Chromatography Forum

Dear All,

I want to identify untargeted metabolites from various samples from LC-MS/MS data. What kind of data analysis workflow do you people generally use for this application.

1. Objective: Identify small molecules

2. Sample: Extracts from various sources like cell culture extract, plant-extract. We get samples from various users.

3. Instrument: We have an ESI-Q-TOF instrument attached to an LC. Our Instrument manufacturer is Bruker. So, we get data in '.d' (.baf) format. But it is easy to export into 'mzXML' format.

3. Question: What software can help us in this?

I'll be really thankful for any inputs.

I have no experience with Brukers own 'omics'-software, but in general vendor-supplied software is more user-friendly than open-source/freeware alternatives. So I would look there first. If price is an issue, I would check either mzmine 2 (I think 3 is under development, not sure how active) or XCMS for R. Nice review article to get started: Data analysis strategies for targeted and untargeted LC-MS metabolomic studies: Overview and workflow

Thanks Poly Styrene