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sgibb / topdownr

R-package for the analysis of Thermo Orbitrap Fusion Top-Down Proteomic Data.
https://sgibb.github.io/topdownr/
GNU General Public License v3.0
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Intact protein Top-Down in negative mode #82

Open Me9atron opened 6 months ago

Me9atron commented 6 months ago

Hello,

Thank you for developing such a useful tool to perform Top-Down analysis using R. I meet a couple of questions and need your expertise to have a look.

  1. Would it be possible to use topdownr to analyze protein Top-Down data acquired in negative ion mode?
  2. If the data only contains MS2 spectral but no full mass, could this data still be analyzed with topdownr?
  3. Usually we select one specific fragmentation method (e.g., HCD, ECD, UVPD) for a analysis, could we specify or include all the types of fragment ions (a, x, b, y, c, z) in the same analysis?

Best wishes,

Zhaowei

sgibb commented 6 months ago
  • Would it be possible to use topdownr to analyze protein Top-Down data acquired in negative ion mode?

I never tried but shouldn't be a problem. Maybe @pavel-shliaha tried it?

  • If the data only contains MS2 spectral but no full mass, could this data still be analyzed with topdownr?

MS1 is not needed. MS2 should be sufficient.

  • Usually we select one specific fragmentation method (e.g., HCD, ECD, UVPD) for a analysis, could we specify or include all the types of fragment ions (a, x, b, y, c, z) in the same analysis?

Yes.

Me9atron commented 6 months ago

Thank you for your support. I am looking forward to hear from @pavel-shliaha.