Hi all,
I'm doing an untargeted metabolomics project using LC/MS. This means I'll be removing media blanks from lots of samples to look at metabolites under each growth condition.
So far I've been doing this one sample at a time using the vendor software (Waters, Masslynx). I haven't found an option to automate this, or do more than one sample at a time - does anyone know of any (ideally free!) software that can do this job?
Thanks!
Hi Joshua,
there are several free tools and workflows out there which could be used to achieve what you want to do. Which one to use depends a bit on what else you want to do with the experimental data (further analysis steps) and how good you are learning new software or even do programming.
In any case you will need to get your samples evaluated all together to produce a intensity matrix for all (preferably non-redundant) peaks. My suggestion would be to use xcms for this purpose. Including the blank samples in this step allows you to next filter all peaks which are not n-times higher in your experimental data compared to your blank samples (which is the task you described) in Excel, R or whatever you prefer.
Have fun. Jan
Hi Joshua,
I can also recommend XCMS it is a very good tool. In case you are not familiar with R you can try XCMS online or MZmine.
As mentioned by Jan, you will/ want to generate a peak table containing all your samples and blanks as a starting point and than do a filtering.
Best, Frederik
Hi Jan & Frederik,
Thanks for your answers. I'm already using MZmine/sometimes XCMS Online for the peak lists and it's been great, but subtracting the blanks with the vendor software first. I'll give filtering out the blank peak lists a go instead.
Josh
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