Kenny Helsens

Fully automated and sensitive detection of EGFR exon 18, 19, 20 and 21 mutational status in <2.5 hrs from a single FFPE slice.

Erwin Sablon, Martin Reijans, Geneviève Vandercruyssen, Inge Keuleers et autres

e20519 Background: Current molecular testing for mutations and indels in EGFRexons 18, 19, 20 and 21 is still laborious and often requires > 5 days in specialized labs. Multiple slices of FFPE tissue are often needed. Lack of experience, time or tissue …

be (code pays fourni par la source)

LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures

Pieter‐Jan Volders, Kenny Helsens, Lennart Martens, Kris Gevaert et autres

Long non-coding RNAs (lncRNAs) constitute a large and diverse class of non-coding RNA genes. While several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) …

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

Niklaas Colaert, Davy Maddelein, Francis Impens, Petra Van Damme et autres

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 database …

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LNCipedia: a database for annotated human lncRNA transcript sequences and structures

Pieter‐Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten et autres

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 …

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Sigpep: Calculating unique peptide signature transition sets in a complete proteome background

Kenny Helsens, Michael Mueller, Niels Hulstaert, Lennart Martens

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 …

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Enabling Computational Proteomics by Public and Local Data Management Systems

Kenny Helsens, Lennart Martens

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Lncipedia: a novel database for annotated lncRNA sequences and structures

Pieter‐Jan Volders, Kenny Helsens, Xiaowei Wang, Lennart Martens et autres

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists

Eric W. Deutsch, Matthew Chambers, Steffen Neumann, Fredrik Levander et autres

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, …

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Analysis of the Resolution Limitations of Peptide Identification Algorithms

Niklaas Colaert, Sven Degroeve, Kenny Helsens, Lennart Martens

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) …

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jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions

Kenny Helsens, Mi‐Youn Brusniak, Eric W. Deutsch, Robert L. Moritz et autres

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 …

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

Petra Van Damme, Kristine Hole, Ana Pimenta-Marques, Kenny Helsens et autres

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 …

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thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files

Niklaas Colaert, Harald Barsnes, Marc Vaudel, Kenny Helsens et autres

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 …

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