fix_MSMS: Transform the MS/MS output to publication ready

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

Transform the MS/MS output to publication ready

Description

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 MetaboSet object
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)

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)

Value

MetaboSet object as the one supplied, with publication-ready MS/MS peak information

Examples

# Spectra before fixing
fData(merged_sample)$MS_MS_spectrum[!is.na(fData(merged_sample)$MS_MS_spectrum)]
# Fixing spectra with default settings
fixed_MSMS_peaks <- fix_MSMS(merged_sample)
# Spectra after fixing
fData(fixed_MSMS_peaks)$MS_MS_Spectrum_clean[!is.na(fData(fixed_MSMS_peaks)$MS_MS_Spectrum_clean)]

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.