Noise in MS2 data

[sdrogers]

Presently, no noise is added to MS2 peaks. Need to:

• understand how their mz is generated and then
• allow the system to either
  • inherit the m/z deviation from their parent chromatogram or
  • add (normal) noise, with a sd set from a set of known ROIs

Check that intensity noise is added to the MS2

[joewandy]

The skeleton codes to add MS2 noise are already there, but we forgot to actually implement it. See https://github.com/sdrogers/vimms/blob/master/vimms/DataGenerator.py#L579-L585.

[sdrogers]

Thanks @joewandy -- to do comparisons between DIA and DDA I think we need to implement both (maybe; but no harm in doing it).

Can we add normal noise to both?

[joewandy]

Added the following commits:

• https://github.com/sdrogers/vimms/commit/d0efae50fa0340a5bc308b14e39216afcd2d0311
• https://github.com/sdrogers/vimms/commit/164efd5d20b7cdb0018922f395e7f6a0e6caab1c.

Two noise classes have been added: NoPeakNoise and GaussianPeakNoise.

We can pass an instance of this noise class when initialising the Mass Spec:

        peak_noise = GaussianPeakNoise(0.1, 1000)
        mass_spec = IndependentMassSpectrometer(ionisation_mode, fragscan_dataset_peaks, fragscan_ps, peak_noise=peak_noise)

This class is then used to apply noise when generating the m/z and intensity values of a peak: https://github.com/sdrogers/vimms/blob/master/vimms/MassSpec.py#L592-L598

        noisy_mz_peaks = []
        for i in range(len(mz_peaks)):
            original_mz, original_intensity = mz_peaks[i]
            noisy_mz = self.peak_noise.get_mz(original_mz, query_rt, original_intensity, ms_level)
            noisy_intensity = self.peak_noise.get_intensity(original_mz, query_rt, original_intensity, ms_level)
            noisy_mz_peaks.append((noisy_mz, noisy_intensity))
        return noisy_mz_peaks

I think some student is supposed to improve the noise process? It can be done by improving the classes above, or making a new one.

[joewandy]

The noise class is further improved in issue #69.