mzTab settings

LDA provides the possibility to export metadata in the mzTab format. None of this information is mandatory for the mzTab export, but helps for the reproducibility of your data. All changes in these settings require a restart of the LDA application.
The metadata is split in two configuration files: i) .properties file containing information about the mass spectrometer ii) mzTab.properties containing experiment specific information such as affiliations and sample origin information.

MS instrument specific settings (.properties)

In the current implementation, the following metadata can be exported in mzTab format:

- mzTabInstrumentName: the name of the instrumentation
 
- mzTabInstrumentIonsource: the ion source of the instrumentation (e.g. ESI, or MALDI)
 
- mzTabInstrumentAnalyzer: the analyzer of the instrument (e.g. ion trap, FT-ICR, etc.)
 
- mzTabInstrumentDetector: the ion detector (e.g. electron multiplier)
 

Examples are provided within the files. Be sure for all parameters that the entries contain always three "," otherwise this setting will be neglected. If you are using (as recommended) controlled vocabulary, please crosscheck its validity (http://www.ebi.ac.uk/ontology-lookup/).

Other mzTab settings (mzTab.properties)

All the other metadata for mzTab is stored in this file. The entries here must contain three commas such as in the MS instrument specific settings. The exception is the contact settings, which must contain at least two commas. The first comma separates the name, the second one the email address, and the rest of the commas are included in the affiliation. The contacts have to start with one, and MUST have consecutive numbers, e.g.
contact_1=$name_first_contact$,$email_first_contact$,$affiliation_first_contact$
contact_2=$name_second_contact$,$email_second_contact$,$affiliation_second_contact$
Other supported metadata settings of this file are:

- species: from which species originates the sample
- tissue: from which tissue originates the sample
- celltype: the cell type of the sample

If any of the values are unknown or cannot be assigned, they should be commented or left out. The export to mzTab is possible with missing values.