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Novel bioinformatics methods for identification and quantification of deamidation in shotgun...
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Novel bioinformatics methods for identification and quantification of deamidation in shotgun proteomics experiments
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http://www.ohsu.edu/xd/education/library/services/theses-dissertations/rights-statement.cfm
Title
Novel
bioinformatics
methods
for
identification
and
quantification
of
deamidation
in
shotgun
proteomics
experiments
Creator.PersonalName
Dasari
,
Surendra
Thesis.Degree
Ph.D.
Thesis.Major
Biomedical Informatics
Thesis.DateDegreeAwarded
May
2008
Institution
Oregon Health & Science University
School
School of Medicine
Department
Dept. of Medical Informatics and Clinical Epidemiology
Thesis.Chair
McWeeney, Shannon K.
Thesis.Committee
Nagalla, Srinivasa R.
David, Larry L.
Dubay, Christopher J.
Jimison, Holly Brugge
Subject.MeSH
Protein Processing, Post-Translational
Chromatography, Liquid
Lens, Crystalline
Proteomics
Call Number
Q171 D2291 2008
Description.Abstract
Reliable
identification
of
deamidation
remains
challenging
when
using
low-resolution
mass
spectrometry
due
to the
MS/MS
mis-triggers
on
first
isotopic
peak
of
unmodified
peptide
and
limited
mass
resolution
.
We
developed
a
bioinformatics
method
that
utilizes
differential
chromatographic
behavior
and
corrected
peptide
masses
of the
amidated
and
deamidated
peptides
to
validate
deamidation
identifications
. The
method
has been
automated
to
facilitate
rapid
validation
of
deamidation
identifications
in
large-scale
proteomics
experiments
.
Accurate
quantification
of
deamidation
is
necessary
for
reliable
protein
pharmaceutical
shelf
life
measurements
,
minimizing
deamidation
in
sample
processing/purification
methods
, and
differentiating
between
healthy
and
diseased
tissue
in
protein
aggregation
diseases
.
Deamidation
quantification
is
complicated
by
coelution
of
modified
and
unmodified
peptide
forms
,
interference
from
other
peptides
with
similar
elution
times
, and
poor
chromatography
peak
shapes
.
We
developed
a
robust
mathematical
quantification
technique
that
uses
Gaussian
isotopic
envelope
modeling
with
peptide
mixture
models
. This
method
estimates
the
abundance
of
deamidation
by
comparing
the
predicted
isotopic
envelope
of
deamidated
and
amidated
peptide
forms
to the
experimentally
measured
isotopic
envelope
. The
technique
has
undergone
extensive
manual
validation
during
development
and a
semi-automated
graphical
user
interface
has been
designed
to
estimate
the
abundance
of
deamidations
in
large-scale
proteomics
experiments
.
We
have
applied
these
methods
to
estimate
deamidation
abundances
in an
aged
series
of
human
lens
tissues
.
Increased
deamidation
abundance
at
three
sites
in
gS
lens
crystallin
is
correlated
with
increasing
age
,
loss
of
protein
solubility
, and
changes
in
3-dimensional
protein
structure
.
Language
eng
Type
Text
Format.Use
Needs Adobe Acrobat to view
Format.FileSize
2737923 Bytes
OCLC number
232664013
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