[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


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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