Code used to query the Metlin database for mass and MSn data
This code is currently deprecated, as recent updates to Metlin's access guidelines prohibit scripted access. Using these functions may result in a temporary or permanent ban from the website.
The Metlin database is a massive repository of mass-spectrometry data, but it can be hard to access via scripts. This repository contains code and examples illustrating a couple convenient wrapper functions I've written to ask Metlin for various bits of data and get them into R nicely.
- httr
- dplyr
- xml2
These wrappers essentially interact with the "Advanced Search" option on the Metlin website, but do NOT require an authorization or login. There are 3 main functions currently written. The first, getMetlinName, queries the Metlin database for a specific compound name and returns a list of all entries matching that name. getMetlinMz queries the database for a given m/z and ppm error (defaults to 2.5) and returns all entries that have a documented mass within that window, i.e. all isomers. getMetlinMS2 extracts the MS/MS data for a given compound, and operates on a specific compound ID assigned within the Metlin database - typically, a call to getMetlinMz or getMetlinName is performed first, both of which return the compound ID. See the vignette for more detailed functionality and the code.
These functions have also been wrapped into a neat package with helpful documentation, generated via Roxygen. To download and install the package, grab the "getMetlin_0.1.0.tar.gz" file from "Package things" and install it via the below code, to be run in R:
install.packages("path/to/tar/file", source = TRUE, repos=NULL)