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michalsta / opentims

Open-source C++ and Python module for opening binary timsTOF data files.
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XIC #2

Open im281 opened 3 years ago

im281 commented 3 years ago

Great utilities! Is there a function to generate extracted ion chromatograms (XIC) from a given mass and ppm tolerance?

MatteoLacki commented 3 years ago

That's on the to-do list on TimsPy: just working on it. Stay tuned.

jsundaram-seer-bio commented 3 years ago

Looking forward to seeing this supported functionality!

MatteoLacki commented 3 years ago

Hi,

Could you precise the input and output of the requested procedure? What can be easily done is to set up some intervals in m/z and simply sum intensities of peaks falling in that intervals per one retention time moment [i.e. on per frame basis]. In that scenario, you would supply me with left and right borders for some mass to charge ratios, and I would sum intensities in MS1 frames (or MS2, what you want?) within each frame. The output could look like a matrix with columns corresponding to different intervals and rows to different frames. Is that what you want?

baderd commented 1 year ago

I am interested in a very similar question:

I would like to query by a MS1 mz range and by an ion mobility range. Then plot remaining all MS2 spectra.

How can this be achieved?

Thanks for your help!

I also placed it here: https://github.com/MatteoLacki/timsr/issues/2