular targets for the metastasis-promoting S100A4 protein

(2009) Jörg Klingelhöfer et al.   FEBS Journal

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

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

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