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Dániel Hüse

Gedeon Richter (Hungary)

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Péter Buglyó

University of Debrecen

Attila Bényei

University of Debrecen

Linda Bíró

University of Debrecen

János Patalenszki

University of Debrecen

Ágnes Révész

HUN-REN Research Centre for Natural Sciences

Dany Jeanne Dit Fouque

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Antony Memboeuf

Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique

Tibor András Rokob

HUN-REN Research Centre for Natural Sciences

Lilla Turiák

HUN-REN Research Centre for Natural Sciences

László Drahos

HUN-REN Research Centre for Natural Sciences

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Hungarian Academy of Sciences

Eötvös Loránd University

HUN-REN Research Centre for Natural Sciences

Institute of Organic Chemistry

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University of Debrecen

Semmelweis University

Hungarian Research Network

Czech Academy of Sciences

Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry

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Optimal Collision Energies and Bioinformatics Tools for Efficient Bottom-up Sequence Validation of Monoclonal Antibodies

Analytical Chemistry (2019)

Ágnes Révész Tibor András Rokob Dany Jeanne Dit Fouque Dániel Hüse Viktor Háda

Rigorous validation of amino acid sequence is fundamental in the characterization of original and biosimilar protein biopharmaceuticals. Widely accepted workflows are based on bottom-up mass spectrometry, and they often require multiple techniques and significant manual work. Here, we demonstrate that optimization of a set of tandem mass spectroscopy (MS/MS) collision energies and automated combination of all available information in the measurements can increase the sequence validated by one technique close to the inherent limits. We created a software (called "Serac") that consumes results of the Mascot database search engine and identifies the amino acids validated by bottom-up MS/MS experiments using the most rigorous, industrially acceptable definition of sequence coverage (we term this "confirmed sequence coverage"). The software can combine spectra at the level of amino acids or fragment ions to exploit complementarity, provides full transparency to justify validation, and reduces manual effort. With its help, we investigated collision energy dependence of confirmed sequence coverage of individual peptides and full proteins on trypsin-digested monoclonal antibody samples (rituximab and trastuzumab). We found the energy dependence to be modest, but we demonstrated the benefit of using spectra taken at multiple energies. We describe a workflow based on 2-3 LC-MS/MS runs, carefully selected collision energies, and a fragment ion level combination, which yields ∼85% confirmed sequence coverage, 25%-30% above that from a basic proteomics protocol. Further increase can mainly be expected from alternative digestion enzymes or fragmentation techniques, which can be seamlessly integrated to the processing, thereby allowing effortless validation of full sequences.

10.1021/acs.analchem.9b03362

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Citations (11)

Interaction of [Ru(η6-p-cym)(H2O)3]2+ with citrate and tricarballate ions in aqueous solution; X-ray crystal structure of novel half-sandwich Ru(II)-citrato complexes

Journal of Inorganic Biochemistry (2012)

Linda Bíró Dániel Hüse Attila Bényei Péter Buglyó

Stoichiometry

10.1016/j.jinorgbio.2012.07.020

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CCDC 1008620: Experimental Crystal Structure Determination

The Cambridge Structural Database (2014)

Dániel Hüse Linda Bíró János Patalenszki Attila Bényei Péter Buglyó

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Crystal (programming language)

10.5517/cc12vk4m

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Complex Formation between [(η⁶‐p‐cymene)Ru(H₂O)₃]²⁺ and Hydroxycarboxylates or their Sulfur Analogues – The Role of Thiolate Groups in Metal Ion Binding

European Journal of Inorganic Chemistry (2014)

Dániel Hüse Linda Bíró János Patalenszki Attila Bényei Péter Buglyó

Abstract The interactions between [(η 6 ‐ p ‐cymene)Ru(H 2 O) 3 ] 2+ and L ‐malic acid (H 2 mal), L ‐tartaric acid (H 2 tart), and their sulfur‐containing analogues dl ‐thiomalic acid (H 3 thiomal) and meso ‐2,3‐dimercaptosuccinic acid (H 4 dmsa) were studied by pH potentiometry, NMR spectroscopy, and ESI‐MS. The hydroxycarboxylates are potent metal ion binders and prevent hydrolysis at pH 7.4 in aqueous solution. Although H 2 mal forms mononuclear complexes with different degrees of protonation by the involvement of the alcohol/alkoxide group in addition to the carboxylate groups, the presence of binding isomers is detected for the H 2 tart system. The replacement of the alcohol group by a thiolate group results in the formation of dinuclear [Ru 2 A 2 ] complexes as the single species over a wide pH range. Complexes with identical binding modes with H 3 thiomal or polymeric species with H 4 dmsa are identified, and the X‐ray structure of [{(η 6 ‐ p ‐cym)Ru} 2 (Hthiomal) 2 ] is reported. The stereochemistry of the chiral‐at‐metal complexes was explored by NMR spectroscopy and is also discussed.

Carboxylate

Tartaric acid

Alkoxide

10.1002/ejic.201402559

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Citations (8)