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Topic: Alignment: MS1/RT factor, N% detected in at least one group (Read 180 times) previous topic - next topic

Alignment: MS1/RT factor, N% detected in at least one group


I have some question with respect to specific alignment parameters.

1.) My first question refers to the parameters "MS1 factor" and "RT factor". As I understood right, the parameters determine the weighting of mass and retention time (deviations) used for calculating the total score of a feature matching the post-identification process. Up to now, my inetention was that the total sum of both parameters should be 1, e.g. 0.5 for MS1 and 0.5 for RT. However, I recognized that you can process your data also with parameter values whose sum is bigger than 1.
So, I am not sure how this weighting finally works?

2.) The second question concerns the “N% detected in at least one group” parameter. Does “one group” also includes the QC and the blank group, respectively?
If the value is smaller than the given parameter setting (valid for all sample groups, but not for QC/blank group), what will be the consequence? Is such a feature completely eliminated from the alignment output or is it only eliminated from the sample groups but not from the QC or blank group (and thus it would remain in the feature list)?