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mz med

Hi,

I am using XCMS online for processing and analysing a metabolomic data from UPLC - TOF (Agilent). I have downloaded the XCMS online package from bioconductor, also using R 2.15.2.

Somebody please tell me the best parameters for UPLC TOF [I have used general : retention time format - minutes, feature detection: ppm =10, min peak - 5, max peak - 20,retention time corretion: method - obiwarp,prof Step -1, alignment and statistics kept as default value,Annotation : search for - isotopes+adducts, ppm - 10, Identification: H+,NH4+,Na+]. Then I changed the retension time to seconds, when I checked the result for the cloud plot, It didnt show the feature points the plot.What will be the reason? I changed it into seconds as the limits are 5-20 seconds.

After analysing with this parameters for positive polarity, I met with some issues with diff report

Issue 1 - mz med value in diff report is the normal mass of the compound or with adducts?
Issue 2 - The column METLIN in result.tsv shows many compound names for the same feature. Which one is appropriate to select or do you have any standard scoring system to pick one with max score.
Issue 3 -  What is the difference between obiwarp and peak groups.

My objective is to compare the XCMS online result with Mass profile Pro result.

The fast responses will be highly appreciated.
Thank you,
Sithara

Re: mz med

Reply #1 –
I am surprised to see no responses for my query.

I would like to update that I found answer for first query, mz med value is with the adducts. But how to select one compound for a particular feature? Is OBIwarp is good for LCMS/ UPLC QTOF data?

Please somebody give suggestions

Re: mz med

Reply #2 –
2. These are putative IDs which have to be verified using e.g. MS/MS data. Also see here
3. These are different retention time correction methods :
    the
obiwarp method is based on correlations of the raw data, method is described in Prince et al.
the peakgroups method uses "well behaved" peak groups and nonlinear regression to calculate retention time deviations for every time point of each sample, method described in the original XCMS publication by Smith et. al.[/list]

Re: mz med

Reply #3 –
Dear Ralf,

With due respect for creating such a wonderful software I would like to thank you for the support. I really appreciate your help. I need to learn the basics of Metabolomics as I am from a public health background.

Thanks alot and expecting the same in future.

Regards,

Sithara

Re: mz med

Reply #4 –
Hi Ralf,

Thank you so much for your support.

I have a good question for you and I really need your advice to proceed in XCMS online.

I have run the standards in XCMS online , which contain a mix of 9 compounds [attachment=1:2kl8ijyk]12_Compounds_mix.xlsx[/attachment:2kl8ijyk]. I have rum 4 mzXML file in each data set and customized the parameters for UPLC TOF.Please see the attachment for logarith [attachment=0:2kl8ijyk]Log _XCMSOnline  version  1.docx[/attachment:2kl8ijyk].
Please see the result,[attachment=2:2kl8ijyk]Result_standard_poshilic.xlsx[/attachment:2kl8ijyk] I have sorted it based on intensities and removed the low intensity features for easy uploading in the forum, I got only five compound features matching with the standards run. I dont know where it went wrong. If the software is not running properly for the standards, which we know already,how will we use it for research. Please accept my apologies if I am wrong.

Could you please look into the data and let me know why I am not getting all the standards in the result. Also why I am getting K+ adducts if at all I didnt select it.
Hope to hear from you soon :)
Thanks alot,

Sithara

[attachment deleted by admin]

Re: mz med

Reply #5 –
You reduced the accuracy for feature detection from 30 (in the Agilent TOF parameterset) down to only 10 ppm, which is most likely the reason that not all features were detected.

Re: mz med

Reply #6 –
Hi Ralf,

Thank you so much!

ppm reduction may be the reason for not getting all compound features in the result. When I run the same with 30 ppm I got Niacin, bit satisfactory. But how am I getting the K+ adduct in the result? Is it an impurity or a bug?

Re: mz med

Reply #7 –
In which column do you see the K+ ?  If it's in the adduct column then this is on purpose - XCMS Online is trying to deconvolve and detect (using CAMERA) possible adducts, including pretty much all possibilities.
But for the METLIN search it will only use the additional adducts that you selected in the identification tab.