Further Calculation Functions¶
MS Peak Assignment¶
The MS assignment features of Peptide Calculator and Peptoid Calculator can be accessed through Pep-Calc API using the Mass Assignment resource.
The following example illustrates assignment of the peak list '1201.4, 1301.7, 1320.8, 1348.1, 1601.3'
for the peptide sequence 'RPKPQQFFGLM'
. Pep-Calc API returns a nested JSON object with the input peaks at the top level.
Top level keys point to arrays of successful assignments. A calculated mass (calcMass
) is given for each assignment, alongside the deduced deletions and adducts contained within the arrays dels
and mods
respectively. The boolean molecular
indicates whether or not an assignment corresponds to a molecular ion.
Request:
GET /peptide/mass?seq=RPKPQQFFGLM&N_term=H&C_term=OH&mz=1201.4%2C+1301.7%2C+1320.8%2C+1348.1%2C+1601.3
Response:
{
"1201.40": [
{
"calcMass": "1201.6510",
"dels": ["F"],
"mods": null,
"molecular": false
}
],
"1301.70": [
{
"calcMass": "1301.5017",
"dels": ["K", "P", "P"],
"mods": ["Na+", "Pbf"],
"molecular": false
},
{
"calcMass": "1301.5381",
"dels": ["P", "P", "Q"],
"mods": ["Na+", "Pbf"],
"molecular": false
}
],
"1320.80": null,
"1348.10": [
{
"calcMass": "1348.7194",
"dels": null,
"mods": null,
"molecular": true
}
],
"1601.30": [
{
"calcMass": "1601.7194",
"dels": null,
"mods": ["Pbf"],
"molecular": false
}
]
}
See here for a comparison with the output from Peptide Calculator’s web interface.
Beta Contiguity Calculation¶
The Beta Contiguity resource can be used to return an array of -strand propensity values for a peptide sequence, ordered by residue number. For example:
Request:
GET /peptide/betacontiguity?seq=RPKPQQFFGLM&N_term=H&C_term=OH
Response:
{
"betaContiguity": [
[1, "R", "0.0000"],
[2, "P", "0.0000"],
[3, "K", "0.0000"],
[4, "P", "1.2034"],
[5, "Q", "4.8810"],
[6, "Q", "6.0936"],
[7, "F", "7.2982"],
[8, "F", "7.2982"],
[9, "G", "4.8419"],
[10, "L", "3.6357"],
[11, "M", "3.6357"]
]
}
Please refer to the article published in the Journal of Computer-Aided Molecular Design for details of the methods used for calculation of -strand propensity values.