[talks] [Released] Z Khan preFPO
Melissa Lawson
mml at CS.Princeton.EDU
Wed Jul 7 09:15:19 EDT 2010
Zia Khan will present his preFPO on Friday, July 23, 2010 at 1:30pm in
Carl Ichan Lab (CIL) 200. The members of his committee are: Mona Singh
(CS) advisor, Leonid Kruglyak (EEB) advisor, Ben Garcia (MOL) reader,
Hillary Coller (MOL), and Saeed Tavazoie (MOL) nonreaders. Everyone is
invited to attend his talk. His abstract follows below.
Title: Efficient Algorithms for Liquid Chromatography Coupled Mass
Spectrometry Based Protein Quantification
Abstract:
One of the driving aims of studies that conduct comprehensive,
quantitative surveys of proteins and across many experimental samples
and replicates is the identification of genes and genetic pathways
effected in disease and disease treatment. The prevailing experimental
tool for such surveys is instrumentation known as liquid chromatography
coupled tandem mass spectrometry (LC-MS/MS). LC-MS/MS generates large
data sets in the form of thousands to millions of mass spectra in a
single experiment. Converting these spectra into interpretable
quantitative output that shows changes in amounts of proteins, their
peptide fragments, or enrichment and depletion of post translational
modifications presents a substantial computational challenge. This
thesis describes a new application of space partitioning data
structures: a series of algorithms that leverage fast geometry queries
supported by these data structures to significantly improve the speed
and quality LC-MS/MS data analysis. In addition, this thesis develops a
collection methods, implemented in an open-source software system called
PVIEW (http://compbio.cs.princeton.edu/pview), that use the output of
these algorithms to enable accurate quantification of proteins, protein
fragments, and post translational modifications. These methods are
evaluated for quantitative quality and computational efficiency on a
wide range of experimental data sets spanning several experimental
methodologies and source protein samples.
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