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experiments.
121
A probe was created that targeted
19 active proteins in the hepatitis C virus (HCV)
proteome. These proteins were then used to eval-
uate the pathological state of HCV replication.
121
The clinical manifestations of ABPs have not
quite yet come to fruition. A recent review
highlights pro
sera, which has improved LOD and LOQ
compared to global quantitative pro
ling
methods, is being exploited for quantifying
low-abundant protein targets. Ideally, these MS
methods can afford accurate quantitation of
a large amount of clinical samples in a short
time period.
130
ling in cancer for pathway
discovery.
114
The discussion for their use in the
clinical setting is often foreshadowed. To echo
this sentiment, a more recent review of preclinical
drug discovery suggests ABPs
Multiple Reaction Monitoring or Selected
Reaction Monitoring MS
Technique Overview
Multiple reaction monitoring (MRM) or
selected reaction monitoring (SRM) MS offers
highly sensitive, speci
future use in the
clinical setting.
122
Due to the complicated
synthetic procedures and the diverse structural
requirements for different enzyme classes, the
activity-based biomarker discovery is likely to be
'
c, and cost-effective anal-
ysis for simultaneous quantitation of hundreds to
several thousands of targeted peptides in a single
experiment.
131,132
firstly successful in several pioneer groups in the
chemical proteomic
field. However, the emerging
availability of commercial APBs is expected to
stimulate the broad exploration of the technology
for discovering novel, activity-based protein
biomarkers. Another technology, the method of
capture compound MS (CCMS),
123
e
125
which
uses the principle of af
For
simplicity,
the
term
“
is used; in a large portion of the related
literature, SRM is also used with the same
meaning. In themultiplexed analysis mode, these
peptides are signature peptides of hundreds of
candidate protein biomarkers; in the throughput
analysis mode, these peptides are signature
peptides, but with sample-speci
MRM
”
nity labeling of proteins,
79
will provide an alternative option for this type of
biomarker discovery.
c codes, for
only a few protein biomarkers in the later stages
of the biomarker development pipeline.
133
Conventional implementation of MRM MS
experiments uses
TARGETED PROTEOMIC
VALIDATION OF BIOMARKER
CANDIDATES
triple quadrupole
(QqQ)
mass spectrometers (
Figure 2
). The
rst mass
analyzer (Q1) of these tandem instruments can
selectively transmit ions of a particular mass-
to-charge ratio (
m/z
), corresponding to intact
ions of a target analyte; these ions are called
precursor ions. The precursor ions are then sub-
jected to collision-induced dissociation in a colli-
sion cell (q2) with neutral gas at appropriate
pressure. This process produces fragment ions
of the target analyte. The fragment ions with
high ion intensity and speci
Validation of candidate protein biomarkers,
especially in easily accessible and less-invasive
blood samples and body
fluids, is essential to
produce disease biomarkers for the eventual
clinical applications. High speci
c and sensitive
MS provides
flexible measurements for fast
validation.
126,127
biomarker
Tissue-derived,
disease-speci
c proteins typically get diluted in
the bloodstream to the concentration range of
low nanograms per milliliter. Such a low amount
is contained in the large dynamic concentration
range of plasma proteins, which span up to 12
orders of magnitude.
128,129
Therefore, targeted
MS analysis of proteins in human plasma and
city are, once again,
selectively transmitted through a mass analyzer.
However, this time it happens in the second
mass analyzer (Q3) (
Figure 2
). The transmitted
ions
finally reach the ion detector in mass spec-
trometers and the detected signals are recorded
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