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An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis.

Murad W, Singh R, Yen TY - BMC Bioinformatics (2011)

Bottom Line: Additionally, each bond is associated with a confidence score, which aids in interpretation and assimilation of the results.The method was also compared with other techniques at the state-of-the-art.It was found to perform as well or better than the competing techniques.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA. whemurad@sfsu.edu

ABSTRACT

Background: Determining the disulfide (S-S) bond pattern in a protein is often crucial for understanding its structure and function. In recent research, mass spectrometry (MS) based analysis has been applied to this problem following protein digestion under both partial reduction and non-reduction conditions. However, this paradigm still awaits solutions to certain algorithmic problems fundamental amongst which is the efficient matching of an exponentially growing set of putative S-S bonded structural alternatives to the large amounts of experimental spectrometric data. Current methods circumvent this challenge primarily through simplifications, such as by assuming only the occurrence of certain ion-types (b-ions and y-ions) that predominate in the more popular dissociation methods, such as collision-induced dissociation (CID). Unfortunately, this can adversely impact the quality of results.

Method: We present an algorithmic approach to this problem that can, with high computational efficiency, analyze multiple ions types (a, b, bo, b*, c, x, y, yo, y*, and z) and deal with complex bonding topologies, such as inter/intra bonding involving more than two peptides. The proposed approach combines an approximation algorithm-based search formulation with data driven parameter estimation. This formulation considers only those regions of the search space where the correct solution resides with a high likelihood. Putative disulfide bonds thus obtained are finally combined in a globally consistent pattern to yield the overall disulfide bonding topology of the molecule. Additionally, each bond is associated with a confidence score, which aids in interpretation and assimilation of the results.

Results: The method was tested on nine different eukaryotic Glycosyltransferases possessing disulfide bonding topologies of varying complexity. Its performance was found to be characterized by high efficiency (in terms of time and the fraction of search space considered), sensitivity, specificity, and accuracy. The method was also compared with other techniques at the state-of-the-art. It was found to perform as well or better than the competing techniques. An implementation is available at: http://tintin.sfsu.edu/~whemurad/disulfidebond.

Conclusions: This research addresses some of the significant challenges in MS-based disulfide bond determination. To the best of our knowledge, this is the first algorithmic work that can consider multiple ion types in this problem setting while simultaneously ensuring polynomial time complexity and high accuracy of results.

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Related in: MedlinePlus

Spectra samples from tryptic digested protein FucT VII. Spectra (m/z vs. normalized intensity) illustrating the confirmatory matches (whose intensity values were at least 10% of the maximum intensity) found for the disulfide bond between cysteines C318-C321 in protein FucT VII. The spectrum in the left shows the matches found when multiple ions were considered. The spectrum in the right shows the matches when only b/y-ions were considered.
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Figure 7: Spectra samples from tryptic digested protein FucT VII. Spectra (m/z vs. normalized intensity) illustrating the confirmatory matches (whose intensity values were at least 10% of the maximum intensity) found for the disulfide bond between cysteines C318-C321 in protein FucT VII. The spectrum in the left shows the matches found when multiple ions were considered. The spectrum in the right shows the matches when only b/y-ions were considered.

Mentions: The consideration of multiple ion types also contributed to the method’s accuracy in terms of determining specific S-S bonds. Disulfide bonds previously missed due to their low match score could be identified when all ten different ion types were considered. The tryptic-digested protein FucT VII (which underwent CID) constituted one such example. In FucT VII the bond C318-C321 was missed when considering only b/y ions (match score 29, pp=11, pp2 =15). However, as shown in Figure 7, this bond was identified when multiple ions types were included (match score 100, pp=31, pp2=70). The confidence measures pp and pp2 are described in the following section. To explain this improvement we note that C318-C321 was an intra-bond involving cysteines that were close together. Consequently, CID-based fragmentation was poor and the consideration of other ion types essentially improved the signal-to-background contrast. In this particular case, five other ion types - a4, a5, a6, bo7, y*7 - were present in the FucT VII MS/MS data besides the b ions represented in the spectrum on the right in Figure 7. In the following, we present details of how these ions contribute to the match score Vs (from Eq. (4)). We present the two cases: consideration of only b/y-ions (Eq. (5)) and consideration of multiple ion types (Eq. (6)). In the numerator we specify the contribution of each spectrum peak from Figure 7 (the ion corresponding to each VMi × IN term is showed in brackets).(5)(6)


An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis.

Murad W, Singh R, Yen TY - BMC Bioinformatics (2011)

Spectra samples from tryptic digested protein FucT VII. Spectra (m/z vs. normalized intensity) illustrating the confirmatory matches (whose intensity values were at least 10% of the maximum intensity) found for the disulfide bond between cysteines C318-C321 in protein FucT VII. The spectrum in the left shows the matches found when multiple ions were considered. The spectrum in the right shows the matches when only b/y-ions were considered.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3044266&req=5

Figure 7: Spectra samples from tryptic digested protein FucT VII. Spectra (m/z vs. normalized intensity) illustrating the confirmatory matches (whose intensity values were at least 10% of the maximum intensity) found for the disulfide bond between cysteines C318-C321 in protein FucT VII. The spectrum in the left shows the matches found when multiple ions were considered. The spectrum in the right shows the matches when only b/y-ions were considered.
Mentions: The consideration of multiple ion types also contributed to the method’s accuracy in terms of determining specific S-S bonds. Disulfide bonds previously missed due to their low match score could be identified when all ten different ion types were considered. The tryptic-digested protein FucT VII (which underwent CID) constituted one such example. In FucT VII the bond C318-C321 was missed when considering only b/y ions (match score 29, pp=11, pp2 =15). However, as shown in Figure 7, this bond was identified when multiple ions types were included (match score 100, pp=31, pp2=70). The confidence measures pp and pp2 are described in the following section. To explain this improvement we note that C318-C321 was an intra-bond involving cysteines that were close together. Consequently, CID-based fragmentation was poor and the consideration of other ion types essentially improved the signal-to-background contrast. In this particular case, five other ion types - a4, a5, a6, bo7, y*7 - were present in the FucT VII MS/MS data besides the b ions represented in the spectrum on the right in Figure 7. In the following, we present details of how these ions contribute to the match score Vs (from Eq. (4)). We present the two cases: consideration of only b/y-ions (Eq. (5)) and consideration of multiple ion types (Eq. (6)). In the numerator we specify the contribution of each spectrum peak from Figure 7 (the ion corresponding to each VMi × IN term is showed in brackets).(5)(6)

Bottom Line: Additionally, each bond is associated with a confidence score, which aids in interpretation and assimilation of the results.The method was also compared with other techniques at the state-of-the-art.It was found to perform as well or better than the competing techniques.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA. whemurad@sfsu.edu

ABSTRACT

Background: Determining the disulfide (S-S) bond pattern in a protein is often crucial for understanding its structure and function. In recent research, mass spectrometry (MS) based analysis has been applied to this problem following protein digestion under both partial reduction and non-reduction conditions. However, this paradigm still awaits solutions to certain algorithmic problems fundamental amongst which is the efficient matching of an exponentially growing set of putative S-S bonded structural alternatives to the large amounts of experimental spectrometric data. Current methods circumvent this challenge primarily through simplifications, such as by assuming only the occurrence of certain ion-types (b-ions and y-ions) that predominate in the more popular dissociation methods, such as collision-induced dissociation (CID). Unfortunately, this can adversely impact the quality of results.

Method: We present an algorithmic approach to this problem that can, with high computational efficiency, analyze multiple ions types (a, b, bo, b*, c, x, y, yo, y*, and z) and deal with complex bonding topologies, such as inter/intra bonding involving more than two peptides. The proposed approach combines an approximation algorithm-based search formulation with data driven parameter estimation. This formulation considers only those regions of the search space where the correct solution resides with a high likelihood. Putative disulfide bonds thus obtained are finally combined in a globally consistent pattern to yield the overall disulfide bonding topology of the molecule. Additionally, each bond is associated with a confidence score, which aids in interpretation and assimilation of the results.

Results: The method was tested on nine different eukaryotic Glycosyltransferases possessing disulfide bonding topologies of varying complexity. Its performance was found to be characterized by high efficiency (in terms of time and the fraction of search space considered), sensitivity, specificity, and accuracy. The method was also compared with other techniques at the state-of-the-art. It was found to perform as well or better than the competing techniques. An implementation is available at: http://tintin.sfsu.edu/~whemurad/disulfidebond.

Conclusions: This research addresses some of the significant challenges in MS-based disulfide bond determination. To the best of our knowledge, this is the first algorithmic work that can consider multiple ion types in this problem setting while simultaneously ensuring polynomial time complexity and high accuracy of results.

Show MeSH
Related in: MedlinePlus