The false positive rate of the identification algorithm is typically 3 4% with a randomized database appended to the original one, which is five times the size of the original utilized database.
DTA files from each LC-MS analysis were submitted to Mascot (Matrix Science, Boston, MA) searches against a forward-reverse NCBI Danio rerio protein database appended with bovine α, β, and γ casein protein entries.
The mapping of database accession numbers and cross linking is carried out by using the base URL of the database and appending the appropriate tags (referring to the entry in the database) to generate the URLs to relevant entries.
A reverse database was appended and concurrently searched.
Discrepancies were verified with patients' written notes if necessary and the database was appended accordingly.
The genic repeats have been further hyperlinked with their corresponding locus id, and the database is appended with primer3 plus for primer designing of selected repeats with left and right flanking sequences up to 250 bp.
Furthermore, randomized versions of the applied databases were appended to the original databases using the decoy perl script (Matrix Science, Boston, USA) downloadable at.
Proteins were identified by searching the data against human IPI database (v 3.41) appended with decoy (reverse) database using X!Tandem/Trans-Porteomic Pipeline software suite.
The mzXML files were searched using SEQUEST against the Human IPI database version 3.24 appended with an equal number of decoy sequences (reversed sequences from the original database).
Finally, by appending all databases, it was found that 67/72 proteins were secreted.
The databases were reversed "on-the fly" during the database query searches, and appended to the original database to assess the false positive rate of identification.
