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IngallsLabUW / Ingalls_Standards

A repository containing the Ingalls Lab standards list, available for download.
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First pass at a consensus MSMS script #36

Open wkumler opened 1 year ago

wkumler commented 1 year ago

Implementing an initial pass at an MSMS consensus script using hierarchical clustering in m/z space to identify robust fragments. Still needs testing (cross validation?) of the outputs and a general approval for MS2string types

wkumler commented 1 year ago

The first commit above was done because we kept seeing "good" fragment clusters of size 9, 10, or 11. This may get cleaned up by using only a single scan's fragments (ideally the scan with highest MS1 intensity) because I suspect that we're getting superimposed lollipops when the biggest fragments are all from the highest MS1 intensity scan and the smaller fragments are all of another scan. I don't know where else those smaller fragments would be coming from but that requires recompiling the original init_dat data frame with RaMS again (i.e. revisiting the extract_DDA script).