Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics

ProteomicsDB

(2017) Tobias Schmidt et al.   NUCLEIC ACIDS RESEARCH

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

(2017) Pascal Leuenberger et al.   SCIENCE

Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation

(2016) Erik McShane et al.   CELL

Positional proteomics reveals differences in N-terminal proteoform stability

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

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

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

The s2D Method: Simultaneous Sequence-Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins

(2015) Pietro Sormanni et al.   JOURNAL OF MOLECULAR BIOLOGY

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

(2015) Sarah E. Calvo et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

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

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

The N-Terminal Methionine of Cellular Proteins as a Degradation Signal

(2013) Heon-Ki Kim et al.   CELL

Identification and Characterization of a Novel Human Methyltransferase Modulating Hsp70 Protein Function through Lysine Methylation

(2013) Magnus E. Jakobsson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Principles of Cotranslational Ubiquitination and Quality Control at the Ribosome

(2013) Stefanie Duttler et al.   MOLECULAR CELL

Protein synthesis rate is the predominant regulator of protein expression during differentiation

(2013) A. R. Kristensen et al.   Molecular Systems Biology

A Novel Pulse-Chase SILAC Strategy Measures Changes in Protein Decay and Synthesis Rates Induced by Perturbation of Proteostasis with an Hsp90 Inhibitor

(2013) Ivo Fierro-Monti et al.   PLoS One

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

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

Regulatory modules: Coupling protein stability to phopshoregulation during cell division

(2012) Liam J. Holt   FEBS LETTERS

Unique posttranslational modifications in eukaryotic translation factors and their roles in protozoan parasite viability and pathogenesis

(2012) Nimisha Mittal et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

(2012) Jacek R Wiśniewski et al.   Molecular Systems Biology

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Developments in quantitative mass spectrometry for the analysis of proteome dynamics

(2012) Christopher Hughes et al.   TRENDS IN BIOTECHNOLOGY

Systems-wide Proteomic Analysis in Mammalian Cells Reveals Conserved, Functional Protein Turnover

(2011) Sidney B. Cambridge et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

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

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

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

(2011) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

The N-end rule pathway and regulation by proteolysis

(2011) Alexander Varshavsky   PROTEIN SCIENCE

Proteome Half-Life Dynamics in Living Human Cells

(2011) E. Eden et al.   SCIENCE

The dynamic state of protein turnover: It's about time

(2011) Izumi V. Hinkson et al.   TRENDS IN CELL BIOLOGY

New Cdc2 Tyr 4 phosphorylation by dsRNA-activated protein kinase triggers Cdc2 polyubiquitination and G2 arrest under genotoxic stresses

(2010) Cheol-Hee Yoon et al.   EMBO REPORTS

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

Post-translational modifications in signal integration

(2010) Yonathan Lissanu Deribe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity

(2009) Tanya Vavouri et al.   CELL

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

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

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

Diversity of degradation signals in the ubiquitin–proteasome system

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

Global Protein Stability Profiling in Mammalian Cells

(2008) H.-C. S. Yen et al.   SCIENCE

Structural disorder serves as a weak signal for intracellular protein degradation

(2007) P. Tompa et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS