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MoseleyBioinformaticsLab / manuscript.peakCharacterization

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m/z difference histograms #25

Closed rmflight closed 2 years ago

rmflight commented 2 years ago

in the peak comparisons, specifically comparing assigned peaks, we want to do two things for the 97lipid sample.

hunter-moseley commented 2 years ago

Robert,

Split the scanlevel by m/z range. Do not do this for msnbase and xcalibur.

On Wed, Apr 13, 2022 at 10:07 AM Robert M Flight @.***> wrote:

in the peak comparisons, specifically comparing assigned peaks, we want to do two things for the 97lipid sample.

  • Add an inset in the msnbase and xcalibur pieces that is zoomed in so that we can see the bimodal distribution.
  • Split the msnbase and xcalibur by m/z range, and calculate the modes to see if they are actually different. This figure should go in supplemental.

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rmflight commented 2 years ago

OK, I think I figured out the bi-modality. We are reporting mz_difference, which naturally varies by mz, b/c we allow bigger differences as m/z increases.

Here you can see the density of the points where I've decreased transparency to 10%.

scancentric_diff_by_mz

This explains the bimodality. So I think we need to do two things:

  1. Switch to ppm as the difference.
  2. Use absolute value, not raw difference.