Simon Daled
YOU?
Author Swipe
View article: Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline
Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline Open
Liquid chromatography-mass spectrometry (LC-MS/MS) extends the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Zooarcheology by Mass Spectrometry (ZooMS) "mass fingerprinting" approach to species identification by pr…
View article: ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation
ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation Open
LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse datasets containing only a few collagen proteins, rendering target-decoy strategies unusabl…
View article: A mass spectrometry-based workflow to analyze histone post-translational modifications and the associated acid extractome
A mass spectrometry-based workflow to analyze histone post-translational modifications and the associated acid extractome Open
Worldwide, there is an increasing interest in epigenetics because of its involvement in several diseases. An important epigenetic mechanism is the histone post-translational modifications and the histone code they generate. Mass spectromet…
View article: Protein Extraction from Dental Enamel v2
Protein Extraction from Dental Enamel v2 Open
This protocol details a method for extracting proteins from ~5mg of powdered dental enamel for proteomic analysis by LC-MS/MS. This procedure includes the use of alkylating and reducing agents, a sample cleanup step, and features the optio…
View article: First insights into human mobility in Neolithic Belgium using strontium isotopic analysis and proteomics: A case study of Grotte de La Faucille (Sclayn, province of Namur)
First insights into human mobility in Neolithic Belgium using strontium isotopic analysis and proteomics: A case study of Grotte de La Faucille (Sclayn, province of Namur) Open
Objectives So far, no 87 Sr/ 86 Sr mobility studies have been done for Neolithic remains from Belgium and information on the Sr isotopic variability in the region is scarce. This study aims to explore mobility in a Final Neolithic populati…
View article: Proteomic Comparison of Three Wild-Type Pseudorabies Virus Strains and the Attenuated Bartha Strain Reveals Reduced Incorporation of Several Tegument Proteins in Bartha Virions
Proteomic Comparison of Three Wild-Type Pseudorabies Virus Strains and the Attenuated Bartha Strain Reveals Reduced Incorporation of Several Tegument Proteins in Bartha Virions Open
The pseudorabies virus (PRV) vaccine strain Bartha—an attenuated strain created by serial passaging—represents an exceptional success story in alphaherpesvirus vaccination. Here, we used mass spectrometry to analyze the Bartha virion compo…
View article: An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia
An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia Open
The holistic nature of omics studies makes them ideally suited to generate hypotheses on health and disease. Sequencing-based genomics and mass spectrometry (MS)-based proteomics are linked through epigenetic regulation mechanisms. However…
View article: A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics Open
In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisiti…
View article: Analyzing data independent acquisition mass spectrometry with noiseless ion-networks
Analyzing data independent acquisition mass spectrometry with noiseless ion-networks Open
Data-independent acquisition (DIA) mass spectrometry (MS) has introduced deter-ministic, periodic and simultaneous acquisition of all fragment ions. Despite the chimeric side-effects associated with this unprecedented data integrity, DIA d…
View article: A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics Open
In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisiti…
View article: Large Scale Toxicoepigenetics on Histones: A Mass Spectrometry-based Screening Assay Applied to Developmental Toxicity
Large Scale Toxicoepigenetics on Histones: A Mass Spectrometry-based Screening Assay Applied to Developmental Toxicity Open
Toxicoepigenetics is an emerging field that studies the toxicological impact of compounds on protein expression through heritable, non-genetic mechanisms, such as histone post-translational modifications (hPTMs). Due to substantial progres…
View article: Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients
Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients Open
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include acc…
View article: Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions Open
Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential…
View article: Histone sample preparation for bottom-up mass spectrometry: a roadmap to informed decisions
Histone sample preparation for bottom-up mass spectrometry: a roadmap to informed decisions Open
Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential…
View article: The CD147 Protein Complex Is Involved in Entry of Chikungunya Virus and Related Alphaviruses in Human Cells
The CD147 Protein Complex Is Involved in Entry of Chikungunya Virus and Related Alphaviruses in Human Cells Open
Chikungunya virus (CHIKV) is an arbovirus with a global spread and significant public health impact. It is a positive stranded RNA alphavirus belonging to the Togaviridae family. However, many questions about the replication cycle of CHIKV…
View article: An experimental design to extract more information from MS-based histone studies
An experimental design to extract more information from MS-based histone studies Open
Enzymatic treatment of a commercial histone extract as a quantify-first strategy allows isolating ion populations of interest that currently remain in the dark.
View article: Cov-MS: a community-based template assay for clinical MS-based protein detection in SARS-CoV-2 patients
Cov-MS: a community-based template assay for clinical MS-based protein detection in SARS-CoV-2 patients Open
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include acc…
View article: Front Cover: Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
Front Cover: Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries Open
DOI: 10.1002/pmic.201900306 In article number 1900306, Van Puyvelde et al. present a unified graphic called the DIAmond DIAgram which the authors use to sample the currently-available peptide-centric DIA data analysis strategies and assess…
View article: An Alphaherpesvirus Exploits Antimicrobial β-Defensins To Initiate Respiratory Tract Infection
An Alphaherpesvirus Exploits Antimicrobial β-Defensins To Initiate Respiratory Tract Infection Open
How herpesviruses circumvent mucosal defenses to promote infection of new hosts through the respiratory tract remains unknown due to a lack of host-specific model systems. We used the alphaherpesvirus equine herpesvirus type 1 (EHV1) and e…
View article: Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries Open
Data‐independent acquisition (DIA) generates comprehensive yet complex mass spectrometric data, which imposes the use of data‐dependent acquisition (DDA) libraries for deep peptide‐centric detection. Here, it is shown that DIA can be redee…
View article: Interrogation of the CHIKV nsP-host interactome in human and mosquito cells
Interrogation of the CHIKV nsP-host interactome in human and mosquito cells Open
Chikungunya virus is a human pathogen transmitted by mosquitos. After a genetic adaptation of the virus that allows increased spreading by Aedes albopictus mosquitos, the past decade, Chikungunya virus has spread across the globe. In a sig…
View article: The Basigin (CD147)-CD98 protein complex is involved in Chikungunya virus attachment and entry in human cells
The Basigin (CD147)-CD98 protein complex is involved in Chikungunya virus attachment and entry in human cells Open
Chikungunya virus (CHIKV), a positive stranded RNA alphavirus, recently reemerged causing multiple outbreaks around the world. Generally, alphaviruses enter the cell via clathrin-mediated endocytosis. Entry is supported by the structural e…
View article: Ion-networks: a sparse data format capturing full data integrity of data independent acquisition mass spectrometry
Ion-networks: a sparse data format capturing full data integrity of data independent acquisition mass spectrometry Open
Data-independent acquisition (DIA) mass spectrometry (MS) has introduced deter-ministic, periodic and simultaneous acquisition of all fragment ions. Despite the chimeric side-effects associated with this unprecedented data integrity, DIA d…
View article: Removing the hidden data dependency of DIA with predicted spectral libraries
Removing the hidden data dependency of DIA with predicted spectral libraries Open
Data-Independent Acquisition (DIA) generates comprehensive yet complex mass spectrometric data, which imposes the use of data-dependent acquisition (DDA) libraries for deep peptide-centric detection. We here show that DIA can be redeemed f…
View article: Host intestinal biomarker identification in a gut leakage model in broilers
Host intestinal biomarker identification in a gut leakage model in broilers Open
Intestinal health problems are a major issue in the poultry industry. Quantifiable easy-to-measure biomarkers for intestinal health would be of great value to monitor subclinical intestinal entities that cause performance problems and to e…