Introduction

This tool allow to generate quickly and efficiently the molecular formula and monoisotopic mass based on the combination of many groups. The system deals with peptide sequences, non-natural peptide sequences, linked peptides and internal fragments. It is not a problem to generate 50000 possibilites. For natural amino acids you may specify a pH for protonation of the ptpide.

Simple example:

Range example:

The system allows also to generate range

The system will generate the following molecular formula:

Userguide

A group list contains different molecular formula separated by a ".". If there is a "." at the end of the string, it means that this group may be empty.

A group may also contain range and all the possibilities will be generate, like in the case of "(H+)1-3" that allows to add one to three protons.

For natural peptide sequence you may enter just the 1 letter uppercase code, like for example "AALLDD". If you have modified peptides you should use the three letter code and put in parenthesis the modification of the amino acid. For example if you have a phenylated serine you can enter the following sequence: HAlaSer(H-1Ph)AlaOH. The natural amino acid modification will be placed in parenthesis and correct peptide fragmentation (A, B, C, X, Y, Z) will be generate. When you specifiy an amino acid modification you may put as well negative number of atom in order to remove an atom. So in the case of the serine modification, we remove an hydrogen (H-1) and add a phenyl group.

For the fragmentation of peptide you have the choice of "A, B, C, X, Y, Z" but also internal fragments: Y + B and Y + A.

 

The system will display 2 different masses :

em : the monoisotopic mass for the neutral molecular formula

ms em : the mass observed monoisotopic mass, taking into account the charge and the mass of the electron