Understanding mass gaps

[Thys Potgieter]

Hi DeNovoGUI team,

I will appreciate some advice, I was not sure wether mass gaps can be considered the sum of (unsequenced) residues in a spectrum in the tag_matches.txt file, or if I need to take into account the mass of the free H+ on the n terminus, and OH- on the c-terminus?

ie. can an n-terminus mass gap of 131.04049 safely be asssumed to be Methionine (monoisotopic mass of M being identical) or do I first need to subtract the mass of a proton or the mass of H20 from the gap before trying to enumerate possible amino acids that can explain the gap?

I will be very grateful for any advice, here!

Thank you,

Thys

[Marc Vaudel]

Hi Thys,

The mass gap in DenovoGUI is the sum of residues without extra proton(s). Note that this is not necessarily the case for the individual algorithms. So the mass gaps should directly represent the mass of Methionine in your example.

I don't know if you tried this already, but PeptideShaker is able to map mass gaps to a database and the latest version gives quite promising results. This is however a beta feature so there might be glitches and bugs that passed our initial tests...

Best regards,

Marc

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[Thys Potgieter]

Thank you so much Marc! I will have a look at the new feature of PeptideShaker as well,

Kind regards

Thys

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