dc.contributor.author	Cheng, Keding
dc.contributor.author	Sloan, Angela
dc.contributor.author	McCorrister, Stuart
dc.contributor.author	Babiuk, Shawn
dc.contributor.author	Bowden, Timothy R
dc.contributor.author	Wang, Gehua
dc.contributor.author	Knox, J D
dc.date.accessioned	2014-07-17T19:21:30Z
dc.date.available	2014-07-17T19:21:30Z
dc.date.issued	2014-07-10
dc.date.updated	2014-07-17T19:21:30Z
dc.description.abstract	Abstract Background Mass spectrometry (MS) is a very sensitive and specific method for protein identification, biomarker discovery, and biomarker validation. Protein identification is commonly carried out by comparing MS data with public databases. However, with the development of high throughput and accurate genomic sequencing technology, public databases are being overwhelmed with new entries from different species every day. The application of these databases can also be problematic due to factors such as size, specificity, and unharmonized annotation of the molecules of interest. Current databases representing liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based searches focus on enzyme digestion patterns and sequence information and consequently, important functional information can be missed within the search output. Protein variants displaying similar sequence homology can interfere with database identification when only certain homologues are examined. In addition, recombinant DNA technology can result in products that may not be accurately annotated in public databases. Curated databases, which focus on the molecule of interest with clearer functional annotation and sequence information, are necessary for accurate protein identification and validation. Here, four cases of curated database application have been explored and summarized. Findings The four presented curated databases were constructed with clear goals regarding application and have proven very useful for targeted protein identification and biomarker application in different fields. They include a sheeppox virus database created for accurate identification of proteins with strong antigenicity, a custom database containing clearly annotated protein variants such as tau transcript variant 2 for accurate biomarker identification, a sheep-hamster chimeric prion protein (PrP) database constructed for assay development of prion diseases, and a custom Escherichia coli (E. coli) flagella (H antigen) database produced for MS-H, a new H-typing technique. Clearly annotating the proteins of interest was essential for highly accurate, specific, and sensitive sequence identification, and searching against public databases resulted in inaccurate identification of the sequence of interest, while combining the curated database with a public database reduced both the confidence and sequence coverage of the protein search. Conclusion Curated protein sequence databases incorporating clear annotations are very useful for accurate protein identification and fit-for-purpose application through MS-based biomarker validation.
dc.description.version	Peer Reviewed
dc.identifier.citation	BMC Research Notes. 2014 Jul 10;7(1):444
dc.identifier.doi	http://dx.doi.org/10.1186/1756-0500-7-444
dc.identifier.uri	http://hdl.handle.net/1993/23698
dc.language.rfc3066	en
dc.rights	open access	en_US
dc.rights.holder	Keding Cheng et al.; licensee BioMed Central Ltd.
dc.title	Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation
dc.type	Journal Article

Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation

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