&lt;formula formulatype="inline"&gt;&lt;tex Notation="TeX"&gt;${\rm MS2DB}+$&lt;/tex&gt;&lt;/formula&gt;: A Software for Determination of Disulfide Bonds Using Multi-Ion Analysis

Murad, W.A.; Singh, Rahul

doi:10.1109/tnb.2012.2212029

Cited by 7 publications

(6 citation statements)

References 6 publications

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“…Several tools have since been developed which address this problem. Dbond [72, 82] and MS2DB+ [109, 110] can map disulfides from MS/MS data using several characteristic fragmentation peaks of disulfide bonded peptides, including b/y or c/z ions containing intact disulfide bonds. While DBond assigns dipeptides solely from CID data, and includes ions resulting from the occasional CID cleavage of C-S and S-S bonds (resulting in thioaldehydes, persulfides and dehydroalanin ions) [72, 82], the MS2DB+ software can assign disulfides from either CID or ETD data, and the fragment ions considered for CID data include ions resulting from the loss of water or ammonia from b/y ions.…”

Section: Software For Automated Disulfide Bond Assignmentmentioning

confidence: 99%

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins

2017

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Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass spectrometry data, and software tools.

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Section: Software For Automated Disulfide Bond Assignmentmentioning

confidence: 99%

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins

2017

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“…Another program, SlinkS (now XlinkX), assigns ions resulting from S–S and C–S bond cleavage as well as fragment ions containing disulfide bonds and standard backbone fragment ions . MS2DB+ was developed to include a, b, c, x, y, and z fragment ions to facilitate the analysis of disulfide-linked peptides . Kojak-MS has been used for cross-linking analysis of protein complexes and allows the user to search for disulfide-containing peptides by considering each disulfide bond as a cross-link with a mass shift of −2.00965 Da per disulfide bond (−2H) …”

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confidence: 99%

“…30 MS2DB+ was developed to include a, b, c, x, y, and z fragment ions to facilitate the analysis of disulfide-linked peptides. 37 Kojak-MS has been used for cross-linking analysis of protein complexes and allows the user to search for disulfide-containing peptides by considering each disulfide bond as a cross-link with a mass shift of −2.00965 Da per disulfide bond (−2H). 38 In the present study, 193 nm UVPD is used to provide insight into the fragmentation patterns of disulfide-linked peptides.…”

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Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry

et al. 2018

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Deciphering disulfide bond patterns in proteins remains a significant challenge. In the present study, interlinked disulfide bonds connecting peptide chains are homolytically cleaved with 193 nm ultraviolet photodissociation (UVPD). Analysis of insulin showcased the ability of UVPD to cleave multiple disulfide bonds and provide sequence coverage of the peptide chains in the same MS/MS event. For proteins containing more complex disulfide bonding patterns, an approach combining partial reduction and alkylation mitigated disulfide scrambling and allowed assignment of the array of disulfide bonds. The 4 disulfide bonds of lysozyme and the 19 disulfide bonds of serotransferrin were characterized through LC/UVPD-MS analysis of nonreduced and partially reduced protein digests.

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“…34 Alternative software for disulfide bond mapping was released in 2015. 35 pLink-SS represents the method applicable for high-throughput mass spectrometry. These days the method is used for highly complex samples such as Igs 36,37 and mAbs.…”

Section: ■ Introductionmentioning

confidence: 99%

EThcD Benefits for the Sequencing Inside Intramolecular Disulfide Cycles of Amphibian Intact Peptides

Vasileva

Samgina

Meng

et al. 2023

J. Am. Soc. Mass Spectrom.

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Disulfide bonds formed by a pair of cysteine residues in the peptides' backbone represent a certain problem for their sequencing by means of mass spectrometry. As a rule, in proteomics, disulfide bonds should be cleaved before the analysis followed by some sort of chemical derivatization. That step is timeconsuming and may lead to losses of minor peptides of the analyzed mixtures due to incomplete reaction, adsorption on the walls of the vials, etc. Certain problems in the de novo top-down sequencing of amphibian skin peptides are caused by the Cterminal disulfide loop, called the Rana box. Its reduction with or without subsequent derivatization was considered to be an unavoidable step before mass spectrometry. In the present study, EThcD demonstrated its efficiency in sequencing intact disulfidecontaining peptides without any preliminary derivatization. Applied to the secretion of three frog species, EThcD provided the full sequence inside the intramolecular disulfide cycle for all S−S-containing peptides found in the samples, with the only exception being diarginine species. Proteolytic fragments, which are shorter than the original peptides, were helpful in some cases. HCD should be mentioned as a complementary tool to the EThcD tool, being useful as a confirmation method for some sequence details.

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<formula formulatype="inline"><tex Notation="TeX">${\rm MS2DB}+$</tex></formula>: A Software for Determination of Disulfide Bonds Using Multi-Ion Analysis

Cited by 7 publications

References 6 publications

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins

Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry

EThcD Benefits for the Sequencing Inside Intramolecular Disulfide Cycles of Amphibian Intact Peptides

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