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ProGenTomics offers a wide range of mass spectrometry based proteomics services for both the academic community and its industrial partners. We aim to tailor our services and the experimental design to the needs of the project thus ensuring solid data and results.

What can ProGenTomics do for you?

Differential Protein Analysis

Differential protein analysis using state-of-the-art bottom-up liquid chromatography mass spectrometry. This technique enables the accurate quantification and comparison of proteins derived from differentially treated samples such as cells, tissue, plant materials and intact organisms.

Biological Characterization

We offer intact protein analysis for the characterization of proteoforms and unexpected modifications, peptide mapping of biopharmaceuticals, host cell protein analysis and potency assays to monitor expression profiles of e.g. mRNA vaccines.

Histone epigenetics

ProGenTomics has over 12 years of experience with histone epigenetic screening covering over 100 post-translational modification sites. Our advanced data-analysis pipeline not only ensures confident identification but also differential quantification and variant calling. Specific modifications can be targeted upon request.

Timelapse Protein Analysis

Timelapse protein analysis using state-of-the-art bottom-up liquid chromatography mass spectrometry. This enables the accurate monitoring of protein abundances over time during treatments, purification processes, toxicological essays…

Forensic- & Palaeoproteomics

Using bottom-up LC-MS/MS we can identify the 5 most common body fluids in a forensic context. Closely related is our palaeoproteomics branch. Currently, our workflow identifies up to 100 proteins in 5mg of ancient bone and our in-house algorithms enable species identification without much prior knowledge. In addition we can perform sex determination on human enamel and identify proteins/peptides in ancient pottery.

Plasma Proteomics

Our bottom-up protein analysis on plasma is routinely performed on less than 20µL and yields up to 1000 quantifiable- and 1500 identified proteins. This is a fully automated process performed by the Andrew+ pipetting robot (Waters Co.), ensuring minimal technical variation.

A little taste of some past projects

Proteomics

  • Integrative Proteomic Profiling Reveals PRC2-Dependent epigenetic Crosstalk Maintains Ground-State Pluripotency
    By: Guido van Mierlo, René A.M. Dirks, Laura De Clerck, Arie B. Brinkman, Michelle Huth, Susan L. Kloet, Nehmé Saksouk, Leonie I. Kroeze, Sander Willems, Matthias Farlik, Christoph Bock, Joop H. Jansen, Dieter Deforce, Michiel Vermeulen, Jérôme Déjardin, Maarten Dhaenens, Hendrik Marks
    https://doi.org/10.1016/j.stem.2018.10.017

     

    The pluripotent ground state is defined as a basal state free of epigenetic restrictions, which influence lineage specification. While naive embryonic stem cells (ESCs) can be maintained in a hypomethylated state with open chromatin when grown using two small-molecule inhibitors (2i)/leukemia inhibitory factor (LIF), in contrast to serum/LIF-grown ESCs that resemble early post-implantation embryos, broader features of the ground-state pluripotent epigenome are not well understood. We identified epigenetic features of mouse ESCs cultured using 2i/LIF or serum/LIF by proteomic profiling of chromatin-associated complex

    es and histone modifications. Polycomb-repressive complex 2 (PRC2) and its product H3K27me3 are highly abundant in 2i/LIF ESCs, and H3K27me3 is distributed genome-wide in a CpG-dependent fashion. Consistently, PRC2-deficient ESCs showed increased DNA methylation at sites normally occupied by H3K27me3 and increased H4 acetylation. Inhibiting DNA methylation in PRC2-deficient ESCs did not affect their viability or transcriptome. Our findings suggest a unique H3K27me3 configuration protects naive ESCs from lineage priming, and they reveal widespread epigenetic crosstalk in ground-state pluripotency.

In forensic casework analysis, identification of the biological matrix and the species of a forensic trace, preferably without loss of DNA, is of major importance. The biological matrices that can be encountered in a forensic context are blood (human or non-human), saliva, semen, vaginal fluid, and to a lesser extent nasal secretions, feces, and urine. All these matrices were applied on swabs and digested with trypsin in order to obtain peptides. These peptides were injected on a mass spectrometer (ESI Q-TOF) resulting in the detection of several biomarkers that were used to build a decision tree for matrix identification. Additionally, by means of this proteomic approach, species identification was possible. This approach has the advantage that the analysis is performed on the first “washing” step of the chelex DNA extraction, a solution which is normally discarded, and that one single test is sufficient to determine the identity and the species of the biological matrix, while the conventional methods require cascade testing.

Mass spectrometry-based proteomics as a tool to identify biological matrices in forensic science
By: Van Steendam K, De Ceuleneer M, Dhaenens M, Van Hoofstat D, Deforce D.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE, 127(2): 287-298, MAR 2013, DOI: 10.1007/s00414-012-0747-x

The design of engineered gold nanoparticles that can interact with living cells and tissues is important for many biomedical applications, including imaging, diagnostics, and drug delivery. Polymer-decoration of goldNP is attractive to modulate the goldNP properties and to render them colloidally stable in complex media. Also proteins can show different binding properties according to the polymer that is attached to the goldNP. To further investigate this, HEA x MEA y @goldNP were exposed to Foetal bovine serum. Subsequently, the particels were loaded on polyacrylamide gel (PAGE) and subjected to electrophoresis followed by in-gel digestion with trypsin. The bound proteins were identified by means of LC-MS/MS. Additionally, the hydrophobicity of the absorbed proteins was analysed by means of the GRAVY score.

Prenylated chalcone xanthohumol associates with histones in breast cancer cells–a novel target identified by a monoclonal antibody
By: Wyns C, van Steendam K, Vanhoecke B, Deforce D, Bracke M, Heyerick A.
MOLECULAR NUTRITION & FOOD RESEARCH, 56(11): 1688-1696, NOV 2012, DOI: 10.1002/mnfr.201200030

In order to identify the antigens in immune complexes in synovial fluid from patients with rheumatoid arthritis, the immune complexes were first isolated by means of protA and G columns. The eluted fraction was separated by means of two dimensional gel-electrophoresis and immunodetection on nitrocellulose membranes revealed the presence of vimentin and fibrinogen. In addition, by means of Western blotting, citrullination of vimentin was found as a characteristic post-translational modification.

Citrullinated vimentin as an important antigen in immune complexes from synovial fluid of rheumatoid arthritis patients with antibodies against citrullinated proteins
By: Van Steendam K, Tilleman K, De Ceuleneer M, De Keyser F, Elewaut D, Deforce D.
ARTHRITIS RESEARCH & THERAPY, 12(4): R132, 2010, DOI: 10.1186/ar3070

The design of engineered gold nanoparticles that can interact with living cells and tissues is important for many biomedical applications, including imaging, diagnostics, and drug delivery. Polymer-decoration of goldNP is attractive to modulate the goldNP properties and to render them colloidally stable in complex media. Also proteins can show different binding properties according to the polymer that is attached to the goldNP. To further investigate this, HEA x MEA y @goldNP were exposed to Foetal bovine serum. Subsequently, the particels were loaded on polyacrylamide gel (PAGE) and subjected to electrophoresis followed by in-gel digestion with trypsin. The bound proteins were identified by means of LC-MS/MS. Additionally, the hydrophobicity of the absorbed proteins was analysed by means of the GRAVY score.

Tailoring Cellular Uptake of Gold Nanoparticles Via the Hydrophilic-to-Hydrophobic Ratio of their (Co)polymer Coating
By: Zhang, Zhiyue; Van Steendam, Katleen; Maji, Samarendra; et al.
ADVANCED FUNCTIONAL MATERIALS, 25(22): 3433-3439, JUN 2015, DOI: 10.1002/adfm.201500904

Cell lysate from Devriesea agamarum was separated on two dimensional (2D) gel-electrophoresis and stained with Sypro Ruby. In parallel a 2D Western blot was prepared. Immunodetection with serum antibodies and their corresponding secundary and tertiary antibody revealed several immunoreactive spots on Western blot. These spots were excised from the gel and identified by means of mass spectrometry. Aminoacid sequences were matched by Mascot Daemon using the in-house sequenced genome from Devriesea agamarum.

Autovaccination confers protection against Devriesea agamarum associated septicemia but not dermatitis in bearded dragons (Pogona vitticeps)
By: Hellebuyck, T; Van Steendam, K; Deforce, D; Blooi, M; Van Nieuwerburgh, F; Bullaert, E; Ducatelle, R; Haesebrouck, F; Pasmans, F; Martel, A.
PLoS One, 9(12): e113084, DEC 2014, DOI: 10.1371/journal.pone.0113084

Genomics

Recent studies suggest a potent role of the small interfering RNA (siRNA) pathway in the control of bee viruses and its usefulness to tackle these viral diseases. However, the involvement of the siRNA pathway in the defense against different bee viruses is still poorly understood. Therefore, in this study, we comprehensively analyzed the response of the siRNA pathway in bumblebees of Bombus terrestris to systemic infections of the virulent Israeli acute paralysis virus (IAPV) and the avirulent slow bee paralysis virus (SBPV). Our analysis included quantification of abundance of the siRNA core gene expression levels, deep sequencing to examine virus-derived small RNAs, and use of an “RNAi-of-RNAi” approach to determine the effects of a reduced expression of Dicer-2, a core component of the RNAi machinery on viral titers.

In vivo study of Dicer-2-mediated immune response of the small interfering RNA pathway upon systemic infections of virulent and avirulent viruses in Bombus terrestris
By: Niu J, Smagghe G, De Coninck D, Van Nieuwerburgh F, Deforce D, Meeus I.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY, 70: 127-137, MAR 2016, DOI: 10.1016/j.ibmb.2015.12.006

Since the development of in vitro embryo production in cattle, different supplements have been added to culture media to support embryo development, with serum being the most popular. However, the addition of serum during embryo culture can induce high birthweights and low viability in calves (Large Offspring Syndrome). Analysis of global gene expression in bovine embryos produced under different conditions can provide valuable information to optimize culture media for in vitro embryo production. We used RNA sequencing to examine the effect of in vitro embryo production, in either serum-containing or serum-free media, on the global gene expression pattern of individual bovine blastocysts.

Suboptimal culture conditions induce more deviations in gene expression in male than female bovine blastocysts
By: Heras S, De Coninck D, Van Poucke M, Goossens K, Bogado Pascottini O, Van Nieuwerburgh F, Deforce D, De Sutter P, Leroy JL, Gutierrez-Adan A, Peelman L, Van Soom A.
BMC GENOMICS, 17(1): 72, JAN 2016, DOI: 10.1186/s12864-016-2393-z

Chromosomal abnormalities in early embryonic development can give rise to implantation failure, early spontaneous abortions and/or fetuses with multiple congenital anomalies. For couples with a known balanced or unbalanced chromosomal rearrangement, preimplantation genetic diagnosis (PGD) can be offered against unbalanced chromosomal aberrations in the embryo during assisted reproductive technology (ART). At the same time, it is well established that early-stage embryos suffer from a high rate of (mosaic) aneuploidy, reducing embryo survival, implantation potential, and hence the success rate of ART. While many techniques (FISH, aCGH) are used to screen for chromosomal imbalances in embryos, we investigated the potential of shallow whole genome sequencing for this screening. To this end a few cells were isolated from the blastocyst, their DNA was amplified and sequenced at a low (about 0.1x) coverage.

Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts
By: Deleye L, Dheendene A, De Coninck D, Sante T, Christodoulos C, Heindryckx B, Van den Abbeel E, De Sutter P, Deforce D, Menten B, Van Nieuwerburgh F
FERTILITY AND STERILITY, 104(5): 1276-1285, NOV 2015, DOI: 10.1016/j.fertnstert.2015.07.1144

A MiSeq multiplexed 16S rRNA amplicon sequencing of the gut microbiota of wild and indoor-reared Bombus terrestris (bumblebees) confirmed the presence of a core set of bacteria, which consisted of Neisseriaceae (Snodgrassella), Orbaceae (Gilliamella), Lactobacillaceae(Lactobacillus), and Bifidobacteriaceae (Bifidobacterium). In wild B. terrestris we detected several non-core bacteria having a more variable prevalence. Although Enterobacteriaceae are unreported by non next-generation sequencing studies, it can become a dominant gut resident. Furthermore the presence of some non-core lactobacilli were associated with the relative abundance of bifidobacteria. This association was not observed in indoor-reared bumblebees lacking the non-core bacteria, but having a more standardized microbiota compared to their wild counterparts.

16S rRNA Amplicon sequencing demonstrates that indoor-reared bumblebees (Bombus terrestris) harbor a core subset of bacteria normally associated with the wild host
By: Meeus I, Parmentier L, Billiet A, Maebe K, Van Nieuwerburgh F, Deforce D, Wäckers F, Vandamme P, Smagghe G.
PLOS ONE, 10(4): e0125152, APR 2015, DOI: 10.1371/journal.pone.0125152

Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies.

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)
By: Broeckx B, Coopman F, Verhoeven G, Bavegems V, De Keulenaer S, De Meester E, Van Nieuwerburgh F, Deforce D.
SCIENTIFIC REPORTS, 4: 5597, JUL 2014, DOI: 10.1038/srep05597

Technical variation induced along the experimental procedure. One way to do this, is the use of multiple reference genes, which are stably expressed throughout all samples analyzed. However, the selection of these references is not always straightforward. For example, when studying human embryonic stem cell (hESC) differentiation, the differentiation process itself might influence reference gene expression stability and render commonly used reference genes not to be the most adequate references anymore. In our experimental setup, we compared 12 candidate-references for retinoic acid-induced differentiating hESC with the geNorm algorithm. It was indeed proven that GAPDH, ACTB and PPIA were not amongst the most stable reference loci; instead, B2M, RPL13A and Alu repeats proved to be the most suitable genes. This again indicates that a reference stability analysis is required for each new experimental setting.

Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells
By: Vossaert L, O’Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D.
BMC MOLECULAR BIOLOGY, 14:21, SEP 2013, DOI: 10.1186/1471-2199-14-21