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Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

Huttenhain, Ruth; Soste, Martin; Selevsek, Nathalie; Roest, Hannes; Sethi, Atul; Carapito, Christine; Farrah, Terry; Deutsch, Eric W.; Kusebauch, Ulrike and Moritz, Robert L., et al. (2012) In Science Translational Medicine 4(142). p.94-142
Abstract
The rigorous testing of hypotheses on suitable sample cohorts is a major limitation in translational research. This is particularly the case for the validation of protein biomarkers; the lack of accurate, reproducible, and sensitive assays for most proteins has precluded the systematic assessment of hundreds of potential marker proteins described in the literature. Here, we describe a high-throughput method for the development and refinement of selected reaction monitoring (SRM) assays for human proteins. The method was applied to generate such assays for more than 1000 cancer-associated proteins, which are functionally related to candidate cancer driver mutations. We used the assays to determine the detectability of the target proteins in... (More)
The rigorous testing of hypotheses on suitable sample cohorts is a major limitation in translational research. This is particularly the case for the validation of protein biomarkers; the lack of accurate, reproducible, and sensitive assays for most proteins has precluded the systematic assessment of hundreds of potential marker proteins described in the literature. Here, we describe a high-throughput method for the development and refinement of selected reaction monitoring (SRM) assays for human proteins. The method was applied to generate such assays for more than 1000 cancer-associated proteins, which are functionally related to candidate cancer driver mutations. We used the assays to determine the detectability of the target proteins in two clinically relevant samples: plasma and urine. One hundred eighty-two proteins were detected in depleted plasma, spanning five orders of magnitude in abundance and reaching below a concentration of 10 ng/ml. The narrower concentration range of proteins in urine allowed the detection of 408 proteins. Moreover, we demonstrate that these SRM assays allow reproducible quantification by monitoring 34 biomarker candidates across 83 patient plasma samples. Through public access to the entire assay library, researchers will be able to target their cancer-associated proteins of interest in any sample type using the detectability information in plasma and urine as a guide. The generated expandable reference map of SRM assays for cancer-associated proteins will be a valuable resource for accelerating and planning biomarker verification studies. (Less)
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type
Contribution to journal
publication status
published
subject
in
Science Translational Medicine
volume
4
issue
142
pages
94 - 142
publisher
American Association for the Advancement of Science (AAAS)
external identifiers
  • wos:000306356000003
  • scopus:84863923380
ISSN
1946-6242
DOI
10.1126/scitranslmed.3003989
language
English
LU publication?
yes
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b6a78db8-4f29-4631-a467-0cc39a533ef8 (old id 2994974)
date added to LUP
2012-09-03 07:18:18
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2017-11-12 03:05:34
@article{b6a78db8-4f29-4631-a467-0cc39a533ef8,
  abstract     = {The rigorous testing of hypotheses on suitable sample cohorts is a major limitation in translational research. This is particularly the case for the validation of protein biomarkers; the lack of accurate, reproducible, and sensitive assays for most proteins has precluded the systematic assessment of hundreds of potential marker proteins described in the literature. Here, we describe a high-throughput method for the development and refinement of selected reaction monitoring (SRM) assays for human proteins. The method was applied to generate such assays for more than 1000 cancer-associated proteins, which are functionally related to candidate cancer driver mutations. We used the assays to determine the detectability of the target proteins in two clinically relevant samples: plasma and urine. One hundred eighty-two proteins were detected in depleted plasma, spanning five orders of magnitude in abundance and reaching below a concentration of 10 ng/ml. The narrower concentration range of proteins in urine allowed the detection of 408 proteins. Moreover, we demonstrate that these SRM assays allow reproducible quantification by monitoring 34 biomarker candidates across 83 patient plasma samples. Through public access to the entire assay library, researchers will be able to target their cancer-associated proteins of interest in any sample type using the detectability information in plasma and urine as a guide. The generated expandable reference map of SRM assays for cancer-associated proteins will be a valuable resource for accelerating and planning biomarker verification studies.},
  author       = {Huttenhain, Ruth and Soste, Martin and Selevsek, Nathalie and Roest, Hannes and Sethi, Atul and Carapito, Christine and Farrah, Terry and Deutsch, Eric W. and Kusebauch, Ulrike and Moritz, Robert L. and Niméus, Emma and Rinner, Oliver and Aebersold, Ruedi},
  issn         = {1946-6242},
  language     = {eng},
  number       = {142},
  pages        = {94--142},
  publisher    = {American Association for the Advancement of Science (AAAS)},
  series       = {Science Translational Medicine},
  title        = {Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics},
  url          = {http://dx.doi.org/10.1126/scitranslmed.3003989},
  volume       = {4},
  year         = {2012},
}