proteome: Proteome
In tsoleary/proteomixr: Label-free quantitative proteomics & D3-Leu turnover

Creates a data frame with an average abundance of the top ionizers for each protein

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proteome(file_name, organism, wt_samps = "all", group = FALSE,
  group_names = NULL, top_pep = 3, min_pep = 3, norm = FALSE,
  norm_method = NULL, norm_pro = NULL, csv = TRUE)

`file_name`	file containing all peptides for all samples with the columns named Annotated.Sequence, Modifications, Master.Protein.Accessions.
`organism`	"mouse", "human" or "rat"
`wt_samps`	"all" if you want to use all samples to weight, otherwise use a pattern that is present in the column names of the samples you wish to use for the weighting
`group`	if you want to group samples then `TRUE`
`group_names`	indicate names of the groups (must be a string pattern present in the samples)
`top_pep`	number of top ionizers used
`min_pep`	minumum number of peptides found in a protein to be incuded in the analysis
`norm`	set to TRUE if normalization is wanted
`norm_method`	indicate normalization method: "protein" or "sum_total"
`norm_pro`	accession of protein used for
`csv`	if result file should be written in working directory

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proteome("WT vs KO all pep.csv", group_names = c("WT", "KO"),
         organism = "mouse", group = TRUE, norm = TRUE,
         norm_method = "protein", norm_pro = "B2RTM0", csv = FALSE)