Match lipid molecules from MS2 data — match

Rule-based matching of lipid molecules in the provided libraries libs using MS2 data (fragments).

match_ms2(ms2, libs, ppm_tol = 30, intensity_cutoff = 1000,
  collapse = TRUE, odd_chain = FALSE, chain_modifs = c("all", "only",
  "none"))

Arguments

ms2	MS2 data frame. Should be the result of `read_ms2`.
libs	Which libraries to match against. Should be the output of `[get_lib]` or `[create_lib]`
ppm_tol	Mass error tolerance between acquired fragments and library. Default tolerance is 30 ppm.
intensity_cutoff	Minimum intensity value for fragments to be taken into account when matching. Default is 1000
collapse	Whether to collapse ambiguous molecules if they have the same sum composition. `TRUE` by default.
odd_chain	Whether to include molecules with odd chain fatty acids.
chain_modifs	Whether to include / exclude molecules with modified chain fatty acids. `FALSE` by default, since odd chains are unlikely in mammals.

Value

A data frame with these columns:

ms2_file, precursor, ms2_rt File, precursor M/Z, precursor RT
name Name of the matching molecules
partial_match Numeric value between 0-1, indicating the percentage of rules satisfied. 1 indicates matching all required fragments and at least one optional fragment. 0 indicates the molecule was matched based on MS1 only.
confirmed Whether all matching rules were satisfied.

This returned values contain all molecules that have a matching precursor regardless of whether the rules are met or not. If you want only molecules that met the rules, filter the dataframe with confirmed == TRUE.

Examples

ms2_file <- system.file("extdata", "ms2file.ms2", package = "lipID")

ms2_data <- read_ms2(ms2_file)
libs <- get_libs()
confirmed_molecules <- match_ms2(ms2_data, libs)
#> Joining, by = c("mz", "ms2_rt")
#> Joining, by = c("precursor", "ms2_rt")
head(confirmed_molecules)
#> # A tibble: 6 x 22
#>   ms2_file precursor ms2_rt name  confirmed ions_matched fragments_inten…
#>   <fct>        <dbl>  <dbl> <chr> <lgl>     <chr>                   <dbl>
#> 1 ms2file       761.   32.3 PC(1… TRUE      [M+H]+;MH-P…        28804189.
#> 2 ms2file       735.   31.8 PC(1… TRUE      [M+H]+;MH-P…        25209814.
#> 3 ms2file       733.   30.2 PC(3… TRUE      [M+H]+;MH-P…        24422286.
#> 4 ms2file       787.   32.8 PC(1… TRUE      [M+H]+;MH-P…        24075173.
#> 5 ms2file       707.   29.5 PC(1… TRUE      [M+H]+;MH-P…        22843936.
#> 6 ms2file       761.   32.2 PC(1… TRUE      [M+H]+;MH-P…        22693128.
#> # … with 15 more variables: partial_match <dbl>, file <chr>, class_name <chr>,
#> #   sum_composition <chr>, odd_chain <lgl>, modifs <chr>, total_cl <dbl>,
#> #   total_cs <dbl>, n_and <int>, n_or <int>, n_and_true <int>, n_or_true <int>,
#> #   and_cols <lgl>, or_cols <lgl>, best_match <lgl>

# Get only the molecules that satisfied all the rules.
confirmed_molecules %>% dplyr::filter(confirmed)
#> # A tibble: 122 x 22
#>    ms2_file precursor ms2_rt name  confirmed ions_matched fragments_inten…
#>    <fct>        <dbl>  <dbl> <chr> <lgl>     <chr>                   <dbl>
#>  1 ms2file       761.   32.3 PC(1… TRUE      [M+H]+;MH-P…        28804189.
#>  2 ms2file       735.   31.8 PC(1… TRUE      [M+H]+;MH-P…        25209814.
#>  3 ms2file       733.   30.2 PC(3… TRUE      [M+H]+;MH-P…        24422286.
#>  4 ms2file       787.   32.8 PC(1… TRUE      [M+H]+;MH-P…        24075173.
#>  5 ms2file       707.   29.5 PC(1… TRUE      [M+H]+;MH-P…        22843936.
#>  6 ms2file       761.   32.2 PC(1… TRUE      [M+H]+;MH-P…        22693128.
#>  7 ms2file       733.   30.2 PC(3… TRUE      [M+H]+;MH-P…        19348695.
#>  8 ms2file       763.   33.8 PC(1… TRUE      [M+H]+;MH-P…        18853109.
#>  9 ms2file       763.   33.8 PC(1… TRUE      [M+H]+;MH-P…        18797276.
#> 10 ms2file       787.   32.8 PC(1… TRUE      [M+H]+;MH-P…        18405277.
#> # … with 112 more rows, and 15 more variables: partial_match <dbl>, file <chr>,
#> #   class_name <chr>, sum_composition <chr>, odd_chain <lgl>, modifs <chr>,
#> #   total_cl <dbl>, total_cs <dbl>, n_and <int>, n_or <int>, n_and_true <int>,
#> #   n_or_true <int>, and_cols <lgl>, or_cols <lgl>, best_match <lgl>