The way of analysing the data will depend on the type of your metabolites as well as on the type and manufacturer of the instrument you measured the data with. In general, the Skyline software package enables the evaluation of many kinds of analyses from several measurement schemes.

Hi,

I like the defenition of metabolomics as "the unbiased identification and quantification of all metabolites in a biological sample" (W. Weckwerth, 2007). So, basically what you are planning to do is not Metabolomics, but sort of a targeted approach. As already pointed out, the to be used software will depend on the kind of analytical approach. There are a number of freely available software packages and webservices  (e.g. MetabolomeExpress for GC-MS data or XCMS online vor LC-MS data) out there to analyse data. Give us further details on the kind of analysis you intend to do and we might be able to give you a better answer.

Hope this helps,

Holger

Thanks for the quick feedback guys, as you can tell I am certainly a 'green horn' at this side of cell characterisation. Essentially I want to get a feel for things both extra-cellular and intra-cellular and any changes over time (14-15 days). Ideally I would like to test for levels of lactate and ammonia from the extra-cellular environment. Then bridging toward intra-cellular I would like to test levels of Pyruvate, Acetyl-CoA, ATP, and NADH. Im not entirely certain about measurements for ATP and NADH though.

In terms of tools for the job, I would ideally want to create as much separation as possible using an LC based method, most likely HPLC. With regards to the columns of use I am aware of various types but I am not sure as to 'the column/s of choice'. Lastly separated samples will be passed through MS analysis, most likely incorporating fourier transformation.

Many thanks,

Chris

Hi there

If you already know what you are looking for the best way is to buy some standards and try separating them using lcms and several different columns (c18, hilic, etc). With the lcms method optmized you can try your real samples.

Regards

Paulo

Thanks Paulo, Ill check out the standards you mentioned. Also thanks for the heads up on the columns to use.

Best,

Chris

Please try DeviumWeb: http://imdevsoftware.wordpress.com/tag/deviumweb/ which is a lot flexible, holistic, free and amazingly easy to use. Apart from it, MetaboAnalyst, MetabolomeExpress, XC-MS, mzMINE, MeltDatabase are immensely helpful too.

Another approach which is not free but is only $2995 and includes the labeling material, software and data analysis package is to label a batch of your CHO cells and spent media with 95% C13 and use these as labeled Internal Standards  to spike into experimental cells and spent media.  The ClusterFinder software will find both labeled metabolites (labeled internal standards) and the unlabeled counterpart (experimental), quantiitate the ratios, remove artifacts and noise. This way you can follow many metabolites and have a built-in standard to each one.  There is an upcoming seminar if you are interested. Registration URL: https://attendee.gotowebinar.com/register/2172682617425316866

Hi

We have on our homepage an example of extracellular metabolites from CHO cells measured with GC-MS. More than 70 compounds varied throughout the study.

Link: www.msomics.com/examples.html

Best,

Morten

www.msomics.com/examples.html