Hi XCMS users,
As many of you aware of this, the metaXCMS protocol is published. The usage of metaXCMS software is thoroughly described on the paper, so please review the paper at Nature Protocols (http://http://www.nature.com/nprot/journal/v7/n3/full/nprot.2011.454.html)
Thank you,
Kevin
Hi Kevin,
I am using XCMS and metaXCMS as descibed in the protocol. But the issue is when I import three .tsv files from pairwise comparisons to meta XCMS (GTK+), I am getting the Venn diagram and excel with the common features. But I think it will be more user friendly if we get the compound name in the result. Could you please tell me how you will select the features and do METLIN search?
Thank you,
Sithara
You can search individual m/z values using METLIN's simple search (http://http://metlin.scripps.edu/metabo_search_alt2.php) or all at once using the batch search. (http://http://metlin.scripps.edu/metabo_batch.php)
Also, an online version of metaXCMS will be available soon, which will automatically search against METLIN.
Hi Ralf,
Many thanks for the information.
But my doubt is that if we do simple/ batch search there are many hits by Metlin for an m/z value(different combinations with the adducts selected, H+, NH4+, Na+ etc). As the process is called untargeted metabolyte profiling, how can I select the compound name for a feature from the listed metlin putative identifications. I think to get to know a way to insert a column for neutral mass of the compound will solve the issue, but how? I am completely depending XCMS/ XCMS online for my analysis, I may lose my project :( if I couldn't find an answer for this, as my mentor already have the compound name and neutral mass from a software Agilent Mass profiler Pro. I am reading the articles suggested by you.
Anticipating a solution for this,
A bunch of thanks for the support :)
Best,
Sithara
XCMS online shows you the neutral mass in the adducts column whenever possible. Sometimes this information is not available when only single peaks/feature are observed. It is mathematically not possible to calculate neutral mass from a single peak. It needs multiple peaks per feature to calculate, otherwise all you can do is to search databases using the most likely adducts like M+H and M+Na. This is what XCMS online is doing.
e.g.
3 UP 5.9 7.12731e-7 859.4871 126.49 1,362 2,432 14,330 [M+H]+ 858.482
where 859.4871 is m/z (M+H) and 858.482 is the neutral mass.
You can only get putative IDs/database hits using exact mass. I don't know what Mass Profiler is showing, but it is not possible to identify compounds based on exact mass only.