Calculating Mass
Proteoforms are polypeptides that contain many amino acid residues joined together in a long strand. To calculate the theoretical mass (measured in Daltons) of a proteoform, one must:
Sum Residue Masses
To begin, one should use a table of masses (reproduced from here) to add together all the residues in your sequence. If you require a very precise value or want to make sure you match an existing example, care must be taken to synchronize isotopic abundance tables and calculate your own table of masses.
| Amino acid | Short | Abbrev. | Mono. mass (Da) | Avg. mass (Da) |
|---|---|---|---|---|
| Alanine | A | Ala | 71.03711 | 71.0779 |
| Cysteine | C | Cys | 103.00919 | 103.1429 |
| Aspartic acid | D | Asp | 115.02694 | 115.0874 |
| Glutamic acid | E | Glu | 129.04259 | 129.1140 |
| Phenylalanine | F | Phe | 147.06841 | 147.1739 |
| Glycine | G | Gly | 57.02146 | 57.0513 |
| Histidine | H | His | 137.05891 | 137.1393 |
| Isoleucine | I | Ile | 113.08406 | 113.1576 |
| Lysine | K | Lys | 128.09496 | 128.1723 |
| Leucine | L | Leu | 113.08406 | 113.1576 |
| Methionine | M | Met | 131.04049 | 131.1961 |
| Asparagine | N | Asn | 114.04293 | 114.1026 |
| Pyrrolysine | O | Pyl | 237.14773 | 237.2982 |
| Proline | P | Pro | 97.05276 | 97.1152 |
| Glutamine | Q | Gln | 128.05858 | 128.1292 |
| Arginine | R | Arg | 156.10111 | 156.1857 |
| Serine | S | Ser | 87.03203 | 87.0773 |
| Threonine | T | Thr | 101.04768 | 101.1039 |
| Selenocysteine | U | Sec | 150.95364 | 150.0489 |
| Valine | V | Val | 99.06841 | 99.1311 |
| Tryptophan | W | Trp | 186.07931 | 186.2099 |
| Tyrosine | Y | Tyr | 163.06333 | 163.1733 |
Consider additional modifications
A proteoform can be decorated with a variety of modifications that will affect its mass. These might include post-translational modifications (PTMs), lipids, or glycosylations.
Just add water
Lastly, the residue masses do not include "stabilizing" atoms that are required for a polypeptide. Specifically, a hydrogen atom must be added to make a complete N-terminus and hydrogen and oxygen atoms must be added to make a complete C-terminus. Simply put, add H2O at the end to complete the proteoform.