[Biojava-dev] Calculation error in MassCalc.getMass()

[Lachlan Coin]

Hi Jerry and Matthew,

I noticed also that MassCalc checks for a protein alphabet, and so will
fall over if the alphabet is a PROTEIN-T alphabet - i.e. protein +
termination symbols. It might be good to fix this at the same time:

Lachlan




>
> Date: Fri, 14 Feb 2003 21:03:56 +0000
> From: Matthew Pocock <matthew_pocock at yahoo.co.uk>
> To: Jerry Thomas <jrt4 at york.ac.uk>
> Cc: biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] Calculation error in MassCalc.getMass()
> Message-ID: <3E4D59BC.3090602 at yahoo.co.uk>
> In-Reply-To: <3E4D2209.3070406 at york.ac.uk>
> References: <3E4D2209.3070406 at york.ac.uk>
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>
> Hi Jerry,
>
> I don't know anything about masses. Could someone else from the list
> seccond this? We should get this sort of thing right.
>
> Matthew
>
> Jerry Thomas wrote:
> > I believe the masses returned by MassCalc.getMass() to be incorrect.
> >
> > The internal residue masses used for amino acids are correct, but the
> > terminii are calculated incorrectly.  Instead of adding H for the
> > N-terminus and OH for the C-terminus, the masses of two OHs are added.
> > For M+H, instead of adding an extra H, the mass of a third hydroxyl is
> > added!
> >
> > For example, MassCalc gives a monoisotopic M+H mass for angiotensin
> > (DRVYIHPFHL) of 1328.6751, whereas the correct value is 1296.6853.  The
> > difference is due to the two extra oxygens (2 * 15.9949 = 31.9898).
> >
> > If there are no objections, I will correct the code, and add a test app
> > to demos.
> >
> > cheers,
> >
> > Jerry
> >