LC/MS matching

An LC/MS matching tool for Galaxy, part of the Workflow4Metabolomics project, and developed during the MetaboHUB project.

The two matching algorithms used in this tool have been imported from developments made at CEA Saclay, inside the DSV/IBITEC-S/SPI. They have been translated from C# to R.

For more information, see the galaxy tool page, help section, available inside galaxy/lcmsmatching.xml.

lcmsmatching script

This is the script, included in this repository, that allows to run on command line an MZ matching on one of the available database types.

Please run lcmsmatching -h for a help page listing all options and presenting some examples.

Dependencies

• R version 3.5.1.
• R packages:
  • getopt >= 1.20.0.
  • biodb >= 1.2.0rc2.

Changelog

4.0.2

• Increase getopt version to 1.20.2.

4.0.1

• Downgrade to Galaxy 18.05. Test in both 18.05 and 18.09.

4.0.0

• Switch to biodb R library (http://github.com/pkrog/biodb).
• Remove Excel and 4TabSql databases from script.
• Remove all dynamic fields in XML (i.e.: fields computed using python scripts, like the list of chromatogaphic columns).
• Use now a single field for in-house file databases column names, whose value is a comma separated list of key/value pairs.
• Update Peakforest URL.

3.4.3

• Returns empty match in case of NA values in mz.low and mz.high.
• Speed up HTML output writing.

3.3.1

• Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns.

3.3.0

• The file database (in-house) field names are now presented in individual choice lists instead of a single text box where you had to insert a very long keys/values string.
• The tool now tries to guess the names of the file database fields, the values of the MS mode column, and the names of the input file columns.
• Allows to select the unit (minutes or seconds) of retention time values inside the input file, but also inside the file database (in-house).