cmmr
CEU Mass Mediator RESTful API
CEU (CEU San Pablo University) Mass Mediator is an on-line tool for aiding researchers in performing metabolite annotation. 'cmmr' (CEU Mass Mediator RESTful API) allows for programmatic access in R: batch search, batch advanced search, MS/MS (tandem mass spectrometry) search, etc. For more information about the API Endpoint please go to < https://github.com/lzyacht/cmmr>.
Consuming CEU Mass Mediator RESTful API in R.
Thank you @albertogilf for your kindness and help!
Please find the CEU Mass Mediator source code repository: CEU Mass Mediator source code on GitHub
The CEU Mass Mediator Website: CEU Mass Mediator
API Endpoint
Batch search http://ceumass.eps.uspceu.es/mediator/api/v3/batch
Advanced search http://ceumass.eps.uspceu.es/mediator/api/v3/advancedbatch
MS/MS search http://ceumass.eps.uspceu.es/mediator/api/msmssearch
About
CEU Mass Mediator is an online tool that aides researchers in identifying metabolites from mass spectrometry experiments. It is currently available as a web interface and a RESTful API. CMMR is a RESTful API implemented for R. This makes it easy to access CEU Mass Mediator programatically in R, integrating search results seamlessly into users custom pipelines and workflows.
Installation
install.packages("cmmr")Development version
To get a bug fix, or use a feature from the development version, you can install cmmr from GitHub.
# install.packages("devtools")devtools::install_github("lzyacht/cmmr")Example
Batch search
Batch search all result in positive mode
library(cmmr) batch_df_pos <- batch_search('http://ceumass.eps.uspceu.es/mediator/api/v3/batch', 'all-except-peptides', '["all-except-mine"]', 'mz', 'positive', '["M+H","M+Na"]', 100, 'ppm', c(670.4623, 1125.2555, 602.6180)) head(batch_df_pos)str(batch_df_pos)Batch search all result in negative mode
library(cmmr) batch_df_neg <- batch_search('http://ceumass.eps.uspceu.es/mediator/api/v3/batch', 'all-except-peptides', '["all-except-mine"]', 'mz', 'negative', '["M-H","M+Cl"]', 100, 'ppm', c(670.4623, 1125.2555, 602.6180)) head(batch_df_neg)str(batch_df_neg)Providing external *.csv files for search
You may want to load your own list of m/zs from a csv or excel file to search the database.
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]) batch_df_neg <- batch_search('http://ceumass.eps.uspceu.es/mediator/api/v3/batch', 'all-except-peptides', '["all-except-mine"]', 'mz', 'negative', '["M-H","M+Cl"]', 10, 'ppm', unique_mz) And save it as a *.csv to the same folder or some other specified folder
# Save to the same folder of the unique_mz.csvwrite.table(batch_df_neg, sub(".csv", "_db_search.csv", unique_mz_file), sep = ",", row.names = FALSE)Save to 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 = paste0( 'http://ceumass.eps.uspceu.es/mediator/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 = '[400.3432, 288.2174]', all_masses = '[]', retention_times = '[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)MSMS Search
library(cmmr) ms_ms_peaks <- matrix( c(40.948, 0.174, 56.022, 0.424, 84.37, 53.488, 101.50, 8.285, 102.401, 0.775, 129.670, 100.000, 146.966, 20.070), ncol = 2, byrow = TRUE) ms2_df <- msms_search(ion_mass = 147, ms_ms_peaks = ms_ms_peaks, ion_mode = 'positive') head(ms2_df)str(ms2_df)