Change the MS/MS output from MS-DIAL format to publication-ready format. Original spectra is sorted according to abundance percentage and clarified. See the example below.
Usage
fix_MSMS(
object,
ms_ms_spectrum_col = "MS_MS_spectrum",
peak_num = 10,
min_abund = 5,
deci_num = 3
)Arguments
- object
a
SummarizedExperimentorMetaboSetobject- ms_ms_spectrum_col
name of column with original MS/MS spectra
- peak_num
maximum number of peak that is kept (Recommended: 4-10)
- min_abund
minimum relative abundance to be kept (Recommended: 1-5)
- deci_num
maximum number of decimals to m/z value (Recommended: >2)
Value
A SummarizedExperiment or MetaboSet object as the one supplied, with publication-ready MS/MS peak information.
Details
Original MS/MS spectra from MS-DIAL: m/z:Raw Abundance
23.193:254 26.13899:5 27.50986:25 55.01603:82 70.1914:16 73.03017:941 73.07685:13 73.13951:120
Spectra after transformation: m/z (Abundance)
73.03 (100), 23.193 (27), 73.14 (12.8), 55.016 (8.7)
Examples
data(example_set)
# Spectra before fixing
ex_set <- example_set
rowData(ex_set)$MS_MS_spectrum <- NA
rowData(ex_set)[1, ]$MS_MS_spectrum <-
"28.769:53 44.933:42 52.106:89 69.518:140"
rowData(ex_set)$MS_MS_spectrum[
!is.na(rowData(ex_set)$MS_MS_spectrum)]
#> [1] "28.769:53 44.933:42 52.106:89 69.518:140"
# Fixing spectra with default settings
fixed_MSMS_peaks <- fix_MSMS(ex_set)
#> INFO [2025-06-23 22:36:33] Saving fixed MS/MS spectra to column 'MS_MS_Spectrum_clean' in rowData
# Spectra after fixing
rowData(fixed_MSMS_peaks)$MS_MS_Spectrum_clean[
!is.na(rowData(fixed_MSMS_peaks)$MS_MS_Spectrum_clean)]
#> [1] "69.518 (100), 52.106 (63.6), 28.769 (37.9), 44.933 (30)"