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Mass spectrometry (MS) promises to be an invaluable tool for
functional genomics, by supporting low-cost, high-throughput
experiments. However, large-scale MS faces the potential problem of
mass degeneracy -- indistinguishable masses for multiple
biopolymer fragments (e.g. from a limited proteolytic digest). This
paper studies the tasks of planning and interpreting MS experiments
that use selective isotopic labeling, thereby substantially reducing
potential mass degeneracy. Our algorithms support an
experimental-computational protocol called Structure-Activity
Relation by Mass Spectrometry (SAR by MS), for elucidating the
function of protein-DNA and protein-protein complexes. SAR by MS
enzymatically cleaves a crosslinked complex and analyzes the resulting
mass spectrum for mass peaks of hypothesized fragments. Depending on
binding mode, some cleavage sites will be shielded; the absence of
anticipated peaks implicates corresponding fragments as either part of
the interaction region or inaccessible due to conformational change
upon binding. Thus different mass spectra provide evidence for
different structure-activity relations. We address combinatorial and
algorithmic questions in the areas of data analysis
(constraining binding mode based on mass signature) and
experiment planning (determining an isotopic labeling strategy to
reduce mass degeneracy and aid data analysis). We explore the
computational complexity of these problems, obtaining upper and lower
bounds. We report experimental results from implementations of our
This report supercedes TR99-359.
To appear in the 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA (Accepted; in press).
Bibliographic citation for this report: [plain text] [BIB] [BibTeX] [Refer]
Or copy and paste:
Chris Bailey-Kellogg, John J. Kelley, Clifford Stein, and Bruce Randall Donald, "Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling." Dartmouth Computer Science Technical Report TR2000-362, February 2000.
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