Proteomic and Mass Spectrometry Technologies for Biomarker Discovery - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 22

microenvironment. 35 Animal models, in contrast
to cell lines, incorporate the effect of the host
microenvironment. In addition, animal models
offer minimum intraindividual variability in
terms of genetic variation and environmental
conditions. Furthermore, animal-derived biolog-
ical samples can be collected at any stage of the
disease development. 36 Nevertheless, whether
animal disease models can be accurately trans-
lated into human disease models remains an
open-ended question.
Regardless of the biological material of choice,
clinical samples should be collected in a stan-
dardized way following prede

invasive procedures that limit their clinical

potential. 28
Diseased tissue is the specimen of choice to
discover tissue-based prognostic and predictive
biomarkers because tissues have high levels of
protein biomarkers. 29 However, biomarker candi-
dates identi

ed by tissue proteomics may not be
detectable in the systemic bloodstream due to
insuf cient leakage from the tissue to blood,

increased degradation by endogenous proteases,
or enhanced clearance by the kidneys. 30 Amajor
obstacle in proteomic analysis of tissues is the
heterogeneity of cellular and extracellular compo-
sition. Laser capture microdissection (LCM) has
been proposed as a tool for isolating pure cell
populations from tissues and thus reducing
such heterogeneity. 31 However, LCM yields
small sample sizes, is labor intensive, and
requires fresh frozen tissues and a high level of
expertise. 32 An advantage of tissues over other
specimens is the ability to obtain adjuvant nonaf-
fected tissues from the same individual to serve as
a control, thus minimizing the effects of biological
heterogeneity. Nevertheless, an adjacent tissue
may also be transformed at the molecular level
and thus may not represent the healthy tissue. 33
Given that

ned standard
operating procedures (SOPs) to minimize varia-
tions due to sample collection, handling, and
storage. 37 Samples should have detailed clinical
annotations, such as gender, race, age, and
concurrent use of medications. Given the limited
availability of clinical samples, it has been
proposed that high-quality samples should be
used at the late stages of biomarker develop-
ment. 38 However, analysis of specimens of
unknown quality at cation phase

increases the risk of generating false positive
markers that will drain

the identi

financial and clinical

n-embedded
(FFPE) tissues were widely collected and
preserved for more than a century, the exploita-
tion of FFPE tissues for biomarker discovery
warrants a detailed investigation. Recent

formalin- xed paraf resources at cation and validation

phases. The issue of sample collection and pres-
ervation for prospective studies along with the
need for storage of very large specimen collec-
tion has driven the development of multiple bio-
banking initiatives. Biobanking incorporates the
proper clinical annotation of specimens along
with managing ethical, legal, and social issues
that may vary in different states and regions. 39
International networking of biobanks facilitates
the use of high-quality biological specimens for
translational and clinical research.

the veri

findings
show that FFPE tissues, a source of potential
biomarkers that has yet to be mined, may be
compatible with mass spectrometry e based pro-
teomic analysis. 34
Ex vivo systems, such as cell lines and animal
models, are also utilized for biomarker
discovery. Cell lines are readily available, allow
for identi cation of low-abundance proteins

due to the reduced sample complexity, and
facilitate studies with minimized biological and
experimental variability due to cell growth
under well-de

PROTEIN IDENTIFICATION
BY MASS SPECTROMETRY

ned conditions. However, no
single cell line can recapitulate disease
heterogeneity and account

Mass spectrometry e based approaches to

for the disease protein identi cation involve either detection of