Kenny Helsens

Kenny Helsens
Ghent University | UGhent · VIB Department of Medical Protein Research

PhD

About

47
Publications
5,247
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3,176
Citations

Publications

Publications (47)
Article
Full-text available
We here present The Online Protein Processing Resource (TOPPR; http://iomics.ugent.be/toppr/), an online database that contains thousands of published proteolytically processed sites in human and mouse proteins. These cleavage events were identified with COmbinded FRActional DIagonal Chromatography proteomics technologies, and the resulting databas...
Article
Full-text available
Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify...
Article
Advances in mass spectrometry have been crucial in enabling high-throughput proteome analysis over the past 2 decades.1 Shotgun proteomics strategies have thereby emerged as the preferred strategy to explore proteomes in combination with tandem mass spectrometry (MS/MS). Both gel-based and chromatography-based methods have been developed to separat...
Article
We have created a new software platform called sigpep that analyzes transition redundancy in selected reaction monitoring assays. Building on this platform, we also created a web application to generate transition sets with unique signatures for targeted peptides. The platform has been made available under the permissive Apache 2.0 open-source lice...
Article
Full-text available
Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more...
Article
Proteome identification using peptide-centric proteomics techniques is a routinely used analysis technique. One of the most powerful and popular methods for the identification of peptides from MS/MS spectra is protein database matching using search engines. Significance thresholding through false discovery rate (FDR) estimation by target/decoy sear...
Article
We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via...
Chapter
In this chapter we focus on the technical improvments that were made to the N -terminal combined fractional diagonal chromatography (COFRADIC) protocol over the past five years. We discuss their general impact on N -terminal peptide coverage as well as on proteome coverage of human blood platelets by comparing the results of a more recent N -termin...
Data
List of 868 unique N-terminal peptides (start position 1 or 2) identified in the proteome of the control yeast strain and/or the yeast strain expressing hNaa60p. (DOC)
Data
List of 1,497 human N-terminal peptides (start position 1 or 2) identified in the hNaa60p overexpression or knockdown experiments in HeLa cells. (DOC)
Data
List of the 72 unique in vivo hNaa60p substrate N-termini identified in yeast. S4A. hNaa60p yeast substrate N-termini (44) which were completely unacetylated in the control setup analyzed. S4B. hNaa60p yeast substrate N-termini (28) which were partially N-Ac in the control setup analyzed. (DOC)
Data
dNAA50 but not dNAA60 dsRNAi treated cells arrest in mitosis. Graph showing mitotic index in control, dNAA60 and dNAA50 dsRNA treated Dmel2 cells. Mitotic index is the percentage of cells positive for phospho-Histone H3 (pSer10). (TIF)
Data
Relating the occurrence of N-Ac and different N-termini in yeast and humans. An unbiased estimation of N-Ac for all methionine-starting yeast (6613) and human SwissProt entries (20102) (SwissProt version 57.8) was performed based on the nature of the N-terminal amino acids and the N-terminal acetylation status uncovered in this study. (DOC)
Data
Amino acid frequencies at position 2 of hNaa60p and dNaa60p substrates. Bar charts of the amino acid frequencies at the 2nd position in the Met- (black bars) and Leu-starting (red bars) oligopeptide substrates identified in proteome-derived peptide library screens of hNaa60p (upper panel) and dNaa60p (lower panel). (TIF)
Data
List of N-termini affected in their N-Ac status by knockdown or overexpression of hNaa60p in HeLa cells. (DOC)
Article
Full-text available
N-terminal acetylation (N-Ac) is a highly abundant eukaryotic protein modification. Proteomics revealed a significant increase in the occurrence of N-Ac from lower to higher eukaryotes, but evidence explaining the underlying molecular mechanism(s) is currently lacking. We first analysed protein N-termini and their acetylation degrees, suggesting th...
Article
The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of...
Article
Initiation of protein translation is a well-studied fundamental process, albeit high-throughput and more comprehensive determination of the exact translation initiation sites (TIS) was only recently made possible following the introduction of positional proteomics techniques that target protein N-termini. Precise translation initiation is of crucia...
Article
Proteins are reckoned to be the key actors in a living organism. By studying proteins, one engages into deciphering a complex series of events occurring during a protein’s life span. This starts at the creation of a protein, which is tightly controlled on both a transcriptional (Williams and Tyler, 2007, Curr Opin Genet Dev 17, 88–93) and a transla...
Data
Full-text available
Compomics-utilities features. A list of compomics-utilities features
Article
Tyrosine nitration is the consequence of a complex machinery of formation and merging of oxygen and nitrogen radicals, and has been associated with both physiological pathways as well as with several human diseases. The latter turned this posttranslational protein modification into an interesting biomarker, being either a consequence of the disease...
Article
Full-text available
The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and in...
Article
Full-text available
Several mass spectrometry-driven techniques allow to map the substrate repertoires and specificities of proteases. These techniques typically yield long lists of protease substrates and processed sites with (potential) physiological relevance, but in order to understand the primary function of a protease, it is important to discern bystander substr...
Article
Full-text available
We present here a novel proteomics design for systematic identification of protease cleavage events by quantitative N-terminal proteomics, circumventing the need for time-consuming manual validation. We bypass the singleton detection problem of protease-generated neo-N-terminal peptides by introducing differential isotopic proteome labeling such th...
Article
Full-text available
We describe a positional proteomics approach to simultaneously analyze N- and C-terminal peptides and used it to screen for human protein substrates of granzyme B and carboxypeptidase A4 in human cell lysates. This approach allowed comprehensive proteome studies, and we report the identification of 965 database-annotated protein C termini, 334 neo-...
Article
Manual validation of regulated proteins found in MS-driven quantitative proteome studies is tedious. Here we present Rover (http://genesis.ugent.be/rover), a tool that facilitates this process. Rover accepts quantitative data from different sources such as MASCOT Distiller and MaxQuant and, in an intuitive environment, Rover visualizes these data s...
Article
MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms_lims (http://genesis.UGent....
Article
Proteolytic processing has recently received increased attention in the field of signal propagation and cellular differentiation. Because of its irreversible nature, protein cleavage has been associated with committed steps in cell function. One aspect of protease biology that boomed the past few years is the detailed characterization of protease s...
Article
Full-text available
A new proteomics technique for analyzing 3-nitrotyrosine-containing peptides is presented here. This technique is based on the combined fractional diagonal chromatography peptide isolation procedures by which specific classes of peptides are isolated following a series of identical reverse-phase HPLC separation steps. Here dithionite is used to red...
Article
Full-text available
Caspase-3 and -7 are considered functionally redundant proteases with similar proteolytic specificities. We performed a proteome-wide screen on a mouse macrophage lysate using the N-terminal combined fractional diagonal chromatography technology and identified 46 shared, three caspase-3-specific, and six caspase-7-specific cleavage sites. Further a...
Article
In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of docum...
Article
Full-text available
N(alpha)-terminal acetylation is one of the most common protein modifications in eukaryotes. The COmbined FRActional DIagonal Chromatography (COFRADIC) proteomics technology that can be specifically used to isolate N-terminal peptides was used to determine the N-terminal acetylation status of 742 human and 379 yeast protein N termini, representing...
Article
Caspase-3 and-7 are considered functionally redundant proteases with similar proteolytic specificities. We performed a proteome-wide screen on a mouse macrophage lysate using the N-terminal combined fractional diagonal chromatography technology and identified 46 shared, three caspase-3-specific, and six caspase-7-specific cleavage sites. Further an...
Article
Full-text available
False positive peptide identifications are a major concern in the field of peptidecentric, mass spectrometry-driven gel-free proteomics. They occur in regions where the score distributions of true positives and true negatives overlap. Removal of these false positive identifications necessarily involves a trade-off between sensitivity and specificit...
Article
We previously described a proteome-wide, peptide-centric procedure for sorting protein N-terminal peptides and used these peptides as readouts for protease degradome and xenoproteome studies. This procedure is part of a repertoire of gel-free techniques known as COmbined FRActional DIagonal Chromatography (COFRADIC) and highly enriches for alpha-am...
Article
Full-text available
Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/ peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, i...
Article
Full-text available
Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/ peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, i...
Article
High-throughput proteomics experiments typically generate large amounts of peptide fragmentation mass spectra during a single experiment. There is often a substantial amount of redundant fragmentation of the same precursors among these spectra, which is usually considered a nuisance. We here discuss the potential of clustering and merging redundant...
Article
Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel-free proteomics techniques. In this review, we discuss several of these gel-free techniques both for monitoring...
Article
Microfluidic interfaces coupled to ESI mass spectrometers hold great potential for proteomics as they have been shown to augment the overall sensitivity of measurements and require only a minimum of operator manipulations as compared to conventional nano-LC interfaces. Here, we evaluated a new type of HPLC-Chips holding larger enrichment columns (t...
Article
MS-based protein identification is an important part of both gel-based and gel-free proteome studies. The MASCOT search engine (http://www.matrixscience.com) provides one of the most popular automated algorithms for this task. Here we present an open-source software library written in Java that parses raw MASCOT results into an easily accessible an...

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