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Messages - manohar.dange

XCMS - Cookbook / MS2 level peak integration using XCMS
Hi, I have a .mzXML file which consists of both MS1 and MS2 level data. Is there any way to specify precursor and its fragment mass to get EIC for both. If someone knows the script for doing this then please let me know. Much needed information for me, thank you.
To be more specific is there any method for peak integration at MS2 level which works like centWAVE works at MS1 level?
Waiting for the response,
XCMS / How to save xcmsSet object from workspace
I am using R 3.2.0 and xcms 1.46.0 version for analysis of metabolomics dataset. I wish to know how can one save the xcmsSet data created in work space. I wish to use this xcmsSet data for running other software's.

XCMS Online / Problems with single job submission
Can someone please tell me what is the output expected from single job submission? I fail to see any identifications for my data. The same file when submitted in pairwise format gives ID's. Since single job submission exists and is supposed to assign ID's, I think it should work. Please see if this problem can be sorted out.

Thank you very much,