maldipickr
In maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(maldipickr)

Quickstart

The {maldipickr} package helps microbiologists reduce duplicate/clonal bacteria from their cultures and eventually exclude previously selected bacteria. {maldipickr} achieve this feat by grouping together data from MALDI Biotyper and helps choose representative bacteria from each group using user-relevant metadata -- a process known as cherry-picking.

{maldipickr} cherry-picks bacterial isolates with MALDI Biotyper:

using taxonomic identification report
using spectra data

Using taxonomic identification report

First make sure {maldipickr} is installed and loaded, alternatively follow the instructions to install the package.

Cherry-picking four isolates based on their taxonomic identification by the MALDI Biotyper is done in a few steps with {maldipickr}.

Get example data

We import an example Biotyper CSV report and glimpse at the table.

report_tbl <- read_biotyper_report(
  system.file("biotyper_unknown.csv", package = "maldipickr")
)
report_tbl %>%
  dplyr::select(name, bruker_species, bruker_log) %>% knitr::kable()

Delineate clusters and cherry-pick

Delineate clusters from the identifications after filtering the reliable ones and cherry-pick one representative spectra.

Unreliable identifications based on the log-score are replaced by "not reliable identification", but stay tuned as they do not represent the same isolates!

report_tbl <- report_tbl %>%
  dplyr::mutate(
      bruker_species = dplyr::if_else(bruker_log >= 2, bruker_species,
                                      "not reliable identification")
  )
knitr::kable(report_tbl)

The chosen ones are indicated by to_pick column.

report_tbl %>%
  delineate_with_identification() %>%
  pick_spectra(report_tbl, criteria_column = "bruker_log") %>%
  dplyr::relocate(name, to_pick, bruker_species) %>% 
  knitr::kable()

Using spectra data

In parallel to taxonomic identification reports, {maldipickr} process spectra data. Make sure {maldipickr} is installed and loaded, alternatively follow the instructions to install the package.

Cherry-picking six isolates from three species based on their spectra data obtained from the MALDI Biotyper is done in a few steps with {maldipickr}.

Get example data

We set up the directory location of our example spectra data, but adjust for your requirements. We import and process the spectra which gives us a named list of three objects: spectra, peaks and metadata (more details in Value section of process_spectra()).

spectra_dir <- system.file("toy-species-spectra", package = "maldipickr")

processed <- spectra_dir %>%
  import_biotyper_spectra() %>%
  process_spectra()

Delineate clusters and cherry-pick

Delineate spectra clusters using Cosine similarity and cherry-pick one representative spectra. The chosen ones are indicated by to_pick column.

processed %>%
  list() %>%
  merge_processed_spectra() %>%
  coop::tcosine() %>%
  delineate_with_similarity(threshold = 0.92) %>%
  set_reference_spectra(processed$metadata) %>%
  pick_spectra() %>%
  dplyr::relocate(name, to_pick) %>% 
  knitr::kable()