The raw data was searched against hβ4-loop protein sequence database using pLink software36.
Metabarcoding data was searched against the relevant sequence database using blastn41, using the script 'blast_with_ncbi.py'blast_with_ncbi.py
The data was searched against a decoy database, with the false discovery rate (FDR) set to 0.01.
After data dependent acquisition, tandem MS data was searched by SEQUEST (v27) against the International Protein Index human protein database (v3.68) and protein identifications were filtered using PeptideProphet.
Given the date the register data was searched, victims were on average 44 years at the end of observation.
There is no "methodology appendix" attached to a keyword search in most commercial platforms that specifies precisely how much data was searched, whether and what kind of sampling was used or how much missing data there is in its index.
A draft genome sequence of A. cellulolyticus (unpublished data) was searched for the xylanase (GH11) genes using In silico Molecular Cloning gene analysis software (In Silico Biology, Inc., Yokohama, Japan) based on the internal amino acid sequence.
The generated PMF data was searched against SWISS-PROT/TrEMBL release 35, using Protein Probe (Micromass), or against a non-redundant database maintained by the National Center for Biotechnology Information (NCBI) using the Mascot (Matrix Science Inc., Boston, MA, USA) search engine ([Helsens et al. 2007]).
LTQ data was searched fully tryptic, while Orbitrap data was searched with partial tryptic specificity.
This data was searched for those motif pairs related to the CHOP promoter element.
Data was searched using the data base search engine Mascot, (London, England).
