TY - JOUR
T1 - Differential plasma glycoproteome of p19ARF skin cancer mouse model using the Corra label-free LC-MS proteomics platform
AU - Letarte, Simon
AU - Brusniak, Mi Youn
AU - Campbell, David
AU - Eddes, James
AU - Kemp, Christopher J.
AU - Lau, Hollis
AU - Mueller, Lukas
AU - Schmidt, Alexander
AU - Shannon, Paul
AU - Kelly-Spratt, Karen S.
AU - Vitek, Olga
AU - Zhang, Hui
AU - Aebersold, Ruedi
AU - Watts, Julian D.
N1 - Funding Information:
Acknowledgments This work was supported with federal funds from the National Cancer Institute, National Institutes of Health, under contract No. N01-CO-12400 (to J.W.), the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract N01-HV-28179 (to R.A.), the National Cancer Institute by Grants R21-CA-114852 (to H.Z.), and by Grant No. 31000-107-67 by the Swiss National Science Foundation (to R.A.).
PY - 2008/12
Y1 - 2008/12
N2 - Introduction: A proof-of-concept demonstration of the use of label-free quantitative glycoproteomics for biomarker discovery workflow is presented in this paper, using a mouse model for skin cancer as an example. Materials and Methods: Blood plasma was collected from ten control mice and ten mice having a mutation in the p19ARF gene, conferring them high propensity to develop skin cancer after carcinogen exposure. We enriched for N-glycosylated plasma proteins, ultimately generating deglycosylated forms of the tryptic peptides for liquid chromatography mass spectrometry (LC-MS) analyses. LC-MS runs for each sample were then performed with a view to identifying proteins that were differentially abundant between the two mouse populations. We then used a recently developed computational framework, Corra, to perform peak picking and alignment, and to compute the statistical significance of any observed changes in individual peptide abundances. Once determined, the most discriminating peptide features were then fragmented and identified by tandem mass spectrometry with the use of inclusion lists. Results and Discussions: We assessed the identified proteins to see if there were sets of proteins indicative of specific biological processes that correlate with the presence of disease, and specifically cancer, according to their functional annotations. As expected for such sick animals, many of the proteins identified were related to host immune response. However, a significant number of proteins are also directly associated with processes linked to cancer development, including proteins related to the cell cycle, localization, transport, and cell death. Additional analysis of the same samples in profiling mode, and in triplicate, confirmed that replicate MS analysis of the same plasma sample generated less variation than that observed between plasma samples from different individuals, demonstrating that the reproducibility of the LC-MS platform was sufficient for this application. Conclusion: These results thus show that an LC-MS-based workflow can be a useful tool for the generation of candidate proteins of interest as part of a disease biomarker discovery effort.
AB - Introduction: A proof-of-concept demonstration of the use of label-free quantitative glycoproteomics for biomarker discovery workflow is presented in this paper, using a mouse model for skin cancer as an example. Materials and Methods: Blood plasma was collected from ten control mice and ten mice having a mutation in the p19ARF gene, conferring them high propensity to develop skin cancer after carcinogen exposure. We enriched for N-glycosylated plasma proteins, ultimately generating deglycosylated forms of the tryptic peptides for liquid chromatography mass spectrometry (LC-MS) analyses. LC-MS runs for each sample were then performed with a view to identifying proteins that were differentially abundant between the two mouse populations. We then used a recently developed computational framework, Corra, to perform peak picking and alignment, and to compute the statistical significance of any observed changes in individual peptide abundances. Once determined, the most discriminating peptide features were then fragmented and identified by tandem mass spectrometry with the use of inclusion lists. Results and Discussions: We assessed the identified proteins to see if there were sets of proteins indicative of specific biological processes that correlate with the presence of disease, and specifically cancer, according to their functional annotations. As expected for such sick animals, many of the proteins identified were related to host immune response. However, a significant number of proteins are also directly associated with processes linked to cancer development, including proteins related to the cell cycle, localization, transport, and cell death. Additional analysis of the same samples in profiling mode, and in triplicate, confirmed that replicate MS analysis of the same plasma sample generated less variation than that observed between plasma samples from different individuals, demonstrating that the reproducibility of the LC-MS platform was sufficient for this application. Conclusion: These results thus show that an LC-MS-based workflow can be a useful tool for the generation of candidate proteins of interest as part of a disease biomarker discovery effort.
KW - Biomarker discovery
KW - Glycoproteomics
KW - LC-MS
KW - Label-free protein quantification
KW - Plasma
KW - Skin cancer
KW - Systems biology
KW - Targeted peptide sequencing
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U2 - 10.1007/s12014-008-9018-8
DO - 10.1007/s12014-008-9018-8
M3 - Article
C2 - 20157627
AN - SCOPUS:62549084737
SN - 1542-6416
VL - 4
SP - 105
EP - 116
JO - Clinical Proteomics
JF - Clinical Proteomics
IS - 3-4
ER -