Aug 05, 2020
Database Preparation and Search for Protein Identification
- 1domnic colvin
- UM-DAE Centre for Excellence in Basic Sciences
Document Citation: avinash.kale 2020. Database Preparation and Search for Protein Identification. protocols.io https://dx.doi.org/10.17504/protocols.io.bjdwki7e
License: This is an open access document distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Created: August 05, 2020
Last Modified: August 05, 2020
Document Integer ID: 40086
Database Preparation and Search for Protein Identification
The mass-spec data were searched against the customized mosquito larvicidal toxin database which included well established larvicidal toxins like Cry1 to Cry73, Bin-A/B, VIP-1/2/3/4, and Mtx-1/2/3. (28). The default search parameters used for the analysis are as follows: (a) trypsin as the proteolytic enzyme with up to one missed cleavage; (b) peptide mass error tolerance of 20ppm; (c) fragment mass error tolerance of 0.1 Da; (d) carb-amido-methylation of cysteine as fixed modification (e) oxidation of methionine as a variable modification. A false discovery rate of 1% was applied while identifying the peptide-spectrum matches. Two criteria used to report a positive find, 1) reported protein/toxin should have least two numbers of peptides in amino acid sequence; and 2) the length of each of the identified peptide sequences using LC-MS has a minimum of 10 amino acids.