TY - JOUR AU - Cheng, Keding AU - Sloan, Angela AU - McCorrister, Stuart AU - Babiuk, Shawn AU - Bowden, Timothy R. AU - Wang, Gehua AU - Knox, J. David PY - 2014 DA - 2014/07/10 TI - Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation JO - BMC Research Notes SP - 444 VL - 7 IS - 1 AB - 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. SN - 1756-0500 UR - https://doi.org/10.1186/1756-0500-7-444 DO - 10.1186/1756-0500-7-444 ID - Cheng2014 ER -