Locating the List of Isotopic Amino Acid Symbols in Bio Tool Kit Software

For research use only. Not for use in diagnostic procedures.

Answer

The Bio Tool Kit microapp can be used for peptide sequencing or fragment matching in PeakView™ or SCIEX OS software. The one-letter codes for amino acids are used when entering potential fragment ions in the Sequence field. To represent isotope-labeled amino acids, square brackets encompassing the mass shift are used to the right of the one-letter code. In Bio Tool Kit software, the information for all heavy amino acids is stored in the AA Modifications tab in the Mass Calculator.

To access this table, select the Show menu, and then select Mass Calculators. The AA Modifications tab contains a table with the symbol to be used in the peptide fragment when representing the heavy amino acid, the mass shift and the name of the isotope-labeled amino acid. For example, isotope-labeled lysine which contains 6 carbon-13 atoms and 2 nitrogen-15 atoms has a mass shift of 8.01420. To represent heavy lysine, the symbol K with the number 8 in brackets is used and appears as K[+08]. See the orange oval in the screenshot below to see how a heavy amino acid is formatted in a peptide fragment. 



Once properly formatted, the theoretical fragment ions can be matched with the acquired MS/MS spectrum.



The red matched fragment ions are labelled in the MS/MS spectrum.