proteomics MS imaging data processing

[yufree]

Hi, Great works for proteomics!
I wonder if this ecosystem will cover MS imaging data with/without ion mobility in the future. Current open source solution is HiTMaP while it will not process data with ion mobility for annotation purpose.

[jalew188]

Hi @yufree , if the data format is similar, I think we can support that

[yufree]

Thanks. For MSI, the open source format is imzML, which is similar to mzML with additional spatial information(x,y,z of the frame). There is a python package pIMZ to perform the MSI segmentation analysis. However, no annotation tool is available for proteomics MSI data. It might be worthwhile to use HDF5 to store MSI data as the size of high spatial resolution data are around 50GB pre sample with ion mobility.

[jalew188]

Is it similar to timsTOF data?

[yufree]

Yes. For Bruker, .D file will contain coords if they are collected in imaging mode.

[jalew188]

Maybe check our alphatims repo for timsTOF loader: https://github.com/MannLabs/alphatims