Project description:Proteomic analysis of six tissues (liver, kidney, blubber, brain, muscle, skin) provided experimental confirmation of 10,402 proteins from 4,711 protein groups, almost 1/3 of the possible predicted proteins in the Atlantic bottlenose dolphin (Tursiops truncatus) NCBI annotation (release 101), which is based on the recently completed NIST Tur_tru v1 genome assembly.
Project description:A Multiple Affinity Removal System (MARS) Human 14 spin cartridge was used to deplete a dolphin serum which was then digested with trypsin and analyzed without prior fractionation by nanoLC-MS/MS. These files are associated with "2011-9-25_Neely-DolphinSerum." Data analysis: raw data generated by the AB Sciex 5600 were converted to a peak list using the AB Sciex MS Data Converter (v. 1.1 beta, July 2011). Protein identifications were made using Mascot (v. 2.3.02) searching against the Ensembl (release 64) turTru1 dolphin genome assembly protein database [16,598 sequences] and the common Repository of Adventitious Proteins database (cRAP; 2012.01.01; the Global Proteome Machine) using the following parameters: trypsin was selected as the enzyme and three missed cleavages were allowed; carbamidomethylation (Cys) was specified as a fixed modification; glucosylgalactosyl (Lys), oxidation (Met, Pro), and 2-succinyl (Cys) were specified as variable modifications; a precursor tolerance of 10 ppm and fragment ion tolerance of 0.5 Da; instrument type was ESI-QUAD-TOF. Additionally, a non-depleted dolphin sera that had been digested followed by quasi-fractionation using SPE, was analyzed by nano-LC-MS/MS which lead to an additional peptide identification, KGEPGESAYVYR, and these files are associated with "2012-12-12 Dolphin IDA".
