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().
Additional arguments passed to makeAdjacencyMatrix().
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