Add MS2 spectra data into mass_dataset class object
Xiaotao Shen
Created on 2021-12-04 and updated on 2026-03-04
Source:vignettes/mutate_ms2.Rmd
mutate_ms2.Rmdmass_data class object can also contain MS2 data.
Data preparation
mass_data class object
We need to create a mass_data class object first; see this
document. Here we use the demo datasets bundled with the
package.
library(massdataset)
data("expression_data")
data("sample_info")
data("variable_info")
object_pos <-
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info
)MS2 data
The MS2 raw data should be converted to mgf format data. Please refer to this document.
Here we use the MGF example bundled with
massdataset.
Add MS2 to mass_dataset class
object
Positive mode.
ms2_dir <- system.file("ms2_data", package = "massdataset")
object_pos2 =
mutate_ms2(
object = object_pos,
column = "rp",
polarity = "positive",
ms1.ms2.match.mz.tol = 10,
ms1.ms2.match.rt.tol = 15,
path = ms2_dir
)Session information
sessionInfo()
#> R version 4.5.2 (2025-10-31)
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#> Running under: macOS Tahoe 26.3
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