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44 results on '"Vissers, Johannes P.C."'

4. Cov2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein

Author

Van Puyvelde, Bart, primary, Van Uytfanghe, Katleen, additional, Van Oudenhove, Laurence, additional, Gabriels, Ralf, additional, Van Royen, Tessa, additional, Matthys, Arne, additional, Razavi, Morteza, additional, Yip, Richard, additional, Pearson, Terry, additional, Drouin, Nicolas, additional, Claereboudt, Jan, additional, Foley, Dominic, additional, Wardle, Robert, additional, Wyndham, Kevin, additional, Hankemeier, Thomas, additional, Jones, Donald, additional, Saelens, Xavier, additional, Martens, Geert, additional, Stove, Christophe P., additional, Deforce, Dieter, additional, Martens, Lennart, additional, Vissers, Johannes P.C., additional, Anderson, N. Leigh, additional, and Dhaenens, Maarten, additional

Published
2022
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5. Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use

Author

Hällqvist, Jenny, primary, Lane, Dan, additional, Shapanis, Andrew, additional, Davis, Kayleigh, additional, Heywood, Wendy E., additional, Doykov, Ivan, additional, Śpiewak, Justyna, additional, Ghansah, Nana, additional, Keevil, Brian, additional, Gupta, Pankaj, additional, Jukes-Jones, Rebekah, additional, Singh, Raj, additional, Foley, Dominic, additional, Vissers, Johannes P.C., additional, Pattison, Rebecca, additional, Ferries, Samantha, additional, Wardle, Robert, additional, Bartlett, Amy, additional, Calton, Lisa J., additional, Anderson, Leigh, additional, Razavi, Morteza, additional, Pearson, Terry, additional, Pope, Matt, additional, Yip, Richard, additional, Ng, Leong L., additional, Nicholas, Benjamin I., additional, Bailey, Alistair, additional, Noel, Dan, additional, Dalton, R. Neil, additional, Heales, Simon, additional, Hopley, Christopher, additional, Pitt, Andrew R., additional, Barran, Perdita, additional, Jones, Donald J. L., additional, Mills, Kevin, additional, Skipp, Paul, additional, and Carling, Rachel S., additional

Published
2022
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6. Paper Spray Ionization Ion Mobility Mass Spectrometry of Sebum Classifies Biomarker Classes for the Diagnosis of Parkinson’s Disease

Author

Sarkar, Depanjan, primary, Sinclair, Eleanor, additional, Lim, Sze Hway, additional, Walton-Doyle, Caitlin, additional, Jafri, Kaneez, additional, Milne, Joy, additional, Vissers, Johannes P.C., additional, Richardson, Keith, additional, Trivedi, Drupad K., additional, Silverdale, Monty, additional, and Barran, Perdita, additional

Published
2022
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9. Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use.

Author

Hällqvist, Jenny, Lane, Dan, Shapanis, Andrew, Davis, Kayleigh, Heywood, Wendy E., Doykov, Ivan, Śpiewak, Justyna, Ghansah, Nana, Keevil, Brian, Gupta, Pankaj, Jukes-Jones, Rebekah, Singh, Raj, Foley, Dominic, Vissers, Johannes P.C., Pattison, Rebecca, Ferries, Samantha, Wardle, Robert, Bartlett, Amy, Calton, Lisa J., and Anderson, Leigh

Subjects
IMMUNOAFFINITY chromatography, LIQUID chromatography-mass spectrometry, PEPTIDES, SARS-CoV-2, MASS spectrometry
Abstract

During 2020, the UK's Department of Health and Social Care (DHSC) established the Moonshot programme to fund various diagnostic approaches for the detection of SARS-CoV-2, the pathogen behind the COVID-19 pandemic. Mass spectrometry was one of the technologies proposed to increase testing capacity. Moonshot funded a multi-phase development programme, bringing together experts from academia, industry and the NHS to develop a state-of-the-art targeted protein assay utilising enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS) to capture and detect low levels of tryptic peptides derived from SARS-CoV-2 virus. The assay relies on detection of target peptides, ADETQALPQRK (ADE) and AYNVTQAFGR (AYN), derived from the nucleocapsid protein of SARS-CoV-2, measurement of which allowed the specific, sensitive, and robust detection of the virus from nasopharyngeal (NP) swabs. The diagnostic sensitivity and specificity of LC-MS/MS was compared with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) via a prospective study. Analysis of NP swabs (n=361) with a median RT-qPCR quantification cycle (Cq) of 27 (range 16.7–39.1) demonstrated diagnostic sensitivity of 92.4% (87.4–95.5), specificity of 97.4% (94.0–98.9) and near total concordance with RT-qPCR (Cohen's Kappa 0.90). Excluding Cq>32 samples, sensitivity was 97.9% (94.1–99.3), specificity 97.4% (94.0–98.9) and Cohen's Kappa 0.95. This unique collaboration between academia, industry and the NHS enabled development, translation, and validation of a SARS-CoV-2 method in NP swabs to be achieved in 5 months. This pilot provides a model and pipeline for future accelerated development and implementation of LC-MS/MS protein/peptide assays into the routine clinical laboratory. [ABSTRACT FROM AUTHOR]

Published
2023
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11. Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment LC-MS Analysis

Author

Hober, Andreas, primary, Hua, Tran-Minh Khue, additional, Foley, Dominic, additional, McDonald, Thomas, additional, Vissers, Johannes P.C., additional, Pattison, Rebecca, additional, Ferries, Samantha, additional, Hermansson, Sigurd, additional, Betner, Ingvar, additional, Uhlen, Mathias, additional, Razavi, Morteza, additional, Yip, Richard, additional, Pope, Matthew E., additional, Pearson, Terry W., additional, Anderson, N. Leigh, additional, Bartlett, Amy, additional, Calton, Lisa, additional, Alm, Jessica J., additional, Engstrand, Lars, additional, and Edfors, Fredrik, additional

Published
2021
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14. Colloid chemical aspects of slurry packing techniques in microcolumn liquid chromatography

Author

Vissers, Johannes P.C., Claessens, Henk A., Laven, Jozua, and Cramers, Carel A.

Subjects
Colloids -- Research, Slurry -- Research, Liquid chromatography -- Research, Chemistry
Abstract

The relationship between the coagulating properties of slurry suspensions, type of packing liquids, and final performance of slurry-packed microcolumns for liquid chromatography (LC) was investigated. The colloidal stability of stationary-phase suspensions was examined by means of sedimentation and [Xi]-potential experiments. Expressions for the theoretical sedimentation rate of noncoagulated particle suspensions were derived for spherical particles with completely and incompletely filled pores and for irregularly shaped particles with incompletely filled pores. The performance of the slurry-packed microcolumns was predominantly determined by the selection of the packing liquid. It is shown that the packing liquid preferably has to be coagulating to obtain efficient and stable packed capillary LC columns. The selection of the slurry liquid on the column performance was of minor importance.

Published
1995

15. Determination of protein haptenation by chemical sensitisers within the complexity of the human skin proteome: protein-sensitiser haptenation of complex cellular lysates

Author

Parkinson, Erika, Aleksic, Maja, Cubberley, Richard, Kaur-Atwal, Gushinder, Vissers, Johannes P.C., and Skipp, Paul

Abstract

Skin sensitisation associated with the development of allergic contact dermatitis (ACD) occurs via a number of specific key events at the cellular level. The molecular initiating event (MIE), the first in the sequence of these events, occurs after exposure of the skin to an electrophilic chemical, causing the irreversible haptenation of proteins within skin. Characterisation of this MIE is a key step in elucidating the skin sensitisation adverse outcome pathway and is essential to providing parameters for mathematical models to predict the capacity of a chemical to cause sensitisation. As a first step to addressing this challenge, we have exposed complex protein lysates from a keratinocyte cell line and human skin tissue with a range of well characterised sensitisers, including dinitrochlorobenzene (DNCB), 5-chloro-2-methylisothiazol-3-one (MCI), cinnamaldehyde (CA) and the non (or weak) sensitiser 6-methyl coumarin (6-MC). Using a novel stable isotope labelling approach combined with ion mobility assisted data independent mass spectrometry (HDMSE), we have characterised the haptenome for these sensitisers. Although a significant proportion of highly abundant proteins were haptenated, we also observed the haptenation of low abundant proteins by all three of the chemical sensitisers tested, indicating that within a complex protein background, protein abundance is not the sole determinant driving haptenation, highlighting a relationship to tertiary protein structure and the amino acid specificity of these chemical sensitisers and sensitiser potency.

Published
2018

16. Excessive dietary lipid intake provokes an acquired form of lysosomal lipid storage disease in the kidney

Author

Rampanelli, Elena, Ochodnicky, Peter, Vissers, Johannes P.C., Butter, Loes M., Claessen, Nike, Calcagni, Alessia, Steenbergen, E., Florquin, Sandrine, Aerts, Johannes M.F.G., and Leemans, Jaklien C.

Subjects
All institutes and research themes of the Radboud University Medical Center, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11]
Abstract

Item does not contain fulltext

Published
2018

17. A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine

Author

Nye, Leanne C., primary, Williams, Jonathan P., additional, Munjoma, Nyasha C., additional, Letertre, Marine P.M., additional, Coen, Muireann, additional, Bouwmeester, Robbin, additional, Martens, Lennart, additional, Swann, Jonathan R., additional, Nicholson, Jeremy K., additional, Plumb, Robert S., additional, McCullagh, Michael, additional, Gethings, Lee A., additional, Lai, Steven, additional, Langridge, James I., additional, Vissers, Johannes P.C., additional, and Wilson, Ian D., additional

Published
2019
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22. Quantitative Proteome Analysis of Mouse Liver Lysosomes Provides Evidence for Mannose 6-phosphate-independent Targeting Mechanisms of Acid Hydrolases in Mucolipidosis II

Author

Markmann, Sandra, primary, Krambeck, Svenja, additional, Hughes, Christopher J., additional, Mirzaian, Mina, additional, Aerts, Johannes M.F.G., additional, Saftig, Paul, additional, Schweizer, Michaela, additional, Vissers, Johannes P.C., additional, Braulke, Thomas, additional, and Damme, Markus, additional

Published
2017
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23. Verification of a Parkinson's Disease Protein Signature by Multiple Reaction Monitoring

Author

McMahon, Kelly, Cuccurullo, Manuela, Gethings, Lee A., Lawless, Craig, Zibetti, Maurizio, Lopiano, Leonardo, Vissers, Johannes P.C., Fasano, Mauro, and Alberio, Tiziana

Subjects
Poster Abstracts
Abstract

OBJECTIVE: Integration of different ‘omics data (genomic, transcriptomic, proteomic) reveals novel discoveries into biological systems. Integration of these datasets is challenging however, involving use of multiple disparate software in a sequential manner. However, the use of multiple, disparate software in a sequential manner makes the integration of multi-omic data a serious challenge. We describe the extension of Galaxy for mass spectrometric-based proteomics software, enabling advanced multi-omic applications in proteogenomics and metaproteomics. We will demonstrate the benefits of Galaxy for these analyses, as well as its value for software developers seeking to publish new software. We will also share insights on the benefits of the Galaxy framework as a bioinformatics solution for proteomic/metabolomic core facilities. METHODS: Multiple datasets for proteogenomics research (3D-fractionated salivary dataset and oral pre-malignant lesion (OPML) dataset) and metaproteomics research (OPML dataset and Severe Early Childhood Caries (SECC) dataset). Software required for analytical steps such as peaklist generation, database generation (RNA-Seq derived and others), database search (ProteinPilot and X! tandem) and for quantitative proteomics were deployed, tested and optimized for use in workflows. The software are shared in Galaxy toolshed (http://toolshed.g2.bx.psu.edu/). Results: Usage of analytical workflows resulted in reliable identification of novel proteoforms (proteogenomics) or microorganisms (metaproteomics). Proteogenomics analysis identified novel proteoforms in the salivary dataset (51) and OPML dataset (38). Metaproteomics analysis led to microbial identification in OPML and SECC datasets using MEGAN software. As examples, workflows for proteogenomics analysis (http://z.umn.edu/pg140) and metaproteomic analysis (http://z.umn.edu/mp65) are available at the usegalaxyp.org website. Tutorials for workflow usage within Galaxy-P framework are also available (http://z.umn.edu/ppingp). CONCLUSIONS: We demonstrate the use of Galaxy for integrated analysis of multi-omic data, in an accessible, transparent and reproducible manner. Our results and experiences using this framework demonstrate the potential for Galaxy to be a unifying bioinformatics solution for ‘omics core facilities.

Published
2014

25. Inside Front Cover: Multi-mode acquisition (MMA): An MS/MS acquisition strategy for maximizing selectivity, specificity and sensitivity of DIA product ion spectra

Author

Williams, Brad J., primary, Ciavarini, Steve J., additional, Devlin, Curt, additional, Cohn, Steven M., additional, Xie, Rong, additional, Vissers, Johannes P.C., additional, Martin, LeRoy B., additional, Caswell, Allen, additional, Langridge, James I., additional, and Geromanos, Scott J., additional

Published
2016
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26. Elevation of glycoprotein nonmetastatic melanoma protein B in type 1 Gaucher disease patients and mouse models

Author

Kramer, Gertjan, primary, Wegdam, Wouter, additional, Donker‐Koopman, Wilma, additional, Ottenhoff, Roelof, additional, Gaspar, Paulo, additional, Verhoek, Marri, additional, Nelson, Jessica, additional, Gabriel, Tanit, additional, Kallemeijn, Wouter, additional, Boot, Rolf G., additional, Laman, Jon D., additional, Vissers, Johannes P.C., additional, Cox, Timothy, additional, Pavlova, Elena, additional, Moran, Mary Teresa, additional, Aerts, Johannes M., additional, and Eijk, Marco, additional

Published
2016
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27. Quantitation and Validation of Low ng/ml Levels of Calcyclin: a Potential Pre-eclampsia Marker – in Serum by SRM

Author

Guzel, Coskun, Bartlett, Amy, Vissers, Johannes P.C., Steegers, Eric A.P., Luider, Theo M., Dekker, Lennard J.M., and Martin, Roy

Subjects
embryonic structures, Scientific Poster Abstracts, reproductive and urinary physiology
Abstract

Pre-eclampsia is a pregnancy-specific disease that complicates 2-8% of all pregnancies. It is associated with serious perinatal and maternal morbidity and mortality. We previously demonstrated that in pre-eclampsia placenta, calcyclin expression is significantly higher compared to controls. The sensitivity of this analysis was improved by Selective Reaction Monitoring (SRM) using a Xevo TQ-S mass spectrometer enabling the quantitation of calcyclin at low attomole levels in trophoblast cells. Next, a method was developed to quantify calcyclin in digested sera to evaluate calcyclin as a potential serum biomarker.

Published
2012

30. Evaluation of MSE based protein quantification methods

Author

Aloria, Kerman, Omaetxebarria, Miren Josu, Azkargorta, Mikel, Vissers, Johannes P.C., Fullaondo, Asier, and Arizmendi, Jesús M.

Subjects
Sistemas biológicos, Biotecnología, Proteómica
Abstract

Comunicaciones a congresos

Published
2010

31. Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics

Author

Helm, Dominic, primary, Vissers, Johannes P.C., additional, Hughes, Christopher J., additional, Hahne, Hannes, additional, Ruprecht, Benjamin, additional, Pachl, Fiona, additional, Grzyb, Arkadiusz, additional, Richardson, Keith, additional, Wildgoose, Jason, additional, Maier, Stefan K., additional, Marx, Harald, additional, Wilhelm, Mathias, additional, Becher, Isabelle, additional, Lemeer, Simone, additional, Bantscheff, Marcus, additional, Langridge, James I., additional, and Kuster, Bernhard, additional

Published
2014
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34. A Probabilistic Framework for Peptide and Protein Quantification from Data-Dependent and Data-Independent LC-MS Proteomics Experiments

Author

Richardson, Keith, primary, Denny, Richard, additional, Hughes, Chris, additional, Skilling, John, additional, Sikora, Jacek, additional, Dadlez, Michał, additional, Manteca, Angel, additional, Jung, Hye Ryung, additional, Jensen, Ole Nørregaard, additional, Redeker, Virginie, additional, Melki, Ronald, additional, Langridge, James I., additional, and Vissers, Johannes P.C., additional

Published
2012
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35. Simulating and validating proteomics data and search results

Author

Geromanos, Scott J., primary, Hughes, Chris, additional, Golick, Dan, additional, Ciavarini, Steven, additional, Gorenstein, Marc V., additional, Richardson, Keith, additional, Hoyes, John B., additional, Vissers, Johannes P.C., additional, and Langridge, James I., additional

Published
2011
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44. Survey of bacterial proteins released in cheese: a proteomic approach

Author

Gagnaire, Valérie, Piot, Michel, Camier, Bénédicte, Vissers, Johannes P.C., Jan, Gwénaël, and Léonil, Joëlle

Subjects
*BACTERIAL proteins, *CHEESE, *TASTE testing of food, *PROTEOMICS
Abstract

During the ripening of Emmental cheese, the bacterial ecosystem confers its organoleptic characteristics to the evolving curd both by the action of the living cells, and through the release of numerous proteins, including various types of enzymes into the cheese when the cells lyse. In Emmental cheese these proteins can be released from thermophilic lactic acid bacteria used as starters like Lactobacillus helveticus, Lb delbruecki subsp. lactis and Streptococcus salivarius subsp. thermophilus and ripening bacteria such as Propionibacterium freudenreichii. The aim of this study was to obtain a proteomic view of the different groups of proteins within the cheese using proteomic tools to create a reference map. A methodology was therefore developed to reduce the complexity of cheese matrix prior to 2D-PAGE analysis. The aqueous phase of cheese was prefractionated by size exclusion chromatography, bacterial and milk proteins were separated and subsequently characterised by mass spectrometry, prior to peptide mass fingerprint and sequence homology database search. Five functional groups of proteins were identified involved in: (i) proteolysis, (ii) glycolysis, (iii) stress response, (iv) DNA and RNA repair and (v) oxidoreduction. The results revealed stress responses triggered by thermophilic lactic acid bacteria and Propionibacterium strains at the end of ripening.Information was also obtained regarding the origin and nature of the peptidases released into the cheese, thus providing a greater understanding of casein degradation mechanisms during ripening. Different peptidases arose from St thermophilus and Lb helveticus, suggesting that streptococci are involved in peptide degradation in addition to the proteolytic activity of lactobacilli. [Copyright &y& Elsevier]

Published
2004
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