It is important to explore PSM results prior to any further
downstream analysies. Two functions, that work on PSM() and
ConnectedComponents() objects can be used for this:
The describeProteins() function describe protein composition
in terms of unique and shared peptides.
The describePeptides() function describe unique/shared peptide
composition.
describeProteins(object)
describePeptides(object)Either an instance of class Matrix, PSM() or
ConnectedComponents().
describePeptides() invisibly return the table of unique
and shared peptides. describeProteins() invisibly returns a
data.frame with logicals indicating the unique/shared
peptide composition of proteins. Both functions are used for
their side effects of printing a short descriptive output
about peptides and proteins.
f <- msdata::ident(full.names = TRUE, pattern = "TMT")
basename(f)
#> [1] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"
psm <- PSM(f) |>
filterPsmDecoy() |>
filterPsmRank()
#> Removed 2896 decoy hits.
#> Removed 155 PSMs with rank > 1.
describePeptides(psm)
#> 2357 peptides composed of
#> unique peptides: 2324
#> shared peptides (among protein):
#> 28(2) 3(3) 2(4)
describeProteins(psm)
#> 1504 proteins composed of
#> only unique peptides: 1455
#> only shared peptides: 38
#> unique and shared peptides: 11