At the Protein Analysis Faciltiy of the University of Lausanne we have our internal list of contaminants.
Since it is a very common task to remove contaminants from MaxQuant outputs (proteinGroups.txt) we implemented a function to find the contaminants in a given file:
# load results from MQ pg_path <- "proteinGroups.txt" pg <- read.table(proteinGroups_path, quote='\"', row.names=NULL, header=TRUE, sep='\t', fill=TRUE, na.strings=c('Non Num\303\251rique')) # remove contaminants is_contaminant <-contaminants_MQ(pg) pg_filtered <- pg[! is_contaminant,]
Alternatively you can find contaminants from a vector of either protein ACs, gene names or a given term (e.g. from a FASTA header):
# by protein AC contaminant_AC(c("A0AVF1", "Q9NZT1", "P02786")) # by gene name contaminant_gene(c("TFRC", "TGM1", "MTFR1")) # by term contaminant_term(c("blibla", "blibla keratin blabla", "Keratinblibla", "kerami mouou"))
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