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XCMS Online / Data processing LTQ Orbitrap MS(n) data
we are just looking for a senseful workflow for processing of high resolution MS(n) data aquired on a Thermo Fischer LTQ. Firstly we converted raw data with "MS Convert" to mzXML files, using the filters "MS1" level and "Peackpicking". Processing the data with XCMS online with the Centwave algorithm led to detection of very much features which didn't represent any senseful peaks. S/N ratio for many features without any peaks still was about 200000. Could this be a problem of the conversion with MS1 filter? Processing the same samples measured without MS(n) didnt lead to so much peaks with S/N usually about 200.
Our main question now is what threshold parameters should be used in the Centwave algorithm in order to process MS(n) data files and if Centwave still makes sense or better matched filter should be used.
Thanks a lot for any ideas and remarks
Chris