Annotate single peaks in mass

Data preparation

library(massdataset)
library(tidyverse)
library(metid)

ms1_data =
  readr::read_csv(file.path(
    system.file("ms1_peak", package = "metid"),
    "ms1.peak.table.csv"
  ))

ms1_data = data.frame(ms1_data, sample1 = 1, sample2 = 2)

expression_data = ms1_data %>%
  dplyr::select(-c(name:rt))

variable_info =
  ms1_data %>%
  dplyr::select(name:rt) %>%
  dplyr::rename(variable_id = name)

sample_info =
  data.frame(
    sample_id = colnames(expression_data),
    injection.order = c(1, 2),
    class = c("Subject", "Subject"),
    group = c("Subject", "Subject")
  )
rownames(expression_data) = variable_info$variable_id

object = create_mass_dataset(
  expression_data = expression_data,
  sample_info = sample_info,
  variable_info = variable_info
)

object
#> -------------------- 
#> massdataset version: 0.99.7 
#> -------------------- 
#> 1.expression_data:[ 100 x 2 data.frame]
#> 2.sample_info:[ 2 x 4 data.frame]
#> 3.variable_info:[ 100 x 3 data.frame]
#> 4.sample_info_note:[ 4 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-02-19 17:25:03

Add MS2 to `mass_dataset` object

path = "./example"
dir.create(path)

ms2_data <- system.file("ms2_data", package = "metid")
file.copy(
  from = file.path(ms2_data, "QC1_MSMS_NCE25.mgf"),
  to = path,
  overwrite = TRUE,
  recursive = TRUE
)
#> [1] TRUE

object =
  massdataset::mutate_ms2(
    object = object,
    column = "rp",
    polarity = "positive",
    ms1.ms2.match.mz.tol = 10,
    ms1.ms2.match.rt.tol = 30
  )
#> 
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Annotate single peaks in mass_dataset

Xiaotao Shen PhD (https://www.shenxt.info/)

Created on 2020-03-28 and updated on 2022-09-19

Data preparation

Add MS2 to `mass_dataset` object

Annotate single peaks in mass_dataset

Xiaotao Shen PhD (https://www.shenxt.info/)

Created on 2020-03-28 and updated on 2022-09-19

Data preparation

Add MS2 to mass_dataset object

Add MS2 to `mass_dataset` object