Threat status was modeled using General Linear Mixed-effects Models, with size, depth and geography treated as fixed effects and taxonomy hierarchy as a random effect to account for phylogenetic non-independence.
The lines are the best fits from General Linear Mixed-effects Models, with maximum body size and geographic distribution traits treated as fixed effects and taxonomy hierarchy as a random effect to account for phylogenetic non-independence.
During the course of the analysis the structure of the taxonomy is fixed.
Database search criteria were as follows – enzyme: trypsin, taxonomy: none, fixed modification: carbamidomethylation, variable modification: methionine oxidation, peptide mass tolerance: 120 ppm, one missed cleavage allowed.
Database search criteria were taxonomy, Homo sapiens, fixed modification; carboxyamidomethylated (+57) at cysteine residue; variable modification; oxidized (+16) at methionine residues, maximum allowed missed cleavage, 1, MS tolerance, 100 ppm.
Both operations are independent of the underlining data set (the selection process is random and the partitioning process is fixed due to the given taxonomy trees), and therefore no privacy budget is required for the h number of iterations.
The MS/MS data were searched against Mascot 2.2 (Matrix Science) applied to NCBInr (released March 2011; 13,473,798 sequences) with the parameters of carbamidomethyl (C) and oxidation (M) as the fixed and variable modifications, respectively: taxonomy, all entries; enzyme, trypsin/P; missed cleavages, 1; peptide tolerance, ± 20 ppm, and MS/MS tolerance, ± 0.02 Da.
Semantic Web technologies enable data integration by allowing the structure and semantics of conceptual entities to be fixed, e.g., as controlled vocabularies, taxonomies, ontologies, etc.
Carcasses were fixed in formalin for α-taxonomy purposes.
