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Topic: rtmin for peaks and groups (Read 4271 times) previous topic - next topic

rtmin for peaks and groups

Hi all,

I'm looking for a clearer definition of 'rtmin' for grouped features. According to the XCMS manual, 'rtmin' for a peak represents 'the leading edge of peak retention time'. For groups, meanwhile, rtmin is defined as the 'minimum retention time of peaks in the group'. In the case of a peak, the definition is very clear. For group rtmin however, things are not so clear. There are two possible interpretations:

1) The group rtmin is taken as the minimum rt value for all peaks in the group (usually defined at the centre of chromatographic peak); e.g. group contains four peaks with rt values of 4.05, 4.07, 4.06, 4.09, so rtmin is stated as 4.05.
2) The group rtmin represents the 'leading edge' value of lowest magnitude among all peaks in the group (i.e. the group rtmin truly represents the start of the curve for a metabolic feature and not just the lowest rt value for a member of the group).

I ask as I wish to gain an understanding of peak width and asymmetry. If option (1) is the correct definition, then this is not appropriate, as I'm not actually learning anything about peak shape, but rather the range of peaks around the median rt.

Many thanks for any help you can offer.
Martin.