## ---- eval=TRUE, echo=FALSE, results='hide', message=FALSE-------------------- require(MSGFplus) ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- par <- msgfPar() show(par) ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- databaseFile <- system.file('extdata', 'milk-proteins.fasta', package='MSGFplus') db(par) <- databaseFile ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- tolerance(par) <- '20 ppm' # Set parent ion tolerance chargeRange(par) <- c(2, 6) # Set the range of charge states to look after lengthRange(par) <- c(6, 25) # Set the range of peptide length to look after instrument(par) <- 'QExactive' # Set the instrument used for acquisition enzyme(par) <- 'Trypsin' # Set the enzyme used for digestion fragmentation(par) <- 0 # Set the fragmentation method protocol(par) <- 0 # Set the protocol type isotopeError(par) <- c(0,2) # Set the isotope error matches(par) <- 2 # Set the number of matches to report per scan ntt(par) <- 1 # Set number of tolerable termini tda(par) <- TRUE # Use target decoy approach par ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- mods(par)[[1]] <- msgfParModification(name = 'Carbamidomethyl', composition = 'C2H3N1O1', residues = 'C', type = 'opt', position = 'any') mods(par)[[2]] <- msgfParModification(name = 'Oxidation', mass = 15.994915, residues = 'M', type = 'opt', position = 'any') nMod(par) <- 2 # Set max number of modifications per peptide par ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- par <- msgfPar(database = databaseFile, tolerance = '20 ppm', tda=TRUE, instrument='QExactive') par ## ---- eval=FALSE, echo=TRUE, results='hide'----------------------------------- # par <- msgfParFromID('/path/to/results/file.mzid') # # par ## ---- eval=FALSE-------------------------------------------------------------- # require(gWidgets) # # par <- msgfParGUI() ## ---- eval=FALSE, echo=TRUE--------------------------------------------------- # res <- runMSGF(par, 'your_rawfile.mzML') ## ---- eval=FALSE, echo=TRUE--------------------------------------------------- # msgf <- runMSGF(par, 'your_rawfile.mzML', async=TRUE) # # while(running(msgf)) { # Sys.sleep(1) # You could arguably do more meaningfull stuff here # } # if(finished(msgf)) { # res <- import(msgf) # } ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- sessionInfo()