Saturday, October 3, 2015

Friday, September 4, 2015

Instructions on how to add custom masses to Peptide Ion Calculator


You will soon be able to add your own custom masses to Peptide Ion Calculator. Here are some instruction on how to calculate the exact mass of your substructure.

Custom masses can likely be divided into two types: 1) Amino Acids, or 2) Side chain modifications of Amino Acids. We'll go step by step for both.

1) Adding new amino acids:

In Chem draw, draw the amino acid as neutrally charged, di-radical species. You can select this using the lasso tool and view your amino acid's exact mass in the analysis window. Here are three examples of exact masses for fictional amino acids, depicting the correct way to draw the structures in Chemdraw in order to calculate the exact mass in a peptide chain:

This is how you compute the exact mass for new amino acids to be compatible with Peptide Ion Calculator

2) Adding new side chain modifications:

In Chem draw, draw the modified side chain, neutrally charged, as well as the unmodified side chain, neutrally charged. The difference in the exact mass between the modified side chain, and unmodified side chain is the exact mass you need to enter for side chain modifications. Here is an example for calculating the exact mass of modifying alcohol side chains with acetyl groups.