README

CMMR provides a programmatic interface in R to interact with the CEU Mass Mediator RESTful API, facilitating automated metabolomics data analysis from mass spectrometry experiments.

The package integrates batch searches, advanced searches, and MS/MS spectral searches, allowing seamless incorporation into R-based metabolomics workflows. Users can leverage this package to process mass spectrometry data efficiently, without manual intervention through the web interface.

For further details on the CEU Mass Mediator platform, visit the CEU Mass Mediator website.

Special Thanks

This package was built on top of the CEU Mass Mediator API by Albert Gil. Special thanks to @albertogilf for his contributions!

API Endpoints

Installation

CRAN Version

install.packages("cmmr")

Development Version

To install the development version, which may include bug fixes or experimental features, use:

# install.packages("devtools")
devtools::install_github("YaoxiangLi/cmmr")

Usage Examples

Batch Search

library(cmmr)

batch_df_pos <- batch_search(
  cmm_url = 'https://ceumass.eps.uspceu.es/api/v3/batch',
  metabolites_type = 'all-except-peptides',
  databases = '["all-except-mine"]',
  masses_mode = 'mz',
  ion_mode = 'positive',
  adducts = '["M+H","M+Na"]',
  tolerance = 10,
  tolerance_mode = 'ppm',
  unique_mz = c(178.1219, 243.9134, 977.6763)
)

head(batch_df_pos)
str(batch_df_pos)

library(cmmr)

batch_df_neg <- batch_search(
  cmm_url = 'https://ceumass.eps.uspceu.es/api/v3/batch',
  metabolites_type = 'all-except-peptides',
  databases = '["all-except-mine"]',
  masses_mode = 'mz',
  ion_mode = 'negative',
  adducts = '["M-H","M+Cl"]',
  tolerance = 100,
  tolerance_mode = 'ppm',
  unique_mz = c(670.4623, 1125.2555, 602.6180)
)

head(batch_df_neg)
str(batch_df_neg)

Batch Search with External Files

# Load unique m/z values from CSV
unique_mz_file <- system.file("extdata", "unique_mz.csv", package = "cmmr")
unique_mz <- read.table(unique_mz_file, sep = ",", stringsAsFactors = FALSE, header = FALSE)
unique_mz <- as.array(unique_mz[, 1])

# Perform batch search using the loaded m/z values
batch_df_neg <- batch_search(
  cmm_url = 'https://ceumass.eps.uspceu.es/api/v3/batch',
  metabolites_type = 'all-except-peptides',
  databases = '["all-except-mine"]',
  masses_mode = 'mz',
  ion_mode = 'negative',
  adducts = '["M-H","M+Cl"]',
  tolerance = 10,
  tolerance_mode = 'ppm',
  unique_mz = unique_mz
)

# Save the results in the same folder as the original CSV
write.table(batch_df_neg, sub(".csv", "_db_search.csv", unique_mz_file), sep = ",", row.names = FALSE)

# Save to the current working directory
write.table(batch_df_neg, "batch_df_neg.csv", sep = ",", row.names = FALSE)

Advanced Batch Search

library(cmmr)

advanced_batch_df <- advanced_batch_search(
  cmm_url = 'https://ceumass.eps.uspceu.es/api/v3/advancedbatch',
  chemical_alphabet = 'ALL',
  modifiers_type = 'none',
  metabolites_type = 'all-except-peptides',
  databases = '["hmdb"]',
  masses_mode = 'mz',
  ion_mode = 'positive',
  adducts = '["all"]',
  deuterium = FALSE,
  tolerance = 7.5,
  tolerance_mode = 'ppm',
  masses = c(400.3432, 288.2174),
  all_masses = '[]',
  retention_times = c(18.842525, 4.021555),
  all_retention_times = '[]',
  composite_spectra = paste0(
    '[ [ { "mz": 400.3432, "intensity": 307034.88 },',
    ' { "mz": 311.20145, "intensity": 400.03336 } ] ]'
  )
)

head(advanced_batch_df)
str(advanced_batch_df)

MS/MS Search

library(cmmr)

# Define MS/MS peaks (m/z and intensity)
ms_ms_peaks <- matrix(
  c(40.948, 0.174,
    56.022, 0.424,
    84.370, 53.488,
    101.500, 8.285,
    102.401, 0.775,
    129.670, 100.000,
    146.966, 20.070),
  ncol = 2,
  byrow = TRUE
)

# Perform MS/MS search
ms2_df <- msms_search(
  ion_mass = 147, 
  ms_ms_peaks = ms_ms_peaks, 
  ion_mode = 'positive'
)

head(ms2_df)
str(ms2_df)

Contribution Guidelines

If you’d like to contribute to the development of CMMR, please follow the tidyverse style guide. Below are a few key conventions to adhere to:

CMMR - CEU Mass Mediator API