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Messages - AdrianaM

6
XCMS Online / Re: Metlin ID in metabolite name in XCMS result table
Basically Metlin database is a searching engine and it takes your peaks and associate with its large repository. Please check manually the metabolites using the spectra, metlind annotation could have a lot of positive falses.

Regards

Adriana
7
Compound identification / How to do manual annotation in metabolomics
> Cordial greeting. Currently I dont know how to perform the manual annotation. I want to find my target compound epicatechin in my data, however when I check the peak list and retention times I get several data like 289.1706, 289.0456, 289.5678 and for each a different retention time.  I went to data bases and I found  
> 
> epicatechin  
> [M - H]- (m/z) MS/MS (m/z)  
> 289         245,205,179 
> >
> But I cant see those ms/ms values in my data. I mean, the ms/ms do not match with 245,205 and 179.  What can I do to resolve this compound? I have seen many people reporting metabolites based on in silico information, and I dont know how can they
>  get that. 
>
 Thanks for your help 

> Adriana 
8
XCMS / XCMS data do not coincide with peak profiles, retention time and m/z
Cordial greeting. I already run two groups of samples (control and treatment, four biological samples in each group ) in XCMS online. It gives me a table of results, telling me what are the metabolites differencially expresed between both set of groups. However if I look for example the m/z given by XCMS I cant find thit in my real data, so,

Is XCMS doing a mean between the four biological samples within groups?

How can I deal with this, I definitively need to compare both groups.

Thanks
9
XCMS / How can I know if I should eliminate a biological sample?
I have four samples in my LC-MS analysis per treatment, and I have 3 treatments. If I see the PCA, score plots shows me there is a biological sample in the first treatment very distant for the rest, however in the others two treatments the distant sample is no the same, how can I know when should I eliminate a biological sample paying attention to the PCA?

Thanks

Adriana
10
XCMS / Re: How can I do the processing data? normalization?
Hi, Im using XCMS online, there, option of normalize with the intensity values by either probabilistic quotient or cyclic loess is presented. Im not sure wich choose.

Other option in the same tab is "values to be used for the diffreport. If value="into", integrated peak intensities are used. If value="maxo", maximum peak intensities are used." I dont know if I choose "into" or "maxo" according to the normalization process.

Thanks

Adriana

.
12
XCMS / How can I do the processing data? normalization?
Hi, I want to analyze my metabolomic data, but, I have all my raw data in .wiff and .scanwiff files. What is the next step? how can I clean and do the normalization for this data?, how can I do it in R?

Thanks

Adriana