In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)

Some times we only want to match one peak. We can use identify_single_peak() function to identify single peak.

library(metid)
library(tidyverse)

Peak information

We need the m/z, rt and MS2 information. MS2 must be a matrix with two columns: mz and intensity.

mz <- 472.3032
rt <- 772.906
ms2 <- data.frame(
  mz = c(81.38455,82.19755,85.02840,86.5934,86.98958,89.48135,90.70250,
         93.03886, 102.09140, 103.03903, 116.01658, 127.98412, 
         134.06819, 152.46967, 162.02180, 162.05521, 162.11261),
  intensity = c(1396.341,1488.730,15473.604, 1740.842,2158.014,1351.686,
                1547.099,1325.864,22441.047,76217.016,17809.395,
                1439.743, 1729.786, 1543.765, 2228.743, 
                3508.225, 529120.000),
  stringsAsFactors = FALSE
)
ms2 %>% head()

Run `identify_single_peak()` function

Load database

First we load the database from metid package and then put them in a example folder.

##create a folder named as example
path <- file.path(".", "example")
dir.create(path = path, showWarnings = FALSE)

##get database from metid
data("snyder_database_rplc0.0.3", package = "metid")
save(snyder_database_rplc0.0.3, file = file.path(path, "snyder_database_rplc0.0.3"))

Now in your ./example, there are one file, namely snyder_database_rplc0.0.3.

annotation_result <- 
  identify_single_peak(ms1.mz = mz, 
                       ms1.rt = rt, 
                       ms2 = ms2, 
                       ms1.match.ppm = 15, 
                       rt.match.tol = 30,
                       ms2.match.tol = 0.5, 
                       database = "snyder_database_rplc0.0.3",
                       path = path)