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24 results on '"Schulte, Douwe"'

1. Into the Dark Serum Proteome: Personalized Features of IgG1 and IgA1 Repertoires in Severe COVID-19 Patients

Author

Bondt, Albert, Hoek, Max, Dingess, Kelly, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, den Boer, Maurits A., Damen, Mirjam, Zwart, Ceri, Barendregt, Arjan, van Rijswijck, Danique M.H., Schulte, Douwe, Grobben, Marloes, Tejjani, Khadija, van Rijswijk, Jacqueline, Völlmy, Franziska, Snijder, Joost, Fortini, Francesca, Papi, Alberto, Volta, Carlo Alberto, Campo, Gianluca, Contoli, Marco, van Gils, Marit J., Spadaro, Savino, Rizzo, Paola, and Heck, Albert J.R.

Published
2024
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5. Into the dark serum proteome: personalized features of IgG1 and IgA1 repertoires in severe COVID-19 patients

Author

Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Bondt, Albert, Hoek, Max, Dingess, Kelly, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, den Boer, Maurits A, Damen, Mirjam, Zwart, Ceri, Barendregt, Arjan, van Rijswijck, Danique M H, Schulte, Douwe, Grobben, Marloes, Tejjani, Khadija, van Rijswijk, Jacqueline, Völlmy, Franziska, Snijder, Joost, Fortini, Francesca, Papi, Alberto, Volta, Carlo Alberto, Campo, Gianluca, Contoli, Marco, van Gils, Marit J, Spadaro, Savino, Rizzo, Paola, Heck, Albert J R, Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Bondt, Albert, Hoek, Max, Dingess, Kelly, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, den Boer, Maurits A, Damen, Mirjam, Zwart, Ceri, Barendregt, Arjan, van Rijswijck, Danique M H, Schulte, Douwe, Grobben, Marloes, Tejjani, Khadija, van Rijswijk, Jacqueline, Völlmy, Franziska, Snijder, Joost, Fortini, Francesca, Papi, Alberto, Volta, Carlo Alberto, Campo, Gianluca, Contoli, Marco, van Gils, Marit J, Spadaro, Savino, Rizzo, Paola, and Heck, Albert J R

Published
2024

6. Reverse-engineering the anti-MUC1 antibody 139H2 by mass spectrometry–based de novo sequencing

Author

Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Infectiebiologie, Infectious Diseases and Immunology - Infection Biology, Sub Structural Biochemistry, Structural Biochemistry, Infectious Diseases and Immunology - KLIF, Peng, Weiwei, Giesbers, Koen, Siborova, Marta, Beugelink, Wouter, Pronker, Matti, Schulte, Douwe, Hilkens, John, Janssen, Bert, Strijbis, Karin, Snijder, Joost, Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Infectiebiologie, Infectious Diseases and Immunology - Infection Biology, Sub Structural Biochemistry, Structural Biochemistry, Infectious Diseases and Immunology - KLIF, Peng, Weiwei, Giesbers, Koen, Siborova, Marta, Beugelink, Wouter, Pronker, Matti, Schulte, Douwe, Hilkens, John, Janssen, Bert, Strijbis, Karin, and Snijder, Joost

Published
2024

8. Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study

Author

Peng, Weiwei, primary, den Boer, Maurits A., additional, Tamara, Sem, additional, Mokiem, Nadia J., additional, van der Lans, Sjors P. A., additional, Bondt, Albert, additional, Schulte, Douwe, additional, Haas, Pieter-Jan, additional, Minnema, Monique C., additional, Rooijakkers, Suzan H. M., additional, van Zuilen, Arjan D., additional, Heck, Albert J. R., additional, and Snijder, Joost, additional

Published
2023
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10. Reverse engineering the anti-MUC1 hybridoma antibody 139H2 by mass spectrometry-based de novo sequencing

Author

Sub Biomol.Mass Spectrometry & Proteom., Infectiebiologie, Sub Structural Biochemistry, Infectious Diseases and Immunology - Infection Biology, Peng, Weiwei, Giesbers, Koen C.A.P., Šiborová, Marta, Beugelink, J. Wouter, Pronker, Matti F., Schulte, Douwe, Hilkens, John, Janssen, Bert J.C., Strijbis, Karin, Snijder, Joost, Sub Biomol.Mass Spectrometry & Proteom., Infectiebiologie, Sub Structural Biochemistry, Infectious Diseases and Immunology - Infection Biology, Peng, Weiwei, Giesbers, Koen C.A.P., Šiborová, Marta, Beugelink, J. Wouter, Pronker, Matti F., Schulte, Douwe, Hilkens, John, Janssen, Bert J.C., Strijbis, Karin, and Snijder, Joost

Published
2023

11. Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Peng, Weiwei, den Boer, Maurits A, Tamara, Sem, Mokiem, Nadia J, van der Lans, Sjors P A, Bondt, Albert, Schulte, Douwe, Haas, Pieter-Jan, Minnema, Monique C, Rooijakkers, Suzan H M, van Zuilen, Arjan D, Heck, Albert J R, Snijder, Joost, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Peng, Weiwei, den Boer, Maurits A, Tamara, Sem, Mokiem, Nadia J, van der Lans, Sjors P A, Bondt, Albert, Schulte, Douwe, Haas, Pieter-Jan, Minnema, Monique C, Rooijakkers, Suzan H M, van Zuilen, Arjan D, Heck, Albert J R, and Snijder, Joost

Published
2023

12. Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study

Author

MMB Research line 1, Infection & Immunity, MMB Medische Staf, MS Hematologie, Cancer, Regenerative Medicine and Stem Cells, MS Nefrologie, Circulatory Health, Peng, Weiwei, den Boer, Maurits A, Tamara, Sem, Mokiem, Nadia J, van der Lans, Sjors P A, Bondt, Albert, Schulte, Douwe, Haas, Pieter-Jan, Minnema, Monique C, Rooijakkers, Suzan H M, van Zuilen, Arjan D, Heck, Albert J R, Snijder, Joost, MMB Research line 1, Infection & Immunity, MMB Medische Staf, MS Hematologie, Cancer, Regenerative Medicine and Stem Cells, MS Nefrologie, Circulatory Health, Peng, Weiwei, den Boer, Maurits A, Tamara, Sem, Mokiem, Nadia J, van der Lans, Sjors P A, Bondt, Albert, Schulte, Douwe, Haas, Pieter-Jan, Minnema, Monique C, Rooijakkers, Suzan H M, van Zuilen, Arjan D, Heck, Albert J R, and Snijder, Joost

Published
2023

13. What Do We (Not) Know About Research Software Engineering?

Author

Lamprecht, Anna-Lena, Martinez-Ortiz, Carlos, Barker, Michelle, Bartholomew, Sadie L., Barton, Justin, Chue Hong, Neil, Cohen, Jeremy, Druskat, Stephan, Forest, Jeremy, Grad, Jean-Noël, Katz, Daniel S., Richardson, Robin, Rosca, Robert, Schulte, Douwe, Struck, Alexander, and Weinzierl, Marion

Subjects
rewards and incentives, science policy, training, career paths, software sustainability, computational science, infrastructure, Library and Information Sciences, eScience, research software engineering, Software, Information Systems
Abstract

As recognition of the vital importance of software for contemporary research is increasing, Research Software Engineering (RSE) is emerging as a discipline in its own right. We present an inventory of relevant research questions about RSE as a basis for future research and initiatives to advance the field, highlighting selected literature and initiatives. This work is the outcome of a RSE community workshop held as part of the 2020 International Series of Online Research Software Events (SORSE) which identified and prioritized key questions across three overlapping themes: people, policy and infrastructure. Almost half of the questions focus on the people theme, which addresses issues related to career paths, recognition and motivation; recruitment and retention; skills; and diversity, equity and inclusion. However, the people and policy themes have the same number of prioritized questions. We recommend that different types of stakeholders, such as RSE employers and policy makers, take responsibility for supporting or encouraging answering of these questions by organizations that have an interest. Initiatives such as the International Council of RSE Associations should also be engaged in this work.&nbsp

Published
2022

14. Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling: Analytical Chemistry

Author

Schulte, Douwe, Peng, Weiwei, Snijder, Joost, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Abstract

Antibodies can target a vast molecular diversity of antigens. This is achieved by generating a complementary diversity of antibody sequences through somatic recombination and hypermutation. A full understanding of the antibody repertoire in health and disease therefore requires dedicated de novo sequencing methods. Next-generation cDNA sequencing methods have laid the foundation of our current understanding of the antibody repertoire, but these methods share one major limitation in that they target the antibody-producing B-cells, rather than the functional secreted product in bodily fluids. Mass spectrometry-based methods offer an opportunity to bridge this gap between antibody repertoire profiling and bulk serological assays, as they can access antibody sequence information straight from the secreted polypeptide products. In a step to meeting the challenge of mass spectrometry (MS)-based antibody sequencing, we present a fast and simple software tool (Stitch) to map proteomic short reads to user-defined templates with dedicated features for both monoclonal antibody sequencing and profiling of polyclonal antibody repertoires. We demonstrate the use of Stitch by fully reconstructing two monoclonal antibody sequences with >98% accuracy (including I/L assignment); sequencing a Fab from patient serum isolated by reversed-phase liquid chromatography (LC) fractionation against a high background of homologous antibody sequences; sequencing antibody light chains from the urine of multiple-myeloma patients; and profiling the IgG repertoire in sera from patients hospitalized with COVID-19. We demonstrate that Stitch assembles a comprehensive overview of the antibody sequences that are represented in the dataset and provides an important first step toward analyzing polyclonal antibodies and repertoire profiling.

Published
2022

15. Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling: Analytical Chemistry

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Schulte, Douwe, Peng, Weiwei, Snijder, Joost, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Schulte, Douwe, Peng, Weiwei, and Snijder, Joost

Published
2022

17. Human plasma IgG1 repertoires are simple, unique, and dynamic

Author

Bondt, Albert, Hoek, Max, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, Schulte, Douwe, van Rijswijck, Danique M H, den Boer, Maurits A, Greisch, Jean-François, Varkila, Meri R J, Snijder, Joost, Cremer, Olaf L, Bonten, Marc J M, Heck, Albert J R, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Sub Intelligent Systems, Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Sub Intelligent Systems, and Biomolecular Mass Spectrometry and Proteomics

Subjects
Mutation rate, Histology, IgG, Clone (cell biology), immunoglobulins, Somatic hypermutation, serology, Computational biology, Top-down proteomics, top-down proteomics, Article, Germline, Pathology and Forensic Medicine, sepsis, Plasma, 03 medical and health sciences, 0302 clinical medicine, de novo sequencing, Humans, antibodies, 030304 developmental biology, Sequence (medicine), mass spectrometry, 0303 health sciences, biology, Repertoire, DNA, Cell Biology, Fab profiling, 3. Good health, LC-MS, Immunoglobulin G, biology.protein, Antibody, Peptides, 030217 neurology & neurosurgery
Abstract

Summary Although humans can produce billions of IgG1 variants through recombination and hypermutation, the diversity of IgG1 clones circulating in human blood plasma has largely eluded direct characterization. Here, we combined several mass-spectrometry-based approaches to reveal that the circulating IgG1 repertoire in human plasma is dominated by a limited number of clones in healthy donors and septic patients. We observe that each individual donor exhibits a unique serological IgG1 repertoire, which remains stable over time but can adapt rapidly to changes in physiology. We introduce an integrative protein- and peptide-centric approach to obtain and validate a full sequence of an individual plasma IgG1 clone de novo. This IgG1 clone emerged at the onset of a septic episode and exhibited a high mutation rate (13%) compared with the closest matching germline DNA sequence, highlighting the importance of de novo sequencing at the protein level. A record of this paper’s transparent peer review process is included in the supplemental information., Graphical abstract, Highlights • Novel LC-MS-based methods enable personalized IgG1 profiling in plasma • Each donor exhibits a simple but unique serological IgG1 repertoire • This repertoire adapts to changes in physiology, e.g., sepsis • Individual plasma IgG1 clones can be identified by combining top-down and bottom-up proteomics, The human body produces immunoglobulins (Igs) to help combat pathogens. The number of distinct IgG molecules our body can produce exceeds several billions. In contrast to this near-infinite theoretical number, we reveal here, as monitored directly by LC-MS, that only a few dozen distinct clones dominate in abundance the total spectrum of plasma IgG1s of both healthy and diseased donors. Our data indicate that each donor’s IgG1 repertoire is distinctively unique. We longitudinally profile an individual’s IgG1 repertoire and observe the occurrence or disappearance of specific IgGs over time in response to changes in physiology, e.g., during a septic episode. As a proof of concept, we show that individual plasma IgG1 clones can be quantified and fully sequenced and identified by using a combination of top-down and bottom-up proteomics.

Published
2021

18. Human plasma IgG1 repertoires are simple, unique, and dynamic

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Sub Intelligent Systems, Biomolecular Mass Spectrometry and Proteomics, Bondt, Albert, Hoek, Max, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, Schulte, Douwe, van Rijswijck, Danique M H, den Boer, Maurits A, Greisch, Jean-François, Varkila, Meri R J, Snijder, Joost, Cremer, Olaf L, Bonten, Marc J M, Heck, Albert J R, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Sub Intelligent Systems, Biomolecular Mass Spectrometry and Proteomics, Bondt, Albert, Hoek, Max, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, Schulte, Douwe, van Rijswijck, Danique M H, den Boer, Maurits A, Greisch, Jean-François, Varkila, Meri R J, Snijder, Joost, Cremer, Olaf L, Bonten, Marc J M, and Heck, Albert J R

Published
2021

19. Human plasma IgG1 repertoires are simple, unique, and dynamic

Author

MMB Research line 1, Infection & Immunity, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectieziekten, Medische Staf Intensive Care, Epi Infectieziekten, Bondt, Albert, Hoek, Max, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, Schulte, Douwe, van Rijswijck, Danique M H, den Boer, Maurits A, Greisch, Jean-François, Varkila, Meri R J, Snijder, Joost, Cremer, Olaf L, Bonten, Marc J M, Heck, Albert J R, MMB Research line 1, Infection & Immunity, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectieziekten, Medische Staf Intensive Care, Epi Infectieziekten, Bondt, Albert, Hoek, Max, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, Schulte, Douwe, van Rijswijck, Danique M H, den Boer, Maurits A, Greisch, Jean-François, Varkila, Meri R J, Snijder, Joost, Cremer, Olaf L, Bonten, Marc J M, and Heck, Albert J R

Published
2021

20. Human Plasma IgG1 Repertoires are Simple, Unique, and Dynamic

Author

Bondt, Albert, primary, Hoek, Max, additional, Tamara, Sem, additional, de Graaf, Bastiaan, additional, Peng, Weiwei, additional, Schulte, Douwe, additional, den Boer, Maurits Arij, additional, Greisch, Jean-François, additional, Varkila, Meri R.J., additional, Snijder, Joost, additional, Cremer, Olaf L., additional, Bonten, Marc J.M., additional, and Heck, Albert J.R., additional

Published
2020
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21. Template-Based Assembly of Proteomic Short Reads For De NovoAntibody Sequencing and Repertoire Profiling

Author

Schulte, Douwe, Peng, Weiwei, and Snijder, Joost

Abstract

Antibodies can target a vast molecular diversity of antigens. This is achieved by generating a complementary diversity of antibody sequences through somatic recombination and hypermutation. A full understanding of the antibody repertoire in health and disease therefore requires dedicated de novosequencing methods. Next-generation cDNA sequencing methods have laid the foundation of our current understanding of the antibody repertoire, but these methods share one major limitation in that they target the antibody-producing B-cells, rather than the functional secreted product in bodily fluids. Mass spectrometry-based methods offer an opportunity to bridge this gap between antibody repertoire profiling and bulk serological assays, as they can access antibody sequence information straight from the secreted polypeptide products. In a step to meeting the challenge of mass spectrometry (MS)-based antibody sequencing, we present a fast and simple software tool (Stitch) to map proteomic short reads to user-defined templates with dedicated features for both monoclonal antibody sequencing and profiling of polyclonal antibody repertoires. We demonstrate the use of Stitch by fully reconstructing two monoclonal antibody sequences with >98% accuracy (including I/L assignment); sequencing a Fab from patient serum isolated by reversed-phase liquid chromatography (LC) fractionation against a high background of homologous antibody sequences; sequencing antibody light chains from the urine of multiple-myeloma patients; and profiling the IgG repertoire in sera from patients hospitalized with COVID-19. We demonstrate that Stitch assembles a comprehensive overview of the antibody sequences that are represented in the dataset and provides an important first step toward analyzing polyclonal antibodies and repertoire profiling.

Published
2022
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22. A Handle on Mass Coincidence Errors in De NovoSequencing of Antibodies by Bottom-up Proteomics

Author

Schulte, Douwe and Snijder, Joost

Abstract

Antibody sequences can be determined at 99% accuracy directly from the polypeptide product by using bottom-up proteomics techniques. Sequencing accuracy at the peptide level is limited by the isobaric residues leucine and isoleucine, incomplete fragmentation spectra in which the order of two or more residues remains ambiguous due to lacking fragment ions for the intermediate positions, and isobaric combinations of amino acids, of potentially different lengths, for example, GG = N and GA = Q. Here, we present several updates to Stitch (v1.5), which performs template-based assembly of de novopeptides to reconstruct antibody sequences. This version introduces a mass-based alignment algorithm that explicitly accounts for mass coincidence errors. In addition, it incorporates a postprocessing procedure to assign I/L residues based on secondary fragments (satellite ions, i.e., w-ions). Moreover, evidence for sequence assignments can now be directly evaluated with the addition of an integrated spectrum viewer. Lastly, input data from a wider selection of de novopeptide sequencing algorithms are allowed, now including Casanovo, PEAKS, Novor.Cloud, pNovo, and MaxNovo, in addition to flat text and FASTA. Combined, these changes make Stitch compatible with a larger range of data processing pipelines and improve its tolerance to peptide-level sequencing errors.

Published
2024
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23. Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling.

Author

Schulte D, Peng W, and Snijder J

Subjects
Antibodies, Monoclonal, High-Throughput Nucleotide Sequencing methods, Humans, Immunoglobulin Light Chains genetics, COVID-19, Proteomics
Abstract

Antibodies can target a vast molecular diversity of antigens. This is achieved by generating a complementary diversity of antibody sequences through somatic recombination and hypermutation. A full understanding of the antibody repertoire in health and disease therefore requires dedicated de novo sequencing methods. Next-generation cDNA sequencing methods have laid the foundation of our current understanding of the antibody repertoire, but these methods share one major limitation in that they target the antibody-producing B-cells, rather than the functional secreted product in bodily fluids. Mass spectrometry-based methods offer an opportunity to bridge this gap between antibody repertoire profiling and bulk serological assays, as they can access antibody sequence information straight from the secreted polypeptide products. In a step to meeting the challenge of mass spectrometry (MS)-based antibody sequencing, we present a fast and simple software tool (Stitch) to map proteomic short reads to user-defined templates with dedicated features for both monoclonal antibody sequencing and profiling of polyclonal antibody repertoires. We demonstrate the use of Stitch by fully reconstructing two monoclonal antibody sequences with >98% accuracy (including I/L assignment); sequencing a Fab from patient serum isolated by reversed-phase liquid chromatography (LC) fractionation against a high background of homologous antibody sequences; sequencing antibody light chains from the urine of multiple-myeloma patients; and profiling the IgG repertoire in sera from patients hospitalized with COVID-19. We demonstrate that Stitch assembles a comprehensive overview of the antibody sequences that are represented in the dataset and provides an important first step toward analyzing polyclonal antibodies and repertoire profiling.

Published
2022
Full Text
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24. Human plasma IgG1 repertoires are simple, unique, and dynamic.

Author

Bondt A, Hoek M, Tamara S, de Graaf B, Peng W, Schulte D, van Rijswijck DMH, den Boer MA, Greisch JF, Varkila MRJ, Snijder J, Cremer OL, Bonten MJM, and Heck AJR

Subjects
Humans, Mass Spectrometry, Peptides, Plasma, DNA, Immunoglobulin G genetics
Abstract

Although humans can produce billions of IgG1 variants through recombination and hypermutation, the diversity of IgG1 clones circulating in human blood plasma has largely eluded direct characterization. Here, we combined several mass-spectrometry-based approaches to reveal that the circulating IgG1 repertoire in human plasma is dominated by a limited number of clones in healthy donors and septic patients. We observe that each individual donor exhibits a unique serological IgG1 repertoire, which remains stable over time but can adapt rapidly to changes in physiology. We introduce an integrative protein- and peptide-centric approach to obtain and validate a full sequence of an individual plasma IgG1 clone de novo. This IgG1 clone emerged at the onset of a septic episode and exhibited a high mutation rate (13%) compared with the closest matching germline DNA sequence, highlighting the importance of de novo sequencing at the protein level. A record of this paper's transparent peer review process is included in the supplemental information., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2021
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