This is the mzTab-M R API and reference implementation.

mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches. This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information.

📌 see the package vignette for examples and an introduction of the provided functionality.

mzTab-M has been developed with a view to support the following general tasks:

1. Facilitate the sharing of final experimental results, especially with researchers outside the field of metabolomics.

2. Export of results to external software, including programs such as Microsoft Excel® and Open Office Spreadsheet and statistical software / coding languages such as R.

3. Act as an output format of (web-) services that report MS-based results and thus can produce standardized result pages.

4. Be able to link to the external experimental evidence e.g. by referencing back to mzML files.

• legacy rmzTabM package
• mzTab-M Standard Specification
• jmzTab-M Reference Implementation and Validator
• jmzTab-M Webapplication and Validator

The R package can be installed from Bioconductor using:

#' Install required packages
install.packages("BiocManager")

#' Install the package
BiocManager::install("RmzTabM")

ℹ️ core functions are expected to take and return single base R data types.

• core functionality to format metadata (MTD section) documentation
• core functionality to format small molecule feature (SMF section) documentation
• core functionality to format the (SML section) documentation
• core functionality to format the (SME section) documentation
• core functionality to extract metadata from an mzTab-M file and reconstruct a sample/experiment data.frame
• core functionality to extract the SMF data table from an mzTab-M file
• core functionality to extract the SME data table from an mzTab-M file
• core functionality to extract the SML data table from an mzTab-M file
• high-level functionality to simplify exporting experimental data in mzTab-M format. documentation
• support for mzTab-M JSON format (will come eventually later)
• mzTab-M file validation (will be added once the java validator for mzTab-M version 2.1 becomes available)

👀 see also the package NEWS for updates.

Please help us improving and completing the package! Any type of contribution welcome 👐 - including discussions, suggestions or actual code. Don't be afraid - we're friendly ☺️! 👉 get involved by opening an issue.

Please also check out the RforMassSpectrometry Contributions Guide.

We follow the RforMassSpectrometry Code of Conduct to maintain an inclusive and respectful community.

We thank the many researchers contributing through discussions or through code. An potentially incomplete list of people:

• Nils Hoffmann
• Steffen Neumann
• Kozo Nishida
• Frank Giacomoni
• Nils Paulhe
• Ozgur Yurekten
• Janik Kokot