SpectraTutorial version 1.0.0

Tutorials and workshops describing the infrastructure for mass spectrometry (MS) data analysis centered around Bioconductor's Spectra package.

The source code of the workshops along with installation information and the docker image with all required data and software package is available at the main SpectraTutorials github repository.

This version of the tutorials bases on Bioconductor release 3.19.

Pre-rendered versions of the tutorials are available here.

The repository provides the following tutorials:

• Seamless integration of mass spectrometry data from different sources: description of the infrastructure explaining the concept and use of different data backends. In the workflow, MS data is imported from mzML files and subsequently filtered, processed, cleaned and visualized. The tutorial shows also how MS2 spectra similarity scores can be calculated and how reference fragment libraries (MassBank) can be accessed through Spectra. At last, an alternative storage option for MS data, in a SQLite database, is presented. A rendered version of this tutorial is available here

• Spectra: an expandable infrastructure to handle mass spectrometry data: this workflow explains different representations of mass spectrometry data and how they can be used and implemented with Spectra. The tutorial provides in addition information on internal data handling and processing enabling also support for analysis of very large data resources. A rendered version of this tutorial is available here.

• MS/MS spectra matching with the MetaboAnnotation package: this workflow describes the user-friendly functionality of the MetaboAnnotation package for spectra similarity scoring and matching of experimental MS2 spectra against a reference database common to LC-MS/MS based untargeted metabolomics experiments. A rendered version of this tutorial is available here.

MsBackendMassbankSql compliant MassBank release 2021-03

This is a MsBackendMassbankSql compliant SQLite version of the MassBank release 2021-03 database. All tables required for the MsBackendMassbankSql backend for Spectra objects are available in this SQLite database.

To use this database with MsBackendMassbankSql:

library(Spectra)
library(MsBackendMassbank)
library(SQLite)

con <- dbConnect(SQLite(), "MassbankSql-2021-03.db")
massbank <- Spectra(con, source = MsBackendMassbankSql())