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Topic: Setting mzwid for high res data (Read 3095 times) previous topic - next topic

Setting mzwid for high res data

I am noticing some irregularities in my EICs from XCMS Online using the Orbitrap II HPLC setting for LTQ-Velos data. There are several noisy "peaks" (just baseline noise) as well as "half peaks" (integration stops near the apex of a peak). 
I looked through the method settings I wasn't really sure where to troubleshoot. I did notice that mzwid is set to 0.015, and this is 75 ppm error at 200 m/z and 15 ppm error at 1000 m/z -- well outside the range of the Orbitrap's resolution. So I turned this setting down to 0.005, and also based on the observed chromatography I adjusted the max peak width to 50 sec. 

I'm wondering if A) I have misinterpreted what mzwid is doing and B) if there are other features the community can suggest to improve peak integration. I can live with noise peaks as those are (relatively) easy to ID and remove from the final feature table. However the "half peaks" are not as easy to spot without close EIC inspection and any help getting rid of them would be appreciated.