TY - JOUR
T1 - Towards proteome standards
T2 - The use of absolute quantitation in high-throughput biomarker discovery
AU - Chao, Tzu Chiao
AU - Hansmeier, Nicole
AU - Halden, Rolf
N1 - Funding Information:
This research was supported in part by the National Institute of Environmental Health Sciences grant 1R01ES015445 .
PY - 2010/6/16
Y1 - 2010/6/16
N2 - The use of proteomics to profile biological fluids and identify therein biomarkers for cancer and other diseases was initially received with considerable excitement. However, results have fallen short of the expectations. Traditionally, protein biomarkers have been identified by measurement of relative expression changes between case and control samples from which differentially expressed proteins are then considered to represent biomarker candidates. We argue that current individual proteomics-based biomarker discovery studies lack the statistical strength for the identification of high-confidence biomarkers. Instead, multi-group efforts are necessary to facilitate the generation of sufficient sample sizes. This is contingent on the ability to collate and cross-compare data from different studies, which will require the use of a common metric or standards. Though profound, the technical challenges for absolute protein quantification can be overcome. The use of matrix specific, shared standards for absolute quantitation presents an opportunity to facilitate the much needed, but currently impossible, comparisons of different studies. In addition to community-wide approaches to standardize pre-analytical biomarker research studies, it is also important to establish means to integrate experimental data from different studies in order to assess the usefulness of proposed biomarkers with sufficient statistical certainty.
AB - The use of proteomics to profile biological fluids and identify therein biomarkers for cancer and other diseases was initially received with considerable excitement. However, results have fallen short of the expectations. Traditionally, protein biomarkers have been identified by measurement of relative expression changes between case and control samples from which differentially expressed proteins are then considered to represent biomarker candidates. We argue that current individual proteomics-based biomarker discovery studies lack the statistical strength for the identification of high-confidence biomarkers. Instead, multi-group efforts are necessary to facilitate the generation of sufficient sample sizes. This is contingent on the ability to collate and cross-compare data from different studies, which will require the use of a common metric or standards. Though profound, the technical challenges for absolute protein quantification can be overcome. The use of matrix specific, shared standards for absolute quantitation presents an opportunity to facilitate the much needed, but currently impossible, comparisons of different studies. In addition to community-wide approaches to standardize pre-analytical biomarker research studies, it is also important to establish means to integrate experimental data from different studies in order to assess the usefulness of proposed biomarkers with sufficient statistical certainty.
KW - Body fluids
KW - Peptide standard
KW - Proteomics
KW - Sample size
KW - Standardization
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U2 - 10.1016/j.jprot.2010.04.004
DO - 10.1016/j.jprot.2010.04.004
M3 - Letter
C2 - 20399287
AN - SCOPUS:77953121793
SN - 1874-3919
VL - 73
SP - 1641
EP - 1646
JO - Journal of Proteomics
JF - Journal of Proteomics
IS - 8
ER -