List of works - Petra Van Damme

A Role for Human N-alpha Acetyltransferase 30 (Naa30) in Maintaining Mitochondrial Integrity

scientific article published on 30 September 2016

A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant

scientific article

A la carte proteomics with an emphasis on gel-free techniques

scientific article published on August 2007

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

scientific article published on 2 October 2014

A review of COFRADIC techniques targeting protein N-terminal acetylation

scientific article

Ablation of elongation factor 2 kinase enhances heat-shock protein 90 chaperone expression and protects cells under proteotoxic stress

scientific article published on 19 March 2019

Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death

scientific article published on 8 January 2008

Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

scientific article published on 10 February 2016

AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1.

scientific article published in March 2006

An organellar nα-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity

scientific journal article

Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs

scientific article published on 3 October 2008

Antigenic peptides: Reviving nuclear translation

scientific article published in December 2013

Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses.

scientific article

Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects

scientific article

C-terminomics screen for natural substrates of cytosolic carboxypeptidase 1 reveals processing of acidic protein C termini

scientific article published on 7 November 2014

C-terminomics: Targeted analysis of natural and posttranslationally modified protein and peptide C-termini

scientific article

Caspase substrates: easily caught in deep waters?

scientific article published on 29 October 2009

Caspase-14 is required for filaggrin degradation to natural moisturizing factors in the skin

scientific article published on 9 June 2011

Caspase-14 protects against epidermal UVB photodamage and water loss

scientific article

Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis

scientific article published in October 2005

Complementary positional proteomics for screening substrates of endo- and exoproteases

scientific article

Conservation of the extended substrate specificity profiles among homologous granzymes across species

scientific article published on 20 June 2013

Contemporary positional proteomics strategies to study protein processing

scientific article published on 03 January 2013

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

scientific article published on 21 February 2013

Degradomics reveals that cleavage specificity profiles of caspase-2 and effector caspases are alike

scientific article

Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?

scientific article

Disentanglement of protease substrate repertoires

scientific article published on April 2008

Dissecting apoptosis the omics way.

scientific article published on 12 November 2013

Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium

scientific article published in 2024

Granzyme M targets topoisomerase II alpha to trigger cell cycle arrest and caspase-dependent apoptosis

scientific article

HPLC-based quantification of in vitro N-terminal acetylation

scientific article published in January 2013

Holistic view on the extended substrate specificities of orthologous granzymes

scientific article published on 10 March 2014

Human and mouse granzyme M display divergent and species-specific substrate specificities

scientific article

Identification of Carboxypeptidase Substrates by C-Terminal COFRADIC.

scientific article published in January 2017

Identification of Serpinb6b as a species-specific mouse granzyme A inhibitor suggests functional divergence between human and mouse granzyme A.

scientific article

Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B.

scientific article

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

scientific article published in April 2008

In-gel N-acetylation for the quantification of the degree of protein in vivo N-terminal acetylation

scientific article published in January 2013

Keeping in Touch with Type-III Secretion System Effectors: Mass Spectrometry-Based Proteomics to Study Effector-Host Protein-Protein Interactions

scientific article published on 19 September 2020

MS-driven protease substrate degradomics

scientific article published on March 2010

Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency

scientific article published on 09 February 2021

N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in

scientific article published on 27 August 2018

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

scientific article

N-terminal acetylation and other functions of Nα-acetyltransferases

scientific article

N-terminal acetylation modulates Bax targeting to mitochondria

scientific article published on 9 December 2017

N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

scientific article

N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases

scientific article

N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men

scientific article

NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation

scientific article

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products

scientific article

Omics assisted N-terminal proteoform and protein expression profiling upon methionine aminopeptidase 1 (MetAP1) deletion

scientific article published on 9 January 2018

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms

scientific article published on 30 April 2019

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

scientific article

Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii

scientific article published on 28 March 2007

Preparation of Arabidopsis thaliana Seedling Proteomes for Identifying Metacaspase Substrates by N-terminal COFRADIC

scientific article published on 01 January 2014

Probing the efficiency of proteolytic events by positional proteomics

scientific article published on 3 November 2010

Protease Substrate Profiling by N-Terminal COFRADIC.

scientific article published in January 2017

Protein N-terminal acetyltransferases act as N-terminal propionyltransferases in vitro and in vivo

scientific article

Protein alpha-N-acetylation studied by N-terminomics

scientific article published on 02 August 2011

Protein processing and other modifications analyzed by diagonal peptide chromatography

scientific article published on 14 September 2006

Protein processing characterized by a gel-free proteomics approach

scientific article

Proteogenomics in Aid of Host-Pathogen Interaction Studies: A Bacterial Perspective

scientific article published on 11 October 2017

Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of N(alpha)-acetyltransferases and point to hNaa10p as the post-translational actin N(alpha)-acetyltransferase

scientific article

Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases.

scientific article

Proteome-wide Identification of HtrA2/Omi Substrates

scientific article

Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity

scientific journal article

Proteomic Identification of Cysteine Cathepsin Substrates Shed from the Surface of Cancer Cells.

scientific article published on 16 June 2015

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

scholarly article

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

scientific article published on 31 August 2017

Ribosome signatures aid bacterial translation initiation site identification

scientific article published on 30 August 2017

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

scientific article published on 14 July 2011

Stable isotopic labeling in proteomics

scientific article published on December 2008

Structure of granzyme C reveals an unusual mechanism of protease autoinhibition

scientific article

Substrate specificities of the granzyme tryptases A and K.

scientific article published on 19 November 2014

T-cell receptor-induced JNK activation requires proteolytic inactivation of CYLD by MALT1.

scientific article

Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes

scientific article published on 30 July 2008

The Arabidopsis metacaspase9 degradome

scientific article published on 20 August 2013

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

scientific article (publication date: 2013)

The chaperone-like protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation

scientific article

The human N-alpha-acetyltransferase 40 (hNaa40p/hNatD) is conserved from yeast and N-terminally acetylates histones H2A and H4

scientific article

The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile

scientific article published in August 2005

The proteome under translational control

scientific article

The substrate specificity profile of human granzyme A.

scientific article

Transcriptional activation of the NF-kappaB p65 subunit by mitogen- and stress-activated protein kinase-1 (MSK1)

scientific article

Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling

scientific article published on 19 January 2021

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

scientific article published on 24 May 2017

List of works by Petra Van Damme

A Role for Human N-alpha Acetyltransferase 30 (Naa30) in Maintaining Mitochondrial Integrity

A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant

A la carte proteomics with an emphasis on gel-free techniques

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

A review of COFRADIC techniques targeting protein N-terminal acetylation

Ablation of elongation factor 2 kinase enhances heat-shock protein 90 chaperone expression and protects cells under proteotoxic stress

Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death

Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1.

An organellar nα-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity

Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs

Antigenic peptides: Reviving nuclear translation

Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses.

Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects

C-terminomics screen for natural substrates of cytosolic carboxypeptidase 1 reveals processing of acidic protein C termini

C-terminomics: Targeted analysis of natural and posttranslationally modified protein and peptide C-termini

Caspase substrates: easily caught in deep waters?

Caspase-14 is required for filaggrin degradation to natural moisturizing factors in the skin

Caspase-14 protects against epidermal UVB photodamage and water loss

Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis

Complementary positional proteomics for screening substrates of endo- and exoproteases

Conservation of the extended substrate specificity profiles among homologous granzymes across species

Contemporary positional proteomics strategies to study protein processing

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

Degradomics reveals that cleavage specificity profiles of caspase-2 and effector caspases are alike

Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?

Disentanglement of protease substrate repertoires

Dissecting apoptosis the omics way.

Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium

Granzyme M targets topoisomerase II alpha to trigger cell cycle arrest and caspase-dependent apoptosis

HPLC-based quantification of in vitro N-terminal acetylation

Holistic view on the extended substrate specificities of orthologous granzymes

Human and mouse granzyme M display divergent and species-specific substrate specificities

Identification of Carboxypeptidase Substrates by C-Terminal COFRADIC.

Identification of Serpinb6b as a species-specific mouse granzyme A inhibitor suggests functional divergence between human and mouse granzyme A.

Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B.

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

In-gel N-acetylation for the quantification of the degree of protein in vivo N-terminal acetylation

Keeping in Touch with Type-III Secretion System Effectors: Mass Spectrometry-Based Proteomics to Study Effector-Host Protein-Protein Interactions

MS-driven protease substrate degradomics

Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency

N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

N-terminal acetylation and other functions of Nα-acetyltransferases

N-terminal acetylation modulates Bax targeting to mitochondria

N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases

N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men

NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products

Omics assisted N-terminal proteoform and protein expression profiling upon methionine aminopeptidase 1 (MetAP1) deletion

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii

Preparation of Arabidopsis thaliana Seedling Proteomes for Identifying Metacaspase Substrates by N-terminal COFRADIC

Probing the efficiency of proteolytic events by positional proteomics

Protease Substrate Profiling by N-Terminal COFRADIC.

Protein N-terminal acetyltransferases act as N-terminal propionyltransferases in vitro and in vivo

Protein alpha-N-acetylation studied by N-terminomics

Protein processing and other modifications analyzed by diagonal peptide chromatography

Protein processing characterized by a gel-free proteomics approach

Proteogenomics in Aid of Host-Pathogen Interaction Studies: A Bacterial Perspective

Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of N(alpha)-acetyltransferases and point to hNaa10p as the post-translational actin N(alpha)-acetyltransferase

Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases.

Proteome-wide Identification of HtrA2/Omi Substrates

Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity

Proteomic Identification of Cysteine Cathepsin Substrates Shed from the Surface of Cancer Cells.

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

Ribosome signatures aid bacterial translation initiation site identification

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

Stable isotopic labeling in proteomics

Structure of granzyme C reveals an unusual mechanism of protease autoinhibition

Substrate specificities of the granzyme tryptases A and K.

T-cell receptor-induced JNK activation requires proteolytic inactivation of CYLD by MALT1.

Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes

The Arabidopsis metacaspase9 degradome

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

The chaperone-like protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation