How to retrieve average mobilogram

[DennisDannecker]

Hello,

Thank you for developing AlphaTIMS, I very helpful data for working with bruker timsTOF data.

I was wondering whether there is a straightforward way to get the average mobilogram, similar to what is done with TIMS Viewer from bruker.
I would like to analyze the data in a broader context and map search results onto this average mobilogram.
I am sure this is possible, but I am not entirely sure how to slice the timsTOF object.
This is not really a feature request, I am just asking whether one can provide me with a couple of lines of code to get this average. Getting the actual average is probably rather computationally expensive, so a smart average estimate would also be good.

Thank you very much for your help and support, much appreciated.

Best,
Dennis

[mschwoer]

Hi,
fed your request into Opus 4.7, here's the answer. Let me know if it was helpful.
best,
Magnus

Opus 4.7:
Computing the (total) MS1 mobilogram is
inexpensive — slicing + one binning pass, a few seconds on a typical run.

import alphatims.bruker
import alphatims.plotting

data = alphatims.bruker.TimsTOF("path/to/your.d")

# Select all MS1 data (precursor_index = 0 == unfragmented / MS1 frames).
ms1_indices = data[:, :, 0, :, "raw"]

# Sum intensities per mobility bin -> 1-D array indexed by scan_index.
mobilogram = data.bin_intensities(ms1_indices, ("mobility_values",))
mobility_axis = data.mobility_values   # 1/K0, same length as mobilogram

# Or plot directly:
alphatims.plotting.line_plot(data, ms1_indices, x_axis_label="mobility")

A few notes:

• For a literal
  per-frame mean, divide by the number of MS1 frames:

  n_ms1 = int((data.frames["MsMsType"] == 0).sum())
  mobilogram_mean = mobilogram / n_ms1

• To restrict to an RT or m/z window (e.g. an extracted ion mobilogram for a
  search hit), use the regular slicing API:
  data[rt_min:rt_max, :, 0, mz_min:mz_max, "raw"], then feed the result into
  bin_intensities the same way.