Swiss Mass Abacus
Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.
An alternative to using Swiss Mass Abacus Web Interface, is a standalone version that can be downloaded from the link below.
How to Use the Abacus
- All masses are monoisotopic and in Dalton. (Reference for Monosaccharides masses: ExPASy GlycoMod; Reference for Amino Acid masses: Mascot)
- Text input can be provided via the interface as well as typed via computer keyboard.The usual keyboard shortcuts (e.g. ctrl-c, ctrl-v) can be used to copy and paste text. Na+, K+, H+ and e- are special ions and they can be inputted by the user typing: NaPlus, KPlus, proton, electron.
- To calculate the mass of a dipeptide, for instance DA, hit the 'Asp' key, then the ‘+’ key, the 'Ala' key and finally the ‘=‘ key to visualise the result in the upper part of the window.
- To calculate the mass of a glycopeptide, the principle is the same. Adding amino acid masses can be complemented by adding monosaccharide composition. For example, if the DAVAL peptide is known to carry Glc(b1-4)Gal(a1-3)GlcNAc, then the formula 2xHex + HexNAc must be added to Asp+Ala+Val+Ala+Leu. If the peptide is known to be doubly charged, the calculated mass should be divided (/) by 2. Electron and proton masses are provided to calculate the actual m/z of the molecule.
- To enable the keyboard input, click on the upper part of the window. In this particular case, one letter amino acid is allowed code. For example the mass of DAVAL can be calculated inputting D+A+V+A+L (no distinction between upper and lower case), and the result is equivalent to typing Asp+Ala+Val+Ala+Leu.
- Some tools compute the mass of a peptide by adding the mass of a water molecule to the sum of amino acid masses. SwissMassAbacus does not add the water molecule automatically, but provides a 'H2O' key for the user to add it if desired.
- SwissMassAbacus applies calculator is using algebraic precedence. which means that binary operators are always applied in the order: exponents and roots, then multiplication and division, and finally addition and subtraction. Of course any brackets can be used to override these precedence rules.
Swiss Mass Abacus was developed in collaboration with members of Dr. Daniel Kolarich group at Max Planck Institute of Colloids and Interfaces in Berlin, Germany.
This work was supported by European Union FP7 GastricGlycoExplorer Innovative Training Network under Grant Agreement No. 316929.