This python script lets users calculate peptide ions (m/z) that will be observed in ESI-MS. It allows users to enter an observed ion, and tells the user what that ion is (e.g., [M+2H]2+)
- Python3
After downloading the repository and ensuring the required Dependencies are installed, navigate to the folder containing the source files using the terminal.
To run the script type: python3 run_PMC.py
Once the script is running, it will first look for a sequence.txt file in the current directory. If it is not there, it will prompt you to make one. Type you amino acid sequence, using the corresponding codes, which are viewable in aaIonMasses.json.
Add the following residues to your sequence if your peptide is:
HOfor linear peptidesCyclicfor cyclic peptides (lactams or lactones)NH2for linear peptides with C-terminal amidesNHCH3for linear peptides with C-terminal methylamides
The script will create the sequence.txt file, and can be rerun so that you do not have to constantly re-input the sequence.
Once your sequence is entered, the script will prompt you for an observed mass. Enter your mass, and the script will return any matching ion that is within 0.3 amu of your queried mass. For example, if you search for 736, the script will return all ions whose m/z is between 735.7 and 736.3. If you do not get a match, try adjusting your queried mass by 0.5 amu, to accommodate fo a possible miss-calibrated instrument.
An important point: Just because your observed ion returns a match, does not mean that the match listed is correct. You should use your best judgement when judging reasonable ions. For example; if you suspect based on one match that you have a single amino acid deletion of alanine, multiple observed ions should match to an alanine deletion. This script just returns a number of potential ions that could explain the m/z you observe...
Currently, the script calculates ions of the form: [l M + i H + j Na + k K]z+, where l, i, j, k, and z are integers. For example: [1M + 2H + K]3+. It will calculate ions with z no larger than 3 (i.e., triply charged ions) and for aggregates no larger than 2.
In the future, I will add the ability for users to specify their own limits to l, i, j, k, and z
The script will compute single and double deletions in addition to single and double additions of amino acids from/to your sequence.
The script will also calculate a number of side reactions that can occur, based on the sequence of the peptide. For example, if your sequence contains lysine residues, the script will also calculate ions that contain the mass for an incomplete deprotection of the Boc protecting group. It will do this for tBu protecting groups, Acm protecting groups, Trityl protecting groups, as well as possible TFA esters, assuming those modifications or possible given the amino acids that comprise your peptide.
Collectively, these side reactions can help diagnose failed syntheses.
When the script is complete, it will create a possible matches.txt file, which contains all of the ions that it has calculated for you sequence.
Amino acid codes, and their corresponding masses, are stored in aaIonMasses.json. Each entry in this .json is formatted as a sting:float, where the string is the amino acid (I've used short names) and the float is the mass of the amino acid. The masses in this .json are not the molecular weight of the amino acids, but instead are the mass that each amino acid adds to the peptide. In other words, these masses are calculated as: exact mass of the new amino acid - H2O.
The amino acid codes can be anything, just ensure that no code is repeated for any amino acid. In the future I will add a tool to ensure amino acids are added to the .json properly.
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