Algorithm-assisted elucidation of disulfide structure: application of the negative signature mass algorithm to mass-mapping the disulfide structure of the 12-cysteine transforming growth factor β type II receptor extracellular domain

Borges, Chad R.; Qi, Jianfeng; Wu, Wei; Torng, Eric; Hinck, Andrew P.; Watson, J. Throck

doi:10.1016/j.ab.2004.01.037

Cited by 8 publications

(4 citation statements)

References 16 publications

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“…Otherwise, in more complicated interpretation schemes such as the negative signature mass algorithm developed by the Watson group for elucidation of protein disulfide bond structures (80) (described next), under-labeling may result in ruling out a correct conclusion and ending up with no valid conclusion whatsoever. In such cases, additional steps may be required to validate and ensure comprehensive labeling of cysteinyl residues (11).…”

Section: Incomplete Labelingmentioning

confidence: 99%

“…This resulted in a routinized laboratory workflow (Fig. 11) for the elucidation of oxidative protein folding intermediates (100,112,117) and complex disulfide structures (11,79)-including proteins with adjacent cysteine residues (116). Other strategically complementary partial reduction strategies based on differential alkylation have also been developed (29,118).…”

Section: Indirect Partial Reduction-based Strategiesmentioning

confidence: 99%

“…This approach operates on the principle of ruling out (rather than ruling in) possible disulfide linkages based on the observations of specific cyanylation-induced cleavage products. In short, the algorithm is driven by the fact that, given complete cyanylation (11,80), the internal cysteine residues of cyanylation-induced cleavage products cannot logically be connected to the cysteines at the peptide termini. Thus, in Figure 11, for example, without fractionation of partially reduced isomers, the observed itz71-150 fragment enables an arrival at the conclusion that Cys71 and Cys 151 may (but not necessarily) be connected to one another, but Cys71 cannot be connected to Cys102 or Cys130-otherwise, there would have been cleavage at the connected residue [or at least massbased evidence of side-chain b-elimination (110)].…”

Section: Indirect Partial Reduction-based Strategiesmentioning

confidence: 99%

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Techniques for the Analysis of Cysteine Sulfhydryls and Oxidative Protein Folding

Borges

Sherma

2014

Antioxidants & Redox Signaling

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The continued development of tools, technical approaches, and corresponding data processing algorithms will, undoubtedly, facilitate site-specific protein sulfhydryl quantification and disulfide structure analysis from within complex biological mixtures with ever-improving accuracy and sensitivity. Fully routinizing disulfide structure analysis will require an equal but balanced focus on sample preparation and corresponding mass spectral dataset reproducibility.

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Section: Incomplete Labelingmentioning

confidence: 99%

Section: Indirect Partial Reduction-based Strategiesmentioning

confidence: 99%

Section: Indirect Partial Reduction-based Strategiesmentioning

confidence: 99%

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Techniques for the Analysis of Cysteine Sulfhydryls and Oxidative Protein Folding

Borges

Sherma

2014

Antioxidants & Redox Signaling

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“…In addition, the ratio of partially reduced protein to unreduced protein is generally low, and therefore a significant quantity of protein is needed for analysis. Most recently, Watson's group introduced an algorithm‐driven method, called ‘negative signature mass algorithm’ (NSMA), for interpreting disulfide mass‐mapping data, which eliminated the need to isolate physically the cyanylated partially reduced protein isoforms 15, 16…”

Section: Introductionmentioning

confidence: 99%

Mass spectrometric determination of selenenylsulfide linkages in rat selenoprotein P

Hill

Burk

et al. 2005

J. Mass Spectrom.

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The reversible formation of a selenenylsulfide linkage in mammalian thioredoxin reductase was identified as having a key role in its activity. Identification of selenenylsulfide and/or diselenide linkages is therefore critical to the determination of the structure and function of selenoproteins. A selenopeptide, (298)SGSAITUQCAENLPSLCSUQGLFAEEK(324) (U=selenocysteine), was isolated from a tryptic digest of rat selenoprotein P. Its two cysteine residues and two selenocysteine (Sec) residues were determined to be present in oxidized form by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The selenopeptide was subjected to partial reduction by dithiothreitol with immediate alkylation by iodoacetamide. This process was monitored by MALDI-TOFMS to determine the number of alkylations that had taken place. The partially reduced and alkylated peptides were then analyzed by nano-electrospray ionization tandem mass spectrometry and the results indicated that selenenylsulfide linkages Sec304-Cys314 and Cys306-Sec316 were present. It is concluded that selenoprotein P contains these two selenenylsulfide bonds.

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Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry

Yang

Liu

2012

Topics in Current Chemistry

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The disulfide bond is one of the most common post-translational modifications in proteins, of which determination is essential to the comprehensive understanding of protein structures. Disulfide bond analysis has undergone great improvement due to the development of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), especially in terms of speed and sensitivity. In general, the characterization of disulfide-containing peptides is achieved by the reduction of disulfide bonds followed by alkylation. In this review we focus on the analysis of disulfide-containing proteins/peptides by some unique methods in MALDI MS. The MALDI in-source decay (ISD) of disulfide bonds and adducts of the matrix and sulfhydryl-containing peptide are discussed in detail. The mechanism of each method is discussed so as to help the reader gain greater insight into it, and examples of its application are also presented. The goal of this review is to provide an understanding of these techniques for analysis of disulfide-linked proteins/peptides in MALDI MS.

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Algorithm-assisted elucidation of disulfide structure: application of the negative signature mass algorithm to mass-mapping the disulfide structure of the 12-cysteine transforming growth factor β type II receptor extracellular domain

Cited by 8 publications

References 16 publications

Techniques for the Analysis of Cysteine Sulfhydryls and Oxidative Protein Folding

Techniques for the Analysis of Cysteine Sulfhydryls and Oxidative Protein Folding

Mass spectrometric determination of selenenylsulfide linkages in rat selenoprotein P

Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry

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