Merge MS2 data with MS1 features

Merge MS2 data with MS1 features

merge_ms2(features, ms2_data, mz_window = 1, rt_window = 2,
  output = c("all", "best_match"))

Arguments

features	two column dataframe, m/z and RT
ms2_data	MS2 data frame. Should be the result of read_ms2.
mz_window	Quadropole isolation window (Daltons).
rt_window	Retention time window.
output	Whether to return all possible matches for each feature all, or only the best match best_match.

Value

A merged data frame containing both MS1 features with their corresponding MS2 data.

Examples

ms2_file <- system.file("extdata", "ms2file.ms2", package = "lipID")
features_file <- system.file("extdata", "features.csv", package = "lipID")
features <- readr::read_csv(features_file)
#> Parsed with column specification:
#> cols(
#>   mz = col_double(),
#>   rt = col_double(),
#>   Sample1 = col_double(),
#>   Sample2 = col_double(),
#>   Sample3 = col_double(),
#>   Sample4 = col_double(),
#>   Sample5 = col_double(),
#>   Sample6 = col_double()
#> )
head(features)
#> # A tibble: 6 x 8
#>      mz    rt   Sample1   Sample2  Sample3  Sample4   Sample5   Sample6
#>   <dbl> <dbl>     <dbl>     <dbl>    <dbl>    <dbl>     <dbl>     <dbl>
#> 1  623.  36.6 11538991  31417167  1721597. 26270387   240068. 146196506
#> 2  649.  37.1  3026293.  4228799  2539904   4811817 34383605    1173481
#> 3  651.  38.1  2715640     71834. 1390301   4208460 18656983   15282626
#> 4  679.  26.9    78211.   942846.  402485. 11245291  2873644.   2362536
#> 5  691.  30.4  3210293   1832204   910287. 29621351   753207.   2049241
#> 6  691.  30.6  7495133.  3902430  8532539.  9627881 27338627    2198889

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")
annotated_features <- merge_ms2(features, confirmed_molecules)
#> Joining, by = c("mz", "rt")
#> Joining, by = c("precursor", "ms2_rt")
head(annotated_features)
#> # A tibble: 6 x 31
#>      mz    rt name  ms2_file precursor ms2_rt best_match partial_match confirmed
#>   <dbl> <dbl> <chr> <fct>        <dbl>  <dbl> <lgl>              <dbl> <lgl>    
#> 1  789.  34.3 PC(3… ms2file       789.   34.2 TRUE                   1 TRUE     
#> 2  747.  33.6 Plas… ms2file       747.   33.5 TRUE                   1 TRUE     
#> 3  747.  33.6 Plas… ms2file       747.   33.5 FALSE                  1 TRUE     
#> 4  783.  30.7 PC(1… ms2file       783.   31.1 TRUE                   1 TRUE     
#> 5  783.  30.3 PC(1… ms2file       783.   31.1 TRUE                   1 TRUE     
#> 6  811.  32.7 PC(1… ms2file       811.   33.2 TRUE                   1 TRUE     
#> # … with 22 more variables: ions_matched <chr>, fragments_intensity <dbl>,
#> #   Sample1 <dbl>, Sample2 <dbl>, Sample3 <dbl>, Sample4 <dbl>, Sample5 <dbl>,
#> #   Sample6 <dbl>, nearest_ms2 <lgl>, 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>