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Your search keyword '"Schulte, Douwe"' showing total 8 results
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8 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. 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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