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In order to investigate if autocatalytic chymotrypsin activity was responsible for the proteasome fragmentation, non-tryptic peptide masses were searched against semi-chymotrypsin cleavages using the FindPept program.
Peak masses were searched against the most current version of the Human Refseq Database National Center for Biotechnology Informationn) and its reversed complement with the following parameters: fixed carbamidomethylation of Cys; variable phosphorylation of Ser, Thr, and Tyr.
Masses were searched against the Homo sapiens database within a mass error of 3 ppm.
Monoisotopic masses were searched within unrestricted protein masses for tryptic peptides.
Peptide masses were searched against the National Center for Biotechnology nonredundant database (NCBInr) using the MASCOT program (http://matrixscience.com/).com/
The generated peptide masses were searched against Uniprot Human protein sequence database using the PLGS 2.5 for protein identification (Waters, UK).
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The resultant peak list with exact masses was searched against metabolite databases, including HMDB and METLIN.
The resulting peptide data from both mass and tandem mass were searched against SWISS-PROT database using MASCOT software on the matrixscience website (www.matrixscience.com).com
According to Google Insights for Search, which tracks what the online masses are searching for within specific times and regions, the former Alaska governor-turned vice presidential nominee-turned media celebrity far surpasses Obama when it comes to Google searches.
Mass spectra and tandem mass spectra were searched against all annotated proteins from strain OM5.
Mass spectra and tandem mass spectra were searched against an in silico trypsin-digested bovine database using TurboSEQUEST™ (Bioworks Browser 3.2; ThermoElectron).
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