Intact protein Top-Down in negative mode

[Me9atron]

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]

• 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]

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