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Sum Formula

KNIME CDK Integration version 1.5.700.v201711101057 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Generates sum formulas based on a given mass. The formula generator assumes input masses to be major isotopic masses.

Generated sum formulas can be filtered by the nitrogen rule, element ratio rule, and by element number restriction. For details on the implemented options, please see the "seven golden rules" by Kind et al., 2007. The following excerpts are taken from the publication.

"The nitrogen rule states that an odd nominal molecular mass implies also an odd number of nitrogens. This rule should only be used with nominal (integer) masses. When using accurate mass measurements this rule becomes unreliable in mass ranges higher than 500 Da."

"The maximum element count can be restricted in a heuristic manner by using the provided sets of element minima und maxima that were derived from NIST and Wiley mass spectra and DNP entries. Maximum element counts are defined for the mass ranges at smaller 500 Da, 1000 Da, 2000 Da, 3000 Da by taking the higher value found in either of the two databases."

"More than 99.7% of all formulas were included with H/C ratios between 0.2–3.1. This range is called the 'common range'. However, a number of chemical classes fall out of this range. The 'extended ranges' covers 99.99% of all formulas in the used database (H vs C 0.1–6). There are extreme cases for which rules of typical H vs C ratios may be overridden, e.g. for the study of fullerenes, which have an extremely low hydrogen/carbon ratio such as in C78H12Cl2N2."

Sum formulas that do not contain a single Carbon atom are always included.

DISABLED Options: 'All elements' and 'Exclude elements' are currently not supported because the matrix required for the calculation exceeds the memory limit of the virtual machine: Math.pow(2, size).

Options

Column with masses
Mass column in input table.
All elements (DISABLED)
Whether to use all elements for the calculation.
Include elements
Whether to use a custom set of elements.
Exclude elements (DISABLED)
Whether to use all elements excluding a set of elements.
Elements
The comma-separated set of elements to be included or excluded.
Carbon limits
The allowed minimum and maximum number of carbon element counts.
Hydrogen limits
The allowed minimum and maximum number of hydrogen element counts.
Other limits
The allowed minimum and maximum number of other element counts.
Mass tolerance
The mass tolerance in 'amu'.
Nitrogen rule
Apply the nitrogen rule.
Element ratio rule
Apply the element ratio check rule.
Element restriction
Apply element occurrence restrictions.

Input Ports

Table with molecular masses.

Output Ports

Input table plus calculated sum formulas.

Best Friends (Incoming)

Best Friends (Outgoing)

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