Linked Life Data

14673818

Source:http://linkedlifedata.com/resource/pubmed/id/14673818

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
24
pubmed:dateCreated
2003-12-15
pubmed:abstractText
Oligosaccharides associated with proteins are known to give these molecules specific conformations and functions. Analysis of proteins would not be complete without studying the glycans. However, high-throughput techniques in proteomics will soon overwhelm the current capacity of methods if no automation is incorporated into glycomics. New capabilities of the StrOligo algorithm introduced for this purpose (Ethier et al., Rapid Commun. Mass Spectrom., 2002; 16: 1743) will be discussed here. Experimental tandem mass spectra were acquired to test the algorithm using a hybrid quadrupole-time-of-flight (QqTOF) instrument with a matrix-assisted laser desorption/ionization (MALDI) source. The samples were N-linked oligosaccharides from monoclonal antibody IgG, beta interferon and fetuin, detached by enzymatic deglycosylation and labeled at the reducing end. Improvements to the program were made in order to reduce the need for user intervention. StrOligo strips the spectra down to monoisotopic peaks only. The algorithm first builds a relationship tree, accounting for each observed loss of a monosaccharide moiety, and then analyzes the tree and proposes possible structures from combinations of adducts and fragment ion types. A score, which reflects agreement with experimental results, is then given to each proposed structure. The program then decides which combination is the best one and labels relevant peaks in the experimental mass spectrum using a modified nomenclature. The usefulness of the algorithm has been demonstrated by assigning structures to several glycans released from glycoproteins. The analysis was completed in less than 2 minutes for any glycan, which is a substantial improvement over manual interpretation.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
0951-4198
pubmed:author
pubmed:copyrightInfo
Copyright 2003 John Wiley & Sons, Ltd.
pubmed:issnType
Print
pubmed:volume
17
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
2713-20
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed-meshheading:14673818-Algorithms, pubmed-meshheading:14673818-Amino Acid Sequence, pubmed-meshheading:14673818-Animals, pubmed-meshheading:14673818-Antibodies, Monoclonal, pubmed-meshheading:14673818-Cattle, pubmed-meshheading:14673818-Computer Simulation, pubmed-meshheading:14673818-Crystallography, pubmed-meshheading:14673818-Databases, Protein, pubmed-meshheading:14673818-Glycoproteins, pubmed-meshheading:14673818-Immunoglobulin G, pubmed-meshheading:14673818-Interferon-beta, pubmed-meshheading:14673818-Models, Molecular, pubmed-meshheading:14673818-Molecular Sequence Data, pubmed-meshheading:14673818-Nitrogen, pubmed-meshheading:14673818-Polysaccharides, pubmed-meshheading:14673818-Protein Subunits, pubmed-meshheading:14673818-Sequence Analysis, Protein, pubmed-meshheading:14673818-Spectrometry, Mass, Matrix-Assisted Laser..., pubmed-meshheading:14673818-alpha-Fetoproteins
pubmed:year
2003
pubmed:articleTitle
Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry.
pubmed:affiliation
Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't, Evaluation Studies, Validation Studies