How to create input data files for RIAssigner from public raw data repo

[kozo2]

I want to use RIAssigner to calculate retention indices (for MS-DIAL) to reanalyze GC-MS data like

• https://ddbj.nig.ac.jp/public/metabobank/project/MTBKS1/
• https://ddbj.nig.ac.jp/public/metabobank/project/MTBKS2/
• https://ddbj.nig.ac.jp/public/metabobank/project/MTBKS3/

However, I could not find what kind of processing should be performed on those data in order to create RIAssigner's query (csv) and reference (msp).

I would appreciate any advice you could provide. Once I understand the workflow, I'd like to contribute by creating a pull request for documentation explaining that workflow.

[hechth]

Hi @kozo2 - so the query file is the file where you want to add retention indices to - normally this would be an MSP output from RAMclustR or metaMS or another tool for spectra deconvolution. The reference is a retention indexed list, similar to the input for MSDial.

There is currently no tool which will detect your alkanes or other RI compounds in a raw sample and outputs that indexed list - this is something that could maybe me added in the future as it might be useful to streamline the overall process. This indexed RI file basically has to be created manually at this point.

[hechth]

@kozo2 I just looked at the public repos and the ALKANE_SERIES.txt files are what you would use as reference :) they just need to be formatted a bit to work with RIAssigner (which is based on matchms) - I can create an issue for this so that the files can be used.