Quality control filters can be applied to spectra using the following steps:

1. Load the library and download the source data:

library(proteoQC) 
online_file <- "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD006247/CS_130530_ORBI_EMCP2156_b2469_narQ_DDM_AmH_X_5.mzXML"

mzxml_file <- file.path(getwd(), "datasets", "ch6", "PXD006247_mz.xml.gz" )

download.file(online_file, mzxml_file, "internal")

2. Create a design file:

design_df <- data.frame(
 file = c(mzxml_file),
 sample = c(1),
 bioRep = c(1),
 techRep = c(1),
 fraction = c(1)
 )
design_file <- file.path(getwd(), "datasets", "ch6", "design_file.txt")
write.table(design_df, file = design_file, quote = FALSE, row.names = FALSE)

3. Set up the QC pipeline and run the following command:

qc <- msQCpipe(
 spectralist = design_file,
 fasta = file.path(getwd(), "datasets", "ch6", "Escherichia_coli.pep.all.fa"),
 outdir = file.path(getwd(), "qc_result"),
 enzyme = 1, varmod = 2, fixmod =1,
 tol = 10, itol = 0.6, cpu = 2,
 mode = "identification"
)