Proteomic and Mass Spectrometry Technologies for Biomarker Discovery - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 32

question of the validation phase is whether the
biomarker candidate addresses the unmet clinical
need that prompted its discovery. However, the
true clinical utility of a biomarker cannot be
assessed without the introduction of the marker
in the clinic and continuous monitoring of its
performance for extended periods of time.

a large number of false discoveries makes
biomarker discovery a quite expensive and not
very effective exercise and may lead to general
frustration in proteomics. Awareness of the meth-
odological limitations of proteomics and mass
spectrometry and careful design of biomarker
development pipelines should decrease the
number of potential biomarkers that never end
up in the clinic and hopefully alleviate disappoint-
ment in proteomics. 126

LIMITATIONS OF MASS
SPECTROMETRY FOR PROTEIN
BIOMARKER DISCOVERY

CONCLUSIONS AND FUTURE
OUTLOOK: INTEGRATED
BIOMARKER DISCOVERY
PLATFORM

Limitations of protein biomarker develop-
ment studies stem from biological factors, such
as intra- and interindividual variation of protein
concentrations, preanalytical variations, such as
protein stability, and technological limitations
of proteomic sample preparation and mass
spectrometry.
Major limitations of proteomics and mass
spectrometry, in general, and as a technique for
biomarker discovery studies, include:

A set of biological concepts and analytical tech-
niques can be incorporated into an integrated
protein biomarker development platform.
Current biomarker discovery strategies often rely
on identi

cation of differentially expressed
proteins and their association with a certain
disease. The exact mechanism of differential
expression and the functional role of protein
biomarkers in disease are often not known and
not studied. An integrated biomarker discovery
platform needs to be complemented with
genomic, transcriptomic, and metabolomic data.
The main purpose of an integrated platform is
not only to make the use of data accumulated by
all -omics technologies but also plan all steps and
phases down the long road that would lead to
the clinical assay approved by health agencies. It
should be always acknowledged that the ultimate
goal of biomarker development is not merely
separate groups of clinical samples, but to provide
reliable guidance for correct decision making in
clinics, such as performing relevant diagnostic
biopsy or surgery or providing relevant therapy.
Thus, the discovery, veri

Lack of the general quantitative relationship
between ion intensity and the amount of
analyte, which makes all MS-based
measurements relative

￿

Signi cant effect of matrix resulting in the ion

suppression and deviation from linear
correlation between protein amount and
spectral intensity of the same analyte

￿

￿ Multiple steps of protein fractionation,

derivatization, and trypsin digestion in
bottom-up proteomic approaches that lead to
high day-to-day variability and low
reproducibility of protein assays

Biological biases and poor quality of clinical
samples, ampli

ed by technological limitations
ofmass spectrometry, often lead to a large number
of false positive discoveries. Taking into account
the high cost of mass spectrometry instruments
and their maintenance, complex data analysis,
and the need for highly experienced personnel,

cation, and validation
steps of the biomarker discovery pipeline should
be tuned for a speci cpurpose d apriori the

biomarker development study.