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MoseleyBioinformaticsLab / manuscript.peakCharacterization

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non-scan level data for assignment #8

Closed rmflight closed 2 years ago

rmflight commented 2 years ago

I had this idea long ago, but completely forgot until now.

To assign peak data that does not intrinsically have scan level data (i.e. the XCaliber data) we can create a fake scan level that just has 20 scans of identical peak information.

This should let it be assigned by SMIRFE.

hunter-moseley commented 2 years ago

This approach may have a problem with estimates of variance in SMIRFE.

On Thu, Mar 10, 2022 at 10:17 PM Robert M Flight @.***> wrote:

I had this idea long ago, but completely forgot until now.

To assign peak data that does not intrinsically have scan level data (i.e. the XCaliber data) we can create a fake scan level that just has 20 scans of identical peak information.

This should let it be assigned by SMIRFE.

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rmflight commented 2 years ago

That is true and something I forgot about.

However, for potentially assigning any of the methods that don't have intrinsic scan level data, or where it is really hard to get scan level data to match aggregate peaks, this is the only option I can see trying without making major modifications to SMIRFE code.

Of course, if this doesn't work, then I'll use peak matching to the PeakChar assignments for evaluation.

rmflight commented 2 years ago

After discussion w/ @hunter-moseley during our lab meeting, we've decided that making SMIRFE assign data this way is like putting a square peg into a round hole, and it doesn't make sense to compare assignments generated like this when SMIRFE expects scan level data.

rmflight commented 2 years ago

I still went ahead and tried doing this, generating scan level m/z values from a normal distribution with 0.5 ppm SD and centered at the centroided m/z.

That still gives the same negative sample error in SMIRFE as we observed in #7 . So no MSnbase assignments. :shrug: