Abstract
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and posttranslational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.
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References
Whiteaker JR, Halusa GN, Hoofnagle AN et al (2014) CPTAC Assay Portal: a repository of targeted proteomic assays. Nat Methods 11:703–704. doi:10.1038/nmeth.3002
Picotti P, Lam H, Campbell D et al (2008) A database of mass spectrometric assays for the yeast proteome. Nat Methods 5:913–914. doi:10.1038/nmeth1108-913
Farrah T, Deutsch EW, Kreisberg R et al (2012) PASSEL: the PeptideAtlas SRMexperiment library. Proteomics 12:1170–1175. doi:10.1002/pmic.201100515
Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20:1466–1467
Remily-Wood ER, Liu RZ, Xiang Y et al (2011) A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin Appl 5:383–396. doi:10.1002/prca.201000115
Yang X, Lazar IM (2009) MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides. BMC Cancer 9:96. doi:10.1186/1471-2407-9-96
Carr SA, Abbatiello SE, Ackermann BL et al (2014) Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics MCP 13:907–917. doi:10.1074/mcp.M113.036095
MacLean B, Tomazela DM, Shulman N et al (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26:966–968. doi:10.1093/bioinformatics/btq054
Sharma V, Eckels J, Taylor GK et al (2014) Panorama: a targeted proteomics knowledge base. J Proteome Res 13:4205–4210. doi:10.1021/pr5006636
Mudunuri U, Che A, Yi M, Stephens RM (2009) bioDBnet: the biological database network. Bioinformatics 25:555–556. doi:10.1093/bioinformatics/btn654
Hornbeck PV, Kornhauser JM, Tkachev S et al (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 40:D261–D270. doi:10.1093/nar/gkr1122
Mani DR, Abbatiello SE, Carr SA (2012) Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics 13(Suppl 16):S9. doi:10.1186/1471-2105-13-S16-S9
Acknowledgements
This work was funded by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the US National Cancer Institute (U24CA160034, U24CA160036, U24CA160019, U24CA159988, and U24CA160035), R01 GM103551, and U01 CA164186.
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Whiteaker, J.R. et al. (2016). Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. In: Sechi, S. (eds) Quantitative Proteomics by Mass Spectrometry. Methods in Molecular Biology, vol 1410. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3524-6_13
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DOI: https://doi.org/10.1007/978-1-4939-3524-6_13
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