Biology Reference
In-Depth Information
nonobstructive azoospermia and postvasectomy
conditions, which has the potential to eliminate
testicular biopsy for diagnosis of male infertility.
Peripheral blood is obviously the
urine sample cohort. Twelve proteins were veri-
fied as credible bladder cancer biomarkers and
a 6-peptide biomarker panel demonstrated better
diagnostic ef
first sample
type that comes to mind when developing assays
to be used in clinics because it is easily obtainable
and generally thought of as representative of
the overall pathophysiology of the patient. A
recent study by Hüttenhain et al.
9
reported the
development of SRM assays for 1,172 cancer-
associated proteins (multiple peptides for each
protein) with 74% and 99% assay generation
success rate per peptide and per protein, respec-
tively. The assays were further applied on
depleted plasma and urine to determine the
detectability of these cancer relevant proteins in
the two widely used clinical sample types. Of
the 1,157 proteins with working SRM assay,
118 proteins were detected in depleted plasma
and 408 targets were detected in urine samples.
The applicability of the generated SRM assays
to biomarker monitoring was demonstrated on
67 ovarian cancer (OVC) patient plasma samples
with 16 benign ovarian tumor patient plasma
samples as control using SID MRM-MS. Among
the 37 proteins targeted in these samples, 4
known OVC biomarkers, and 15 of 33 potential
OVC biomarkers determined according to litera-
ture search and network analysis of the 1,157
proteins were con
cacy for bladder cancer detection in
urine samples. Although more systematic efforts
obviously need to be made, including proper
urine collection protocol, protein normalization
strategy and systematic assay performance
evaluation as have been done in plasma and urine
certainly show great potential to be further inves-
tigated for MRM-MS-based biomarker veri
ca-
tion applications.
CONCLUSIONS AND
PERSPECTIVES
ed
within the discovery phases continues to
increase in size, it is becoming imperative that
high-throughput tools for verifying the utility
of any of these proteins soon become available.
While MRM-MS based approaches for verifying
these potential biomarkers hold promise, each
step in the process requires careful optimization.
It should be kept in mind that the
With the backlog of biomarkers identi
final quantita-
tive results provided by MRM-MS must be
accurate, precise, and highly reproducible. These
requirements are not trivial, as there is not a one-
size-
rmed to differentiate OVC
patient sample and control. The study developed
working SRM assays for 1,157 cancer-relevant
proteins
ts-all method to assay every candidate
biomarker. The peptide selection, sample prepa-
ration method, LC conditions, and MS parame-
ters must be optimized for each potential
biomarker. After systematic evaluation, the
applicability of the MRM-MS-based approach
to potential biomarker veri
that
could be applied for
future
biomarker veri
cation studies in the proteomic
community. It is also interesting to see that almost
40% of these cancer relevant proteins investigated
are readily detectable in urine sample by SRM
assay, compared to 16% detectable in depleted
plasma sample. However, biomarker veri
cation in complex
matrix such as plasma has been well established.
Although it is not trivial, development of
working MRM-MS assays for hundreds to
thousands of proteins has certainly become
achievable and common, as demonstrated in
the literature. With technology advancement of
both software and instrument in the last few
years, absolute quanti
cation
based on the MRM-MS approach has been largely
focusing on its performance and application to
plasma sample. The study by Chen et al.
8
is the
only study that we are aware of that applied
SID MRM-MS for bladder cancer biomarker veri-
cation of hundreds of
proteins in one patient sample reproducibly
fication targeting 63 proteins in a 156-patient
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