Problem with monoisotopic mass calculation in KNIME molecule properties

[Oliver Kohlbacher]

Dear all,

quick question: calculation of monoisotopic mass via the KNIME molecule properties

node leads to incorrect results for compounds containing bromine.

Example: CH3Br yields a monoisotopic mass of 94.94 Da rather than 93.94 Da.

I assume that the calculation does not account for the less common elements.

Is that assumption correct? Is there a way to fix this?

Thanks

  Oliver

[Mikhail Rybalkin]

Hello Oliver,

Monoisotopic mass uses most abundant isotope for each atom independently. Bromine atom has the following isotopic distribution:

79Br - 50.69%, 81Br - 49.31. Monoisotopic mass computation method calculates mass of [79Br] + [12C] + 3x [1H].

Indigo computes 3 masses and for CH3Br they have the following values:

molecularWeight = 94.939

monoisotopicMass = 94.942

mostAbundantMass =  93.942

I took this results from the latest version. We have a page were this masses are explained: http://www.ggasoftware.com/up/indigo-doc/indigo/concepts/mass.html

Could you check that your version of Indigo KNIME nodes returns the same values?

Best regards,

Mikhail

[Oliver Kohlbacher]

Hi Mikhail,

thanks a lot for your reply. Indeed, the KNIME nodes produce the numbers you gave below.

However, the masses seem to be off:

   79Br:  78.918 u

    3x  1H:   3 x 1.008 u

   13 C: 12.000 u

If I sum that up, I get 93.942 rather than 94.942.

Any idea what's going on?

Cheers,

  O.

[Mikhail Rybalkin]

It seems like we have a bug here. Thank you for reporting about this problem! We were using "default isotope" that is calculate as the nearest isotope to the natural atomic weight, but instead of it we have to use most abundant isotope. We were using 80 Br instead of 79 Br. I will fix it shortly and will post message about it.

PS: I support you typed wrong number here:

   13 C: 12.000 u

It should be "12 C: 12.000 u", right?

Best,

Mikhail

[Oliver Kohlbacher]

Dear Mikhail,

thanks a lot for getting that sorted! Indeed, the 13C was a typo ;)

Cheers,

  O.