Using DeNovoGUI for mass spectra obtained in negative ion mode

[mcamen...@gmail.com]

Dear DeNovoGUI developers,

I am an academic at the University of Amsterdam studying protein phosphorylation using a bottom-up proteomics workflow. I would like to begin using negative ion MS since phosphorylated peptides are negatively charged. It follows that I am looking for software that would allow me to undertake peptide mapping using mass spectra obtained with negative ion mode. Could you please let me know if DeNovoGUI would be suitable?

Thanks for your assistance.

Michelle

[Harald Barsnes]

Hi Michelle,

Thank you for your interest in DeNovoGUI.

DeNovoGUI is simply a single user interface for running the four de novo sequencing algorithms Novor, DirecTag, PepNovo+ and pNovo+. DeNovoGUI in itself can therefore only support the settings available in the algorithms themselves, and as far as I know none if the algorithms included in DeNovoGUI supports negative ion mode.

There might be other proteomics software able to analyze such data though, but I'm afraid I cannot think if any at the moment. Maybe somebody else on the list will now.

Best regards,

Harald

On Friday, October 21, 2016 at 3:30:34 PM UTC+2: