OpenMS returning lots of zeroes

[stolltho]

Hi Rick

I am running untargeted metabolomics on a 6545QTOF using patRoon/OpenMS and XCMS for feature extraction. Compared to XCMS, OpenMS is not giving good results, i.e. integrating noise and returning lots of '0' although I bumped up the noise threshold to 5000 (report attached). Standard parameter were optimized w/ patRoon/IPO.

Any idea?

Cheers, Thomas

OpenMS report: featureGroupsOpenMS_noise5000.xlsx

optimizedParameters(ftOpt) Feature detection $chromFWHM [1] 2.5

$mzPPM [1] 8

$minFWHM [1] 1.5

$maxFWHM [1] 45.5

$chromSNR [1] 2.5

$noiseThrInt [1] 5000

optimizedParameters(fgOpt) Feature grouping maxAlignRT [1] 28.5

$maxAlignMZ [1] 0.002

$maxGroupRT [1] 6

$maxGroupMZ [1] 0.0071

[rickhelmus]

Hi Thomas,

The zero values simply mean that a feature from a feature group is not present for all analyses. It might be due to poor grouping, the actual compound simply not being present or often it's just noise or misdetection. For the latter it's always important to post-filter your data. In this case the replicate filter works very well. In fact, this is what XCMS does by default, hence it looks cleaner. The tutorial and handbook should give you examples on how to post filter your data.

[rickhelmus]

Closing this due to inactivity. Feel free to comment if you need more feedback.

[stolltho]

Thanks Rick for the info, it worked.