Prepare a peptides dictionary for global standards normalization

Prepare a peptides dictionary for global standards normalization

makePeptidesDictionary(input, normalization)

Arguments

input	`data.table` in MSstats standard format
normalization	normalization method

Details

This function extracts information required to perform normalization with global standards. It is useful for running the summarization workflow outside of the dataProcess function.

Examples

input = data.table::as.data.table(DDARawData)
peptides_dict = makePeptidesDictionary(input, "GLOBALSTANDARDS")
head(peptides_dict) # ready to be passed to the MSstatsNormalize function
#>      PeptideSequence PrecursorCharge              PEPTIDE
#> 1:       S.PVDIDTK_5               5        S.PVDIDTK_5_5
#> 2:       G.PLTGTYR_8               8        G.PLTGTYR_8_8
#> 3:     K.KDGADFAK_16              16     K.KDGADFAK_16_16
#> 4:     D.GPLTGTYR_23              23     D.GPLTGTYR_23_23
#> 5:     L.VYGEATSR_34              34     L.VYGEATSR_34_34
#> 6: -.PHSHPALTPEQK_35              35 -.PHSHPALTPEQK_35_35