Computational protocol: Mass spectrometry data from a quantitative analysis of protein expression in gills of immuno-challenged blue mussels (Mytilus edulis)

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Protocol publication

[…] The acquired data (.RAW-files) were processed by MaxQuant and database searches were performed using the implemented Andromeda search engine. MS/MS spectra were correlated to a FASTA database containing proteins from Mytilus extracted from the NCBI database (release June 2015). A decoy search database, including common contaminants and a reverse database, was used to estimate the identification false discovery rate (FDR). An FDR of 1% was accepted. The search parameters included: maximum 10 ppm and 0.6 Da error tolerances for the survey scan and MS/MS analysis, respectively; enzyme specificity was trypsin; maximum one missed cleavage site allowed; cysteine carbamidomethylation was set as static modification and oxidation (M) was set as variable modification. For protein identification, only peptides with a minimum of seven amino acids and at least one unique peptide were accepted. […]

Pipeline specifications

Software tools MaxQuant, Andromeda
Application MS-based untargeted proteomics
Organisms Mytilus edulis
Diseases Multiple Sclerosis