Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology

Protein TAILS: when termini tell tales of proteolysis and function

(2013) Philipp F Lange et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Identifying Natural Substrates for Dipeptidyl Peptidases 8 and 9 Using Terminal Amine Isotopic Labeling of Substrates (TAILS) Revealsin VivoRoles in Cellular Homeostasis and Energy Metabolism

(2013) Claire H. Wilson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cell Death Proteomics Database: Consolidating Proteomics Data on Cell Death

(2013) Magnus Ø. Arntzen et al.   JOURNAL OF PROTEOME RESEARCH

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Systems-Level Analysis of Proteolytic Events in Increased Vascular Permeability and Complement Activation in Skin Inflammation

(2013) U. auf dem Keller et al.   Science Signaling

CLIPPER: an add-on to the Trans-Proteomic Pipeline for the automated analysis of TAILS N-terminomics data

(2012) Ulrich auf dem Keller et al.   BIOLOGICAL CHEMISTRY

N-terminal acetylation and other functions of Nα-acetyltransferases

(2012) Jolien Hollebeke et al.   BIOLOGICAL CHEMISTRY

Secretome protein enrichment identifies physiological BACE1 protease substrates in neurons

(2012) Peer-Hendrik Kuhn et al.   EMBO JOURNAL

Deletion of Cysteine Cathepsins B or L Yields Differential Impacts on Murine Skin Proteome and Degradome

(2012) Stefan Tholen et al.   MOLECULAR & CELLULAR PROTEOMICS

Unbiased Selective Isolation of Protein N-terminal Peptides from Complex Proteome Samples Using Phospho Tagging (PTAG) and TiO2-based Depletion

(2012) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

The DegraBase: A Database of Proteolysis in Healthy and Apoptotic Human Cells

(2012) Emily D. Crawford et al.   MOLECULAR & CELLULAR PROTEOMICS

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events

(2012) Niklaas Colaert et al.   NUCLEIC ACIDS RESEARCH

Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis

(2012) K. Shimbo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global kinetic analysis of proteolysis via quantitative targeted proteomics

(2012) N. J. Agard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Qualitative improvement and quantitative assessment of N-terminomics

(2012) Vilém Guryča et al.   PROTEOMICS

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

(2011) Nicholas T. Ingolia et al.   CELL

Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

(2011) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

TopFIND, a knowledgebase linking protein termini with function

(2011) Philipp F Lange et al.   NATURE METHODS

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

(2011) Craig D Wenger et al.   NATURE METHODS

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

Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry

(2011) Oliver Schilling et al.   Nature Protocols

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2011) N. D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation

(2011) Petra Van Damme et al.   PLoS Genetics

Selective isolation of N-blocked peptide by combining AspN digestion, transamination, and tosylhydrazine glass treatment

(2010) Kazuhiro Sonomura et al.   ANALYTICAL BIOCHEMISTRY

Deubiquitylase, DeSUMOylase, and DeISGylase Activity Microarrays for Assay of Substrate Preference and Functional Modifiers

(2010) Christian M. Loch et al.   MOLECULAR & CELLULAR PROTEOMICS

Broad Coverage Identification of Multiple Proteolytic Cleavage Site Sequences in Complex High Molecular Weight Proteins Using Quantitative Proteomics as a Complement to Edman Sequencing

(2010) Alain Doucet et al.   MOLECULAR & CELLULAR PROTEOMICS

Inflammatory Stimuli Regulate Caspase Substrate Profiles

(2010) Nicholas J. Agard et al.   MOLECULAR & CELLULAR PROTEOMICS

A Statistics-based Platform for Quantitative N-terminome Analysis and Identification of Protease Cleavage Products

(2010) Ulrich auf dem Keller et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics

(2010) Anna Prudova et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Complementary positional proteomics for screening substrates of endo- and exoproteases

(2010) Petra Van Damme et al.   NATURE METHODS

Proteome-wide analysis of protein carboxy termini: C terminomics

(2010) Oliver Schilling et al.   NATURE METHODS

Sampling the N-terminal proteome of human blood

(2010) D. Wildes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A proteome-scale study on in vivo protein Nα-acetylation using an optimized method

(2010) Xumin Zhang et al.   PROTEOMICS

A proteomics approach to study in vivo protein Nα-modifications

(2009) Xumin Zhang et al.   Journal of Proteomics

Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini

(2009) G. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A rapid isolation and identification method for blocked N-terminal peptides by isothiocyanate-coupled magnetic nanoparticles and MS

(2009) Liyan Zhao et al.   PROTEOMICS

Tags for labeling protein N-termini with subtiligase for proteomics

(2008) Hikari A.I. Yoshihara et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

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

(2008) Sami Mahrus et al.   CELL

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

(2008) Melissa M. Dix et al.   CELL

Structure and Mechanism of Metallocarboxypeptidases

(2008) F. Gomis-Rüth   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Matrix Metalloproteinase Processing of CXCL11/I-TAC Results in Loss of Chemoattractant Activity and Altered Glycosaminoglycan Binding

(2008) Jennifer H. Cox et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pharmacoproteomics of a Metalloproteinase Hydroxamate Inhibitor in Breast Cancer Cells: Dynamics of Membrane Type 1 Matrix Metalloproteinase-Mediated Membrane Protein Shedding

(2008) G. S. Butler et al.   MOLECULAR AND CELLULAR BIOLOGY

Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites

(2008) Oliver Schilling et al.   NATURE BIOTECHNOLOGY

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

PMAP: databases for analyzing proteolytic events and pathways

(2008) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)

(2008) An Staes et al.   PROTEOMICS