STAT:  A Saccharide Topology Analysis Tool Used in Combination with Tandem Mass Spectrometry

Gaucher, Sara P.; Morrow, Jeff; Leary, Julie A.

doi:10.1021/ac000096f

Cited by 83 publications

(66 citation statements)

References 12 publications

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“…Structural information can be derived from collision-induced dissociation (CID) [12][13][14][15][16][17][18][19][20] or from post-source decay (PSD) time-of-flight (TOF) experiments [21][22][23][24][25][26]. Fragmentation of glycosidic bonds provides information about the monosaccharide sequence and computer algorithms can extract sequence information from web-based catalogs of MS n spectra [27]. However, the assignment of anomeric configuration [28 -35] and linkage [18, 36 -38] within the oligosaccharide structure is not a trivial task.…”

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confidence: 99%

Evidence for long-range glycosyl transfer reactions in the gas phase

Franz

Lebrilla

2002

J. Am. Soc. Mass Spectrom.

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A long-range glycosyl transfer reaction was observed in the collision-induced dissociation Fourier transform (CID FT) mass spectra of benzylamine-labeled and 9-aminofluorene-labeled lacto-N-fucopentaose I (LNFP I) and lacto-N-difucohexaose I (LNDFH I). The transfer reaction was observed for the protonated molecules but not for the sodiated molecules. The long-range glycosyl transfer reaction involved preferentially one of the two L-fucose units in labeled LNDFH I. CID experiments with labeled LNFP I and labeled LNFP II determined the fucose with the greatest propensity for migration. Further experiments were performed to determine the final destination of the migrating fucose. , and post-translational protein modification [6 -8]. Whereas the insight into the physical process of carbohydrate recognition is in its infancy, considerable progress has been made towards the quantitation and structural elucidation of biologically active oligosaccharides. NMR [9] yields structural information about oligosaccharides. Frequently, however, an inherent problem is the limited amount of sample causing NMR experiments to become time-consuming or impossible. The sensitivity and accuracy of mass spectrometry has made this technique the best choice for analysis of oligosaccharides [10,11]. Structural information can be derived from collision-induced dissociation (CID) [12][13][14][15][16][17][18][19][20] or from post-source decay (PSD) time-of-flight (TOF) experiments [21][22][23][24][25][26]. Fragmentation of glycosidic bonds provides information about the monosaccharide sequence and computer algorithms can extract sequence information from web-based catalogs of MS n spectra [27]. However, the assignment of anomeric configuration [28 -35] and linkage [18, 36 -38] within the oligosaccharide structure is not a trivial task. Glycosidase digestion [13, 39 -47] in conjunction with mass spectrometric analysis can be used to assign linkage and stereochemistry. In an alternative approach, CID-fragmentation patterns have been linked to structural motifs in the oligosaccharide (catalog library approach) [12].We recently reported on the use of more nucleophilic benzylogous amines, such as benzylamine and 9-aminofluorene, for the labeling of oligosaccharides and the experimental results of FT-MS experiments with the labeled oligosaccharides [48]. Detection of 5 pmol of 9-amino fluorene-labeled oligosaccharide was achieved with a photo diode array during HPLC separation. The label combines low cost with good nucleophilicity and ease of introduction. The behavior of oligosaccharides derivatized with benzylogous amines such as benzylamine in CID experiments has not been reported, although data obtained from PSD matrix-assisted laser desorption/ionization (MALDI)-TOF experiments have been published [25,49].In this paper, we discuss a long-range glycosyl transfer that occurs during CID for benzylamine-and 9-AmFL-labeled oligosaccharides. The transfer of a fucose across three monosaccharide units was observed only in protonated molecules. To t...

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confidence: 99%

Evidence for long-range glycosyl transfer reactions in the gas phase

Franz

Lebrilla

2002

J. Am. Soc. Mass Spectrom.

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“…Much of the data interpretation discussed above, regarding the topology, were extrapolated using the STAT program, developed previously in our laboratory [17]. STAT utilizes all of the MS n product ions to generate all possible topologies that could result from the observed product ions.…”

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confidence: 99%

“…This is due to the speed of MS, its sensitivity, and the ability to use gas phase isolation, which obviates the need for chromatography [7][8][9][10]. In our laboratory, we have developed several methods for the determination of carbohydrate structure [11][12][13][14][15][16][17]. These include methods for topology, linkage position, stereochemistry, and anomericity determination.…”

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confidence: 99%

“…Initially, the glycoform population present on the cell surface of the bacteria was determined using exact mass measurements on a FTICR mass spectrometer. Subsequently, tandem mass spectrometry (MS n ) was employed to determine the topology of the Hex 3 glycoform (Hex: hexose) from the N. gonorrhoeae bacteria, and confirmed using the STAT computer program [17]. This program has the advantage of generating all structures that are possible from the observed collision-induced dissociation (CID) data, thus possible structures will not be missed.…”

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Mass spectrometric strategy for the characterization of lipooligosaccharides from Neisseria gonorrhoeae 302 using FTICR

Leavell

Leary

Yamasaki

2002

J. Am. Soc. Mass Spectrom.

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The lipooligosaccharides (LOS) of Neisseria gonorrhoeae 302 were profiled using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Using techniques developed in this laboratory, the topology and some of the linkages of the LOS were determined. Mass spectrometric analysis in the negative ion mode yielded a glycoform of the composition: Hex 3 Hep 2 Hxn 1 PEA 1 KDO 2 DPLA. The composition was confirmed through exact mass measurements, which showed only a 2 ppm error between the exact mass and theoretical mass. Although the core structure has been postulated previously, the positioning of the three hexose moieties were in question for this particular strain of N. gonorrhoeae. Topology assignment was performed through collision-induced dissociation analysis of the O-deacylated glycoform in the negative ion mode followed by submission to the saccharide topology analysis tool (STAT) computer program, which confirmed the topology assignment. It was found that the three hexoses were added to the Hep[I] of the conserved core of N. gonorrhoeae in a linear fashion, while Hep[II] remains unbranched. Linkage position analysis was performed through application of a mild acid hydrolysis technique followed by collisioninduced dissociation of the sodiated precursor ions, yielding a 1 3 4 linkage between the terminating and penultimate hexoses. (J Am Soc Mass Spectrom 2002, 13, 571-576)

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“…Many approaches for deriving glycan topologies from mass spectrometry data are based on enumerating all topologies of a particular mass, and comparing a simulated spectrum for each topology against the measured data (Gaucher et al, 2000;Ethier et al, 2003;Goldberg et al, 2006). Counting glycan topologies and, in particular, the number of topologies of a certain mass M allows us to estimate the algorithm's running time before actually running it, or to check its general applicability.…”

Section: Introductionmentioning

confidence: 99%

Counting glycans revisited

Böcker

Wagner

2013

J. Math. Biol.

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Abstract. We present an algorithm for counting glycan topologies of order n that improves on previously described algorithms by a factor n in both time and space. More generally, we provide such an algorithm for counting rooted or unrooted d-ary trees with labels or masses assigned to the vertices, and we give a "recipe" to estimate the asymptotic growth of the resulting sequences. We provide constants for the asymptotic growth of d-ary trees and labeled quaternary trees (glycan topologies). Finally, we show how a classical result from enumeration theory can be used to count glycan structures where edges are labeled by bond types. Our method also improves time bounds for counting alkanes.

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STAT: A Saccharide Topology Analysis Tool Used in Combination with Tandem Mass Spectrometry

Cited by 83 publications

References 12 publications

Evidence for long-range glycosyl transfer reactions in the gas phase

Evidence for long-range glycosyl transfer reactions in the gas phase

Mass spectrometric strategy for the characterization of lipooligosaccharides from Neisseria gonorrhoeae 302 using FTICR

Counting glycans revisited

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