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Bioinformatics. 2009 Feb 1;25(3):365-71. doi: 10.1093/bioinformatics/btn636. Epub 2008 Dec 10.

Glycan family analysis for deducing N-glycan topology from single MS.

Author information

1
Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto CA 94304, USA. goldberg@parc.com

Abstract

MOTIVATION:

In the past few years, mass spectrometry (MS) has emerged as the premier tool for identification and quantification of biological molecules such as peptides and glycans. There are two basic strategies: single-MS, which uses a single round of mass analysis, and MS/MS (or higher order MS(n)), which adds one or more additional rounds of mass analysis, interspersed with fragmentation steps. Single-MS offers higher throughput, broader mass coverage and more direct quantitation, but generally much weaker identification. Single-MS, however, does work fairly well for the case of N-glycan identification, which are more constrained than other biological polymers. We previously demonstrated single-MS identification of N-glycans to the level of 'cartoons' (monosaccharide composition and topology) by a system that incorporates an expert's detailed knowledge of the biological sample. In this article, we explore the possibility of ab initio single-MS N-glycan identification, with the goal of extending single-MS, or primarily-single-MS, identification to non-expert users, novel conditions and unstudied tissues.

RESULTS:

We propose and test three cartoon-assignment algorithms that make inferences informed by biological knowledge about glycan synthesis. To test the algorithms, we used 71 single-MS spectra from a variety of tissues and organisms, containing more than 2800 manually annotated peaks. The most successful of the algorithms computes the most richly connected subgraph within a 'cartoon graph'. This algorithm uniquely assigns the correct cartoon to more than half of the peaks in 41 out of the 71 spectra.

PMID:
19073587
PMCID:
PMC2732296
DOI:
10.1093/bioinformatics/btn636
[Indexed for MEDLINE]
Free PMC Article
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