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An improved program for the estimation of protein theoretical relative molecular mass and uncertainty



Eric L. Kilpatrick


Here is presented the NIST Mass Calculator to provide both a relative molecular mass value (Mr) and an associated uncertainty value of a given protein sequence. The calculation of a protein Mr based on its amino acid residue sequence is performed by many software applications. Unfortunately, many of the results do not agree with each other. Reasons for this lack of consensus may include use of rounded values, calculation errors or alternative calculation methods and it is often not possible to distinguish the source of the differences. Additionally, the result is provided without an estimate of precision. This would imply that the Mr is perfectly known, when in fact it is not. The basis for the calculation, either the Relative Atomic Mass or the Standard Atomic Weight, are themselves provided as estimates. Until the release of the NIST Mass Calculator, there were no applications available to provide both a Mr and an associated uncertainty value. Further, the full disclosure of the computation methods and elemental values allows for independent verification of the results. The uncertainty is obtained via Monte Carlo simulation and is now a useful feature in light of the capability of the high resolution mass spectrometry of intact proteins.
Journal of Proteome Research


high resolution mass spectrometry, Monte Carlo simulation, relative atomic mass, standard atomic weight, software


Kilpatrick, E. (2019), An improved program for the estimation of protein theoretical relative molecular mass and uncertainty, Journal of Proteome Research, [online], (Accessed July 18, 2024)


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Created November 1, 2019, Updated April 19, 2020