Selected article for: "protein sequence database and raw data"
Author: Prashali Bansal; Johannes Madlung; Kristina Schaaf; Boris Macek; Fulvia Bono
Title: An interaction network of RNA-binding proteins involved in Drosophila oogenesis
  • Document date: 2020_1_9
    • ID: 2f9nc2to_15
    Snippet: For label-free MS, raw data files were processed using MaxQuant software suite v.1.6.0.1 (71) at default settings. Using the Andromeda search engine (72) integrated in the software, the spectra were searched against UniProt D. melanogaster (taxonomy ID 7227) complete proteome database (11/07/2017; 23300 protein entries; https://www.uniprot.org/), a database comprising a sequence of the tag alone and a file containing 245 common contaminants. In t.....
    Document: For label-free MS, raw data files were processed using MaxQuant software suite v.1.6.0.1 (71) at default settings. Using the Andromeda search engine (72) integrated in the software, the spectra were searched against UniProt D. melanogaster (taxonomy ID 7227) complete proteome database (11/07/2017; 23300 protein entries; https://www.uniprot.org/), a database comprising a sequence of the tag alone and a file containing 245 common contaminants. In the database search, Trypsin was defined as a cleaving enzyme, up to two missed cleavages were allowed. Carbamidomethylation (Cys) was set as fixed modification, whereas oxidation (Met) and acetylation (protein N termini) were set as variable modifications. The mass tolerances for precursor and fragment ions were set to default values of 20ppm and 0.5Da, respectively.

    Search related documents:
    Co phrase search for related documents
    • acetylation Met oxidation and database search: 1
    • acetylation Met oxidation and mass tolerance: 1
    • acetylation Met oxidation and raw data: 1
    • acetylation Met oxidation and search engine: 1
    • Andromeda search engine and database search: 1, 2, 3
    • Andromeda search engine and fragment precursor: 1
    • Andromeda search engine and mass tolerance: 1, 2, 3
    • Andromeda search engine and raw data: 1, 2
    • Andromeda search engine and search engine: 1, 2, 3, 4, 5
    • cleave enzyme and protein entry: 1
    • Cys carbamidomethylation and raw data: 1