Computational protocol: Comprehensive Assessment of Milk Composition in Transgenic Cloned Cattle

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Protocol publication

[…] The in-solution tryptic digestion proteins (200 µg) were analyzed using 2D-Nano-LC-ESI-MS/MS, performed on a nano Acquity UPLC (Waters) connected to a LTQ Orbitrap XL mass spectrometer (Thermo Fisher). Each scan cycle consisted of one full MS scan in profile mode followed by five MS/MS scans in centroid mode. The acquired MS/MS spectra were used to search against a non-redundant protein Bovidae database using the SEQUEST program in the BioWorks™ 3.3.1 software suite with the following parameters: the mass tolerance of 1.4 Da for precursor ions and 1.0 Da for fragment ions, allowing two missed cleavage. The false discovery rate was less than 1%, which was calculated using a database containing reversed sequences. The peptide identifications were filtered by PeptideProphet with a confidence level of 95% and protein identifications were accepted with greater than 99% probability . […]

Pipeline specifications

Software tools Comet, PeptideProphet
Application MS-based untargeted proteomics
Organisms Bos taurus, Homo sapiens