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Calculate neutral losses from precursor ion mass and fragment ion masses

Source: R/misc.R
calc_neutral_loss.Rd

Calculate neutral loss spectra for all ions with available MSn spectra in data. To calculate neutral losses, MSn spectra are required. See read_mgf. This step is required for subsequent filtering based on neutral losses (filter_neutral_loss). Resulting neutral loss spectra are stored in tibbles in a new list column named Neutral_Loss.

Usage

calc_neutral_loss(data, m_z_col)

Arguments

data

A tidy tibble created by read_featuretable.

m_z_col

Which column holds the precursor m/z? Uses args_data_masking.

Value

A tibble with added neutral loss spectra. A new list column is created named Neutral_Loss.

Examples

toy_mgf %>%
  calc_neutral_loss(m_z_col = PEPMASS)
#> # A tibble: 3 × 6
#>   VARIABLEONE VARIABLETWO VARIABLETHREE PEPMASS MSn              Neutral_Loss
#>         <dbl>       <dbl>         <dbl>   <dbl> <list>           <list>      
#> 1         1.1         1.2           1.3    45.7 <tibble [3 × 2]> <tibble>    
#> 2         2.1         2.2           2.3   679.  <tibble [5 × 2]> <tibble>    
#> 3         3.1         3.2           3.3  5890.  <tibble [6 × 2]> <tibble>