This function combines a set of proteins with a set of PTM compositions ("modcoms") and calculates the masses of the resulting proteoforms (i.e., the different molecular forms in which the protein product of a single gene can be found due to changes introduced by posttranslational modifications).
assemble_proteoforms(p, m, mass_set = "average")
| p | A protein specification as returned by |
|---|---|
| m | A modcom specification as returned by |
| mass_set | Atomic masses that should be used for mass calculation. |
A data frame containing \(p \times m\) proteoforms, obtained
by combining information on \(p\) proteins (i.e., number of rows in p)
with information on \(m\) PTM compositions (i.e., number of rows in m).
This data frame comprises two columns derived from the input data frames
(protein_name and modcom_name, respectively) and two new columns
formula (overall molecular formula) and mass (calculated proteoform
masses).
get_mass() for predefined mass sets
proteins <- define_proteins( system.file("extdata", "mab_sequence.fasta", package = "fragquaxi"), .disulfides = 16 ) modcoms <- define_ptm_compositions(sample_modcoms) assemble_proteoforms(proteins, modcoms)#> # A tibble: 6 x 4 #> protein_name modcom_name formula mass #> <int> <chr> <mol> <dbl> #> 1 1 G0F/G0 C6570 H10124 N1714 O2088 S44 147942. #> 2 1 G0F/G0F C6576 H10134 N1714 O2092 S44 148088. #> 3 1 G0F/G1F C6582 H10144 N1714 O2097 S44 148250. #> 4 1 G1F/G1F C6588 H10154 N1714 O2102 S44 148412. #> 5 1 G1F/G2F C6594 H10164 N1714 O2107 S44 148574. #> 6 1 G2F/G2F C6600 H10174 N1714 O2112 S44 148737.