Tutorials and workshops for the use of the
Spectra Bioconductor package to analyze mass spectrometry (MS) data.
This (instructor-led live demo) workshop explains the
Spectra package and shows how this new infrastructure can be used to represent and analyze Mass Spectrometry (MS) data. In a simple use case in which experimental MS2 spectra are matched against public spectral database the seamless integration and analysis of MS data from a variety of input formats is illustrated.
Get the docker image of this tutorial with
docker pull jorainer/spectra_tutorials:latest.
Start docker using
docker run \ -e PASSWORD=bioc \ -p 8787:8787 \ jorainer/spectra_tutorials:latest
http://localhost:8787 in a web browser and log in with username
rstudio and password
Open this R-markdown file (vignettes/analyzing-MS-data-from-different-sources-with-Spectra.Rmd) in the RStudio server version in the web browser and evaluate the R code blocks.
To get the source code: clone this github repository, e.g. with
git clone https://github.com/jorainer/SpectraTutorials.
Optionally, to run also the code to import the MS2 spectra from HMDB the All Spectra Files (XML) archive from the hmdb downloads page has to be downloaded. The contents of the hmdb_all_spectra.zip archive should then be unzipped into the folder data/hmdb_all_spectra.
For more advanced users it is also possible to manually install all the resources required for this tutorial. In addition to R version >= 4, specifically for the examples involving the MassBank database, a running MySQL/MariaDB server is also required.
The required R packages can be installed with the code below:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true") install.packages(c("devtools", "rmarkdown", "BiocManager")) BiocManager::install(c("BiocStyle", "MsCoreUtils", "Spectra", "pheatmap")) devtools::install_github("RforMassSpectrometry/MsBackendHmdb") devtools::install_github("RforMassSpectrometry/MsBackendMgf") devtools::install_github("michaelwitting/MsBackendMassbank") devtools::install_github("jorainer/SpectraTutorials")
A MySQL database dump of the
MassBank database can be downloaded from the official github page. A database named
MassBank should then be created in the local MySQL/MariaDB server. The downloaded .sql.gz needs to be unzipped and can then be installed with
mysql MassBank < *.sql.
The source code for all tutorials in this package can be downloaded with:
git clone https://github.com/jorainer/SpectraTutorials
Then open the R-markdown (Rmd) files of one of the tutorials (which are located within the vignettes folder with the editor of choice (e.g. RStudio, emacs, vim, …) and evaluate the R-code in the tutorial interactively.
Other R packages not (yet) in Bioconductor:
|MS data import and handling||5min|
|Data processing and manipulation||5min|
|Spectrum data comparison||5min|
|Comparing spectra against MassBank||10min|
|(Comparing spectra against HMDB)||(5min)|
Spectrato work with MS data from various sources.