{

// generate AASequence object from String

const String s = "DEFIANGER";

AASequence peptide1 = AASequence::fromString(s);

// ... or generate AASequence object from string literal

AASequence peptide2 = AASequence::fromString("PEPTIDER");

// extract prefix and suffix of the first/last AA residues

AASequence prefix(peptide1.getPrefix(2)); // "PE"

AASequence suffix(peptide1.getSuffix(3)); // "DER"

cout << peptide1.toString() << " " << prefix << " " << suffix << endl;

// create chemically modified peptide

AASequence peptide_meth_ox = AASequence::fromString("PEPTIDESEKUEM(Oxidation)CER");

cout << peptide_meth_ox.toString() << " --> unmodified: " << peptide_meth_ox.toUnmodifiedString() << endl;

// mass of the full, uncharged peptide

double peptide_mass_mono = peptide_meth_ox.getMonoWeight();

cout << "Monoisotopic mass of the uncharged, full peptide: " << peptide_mass_mono << endl;

double peptide_mass_avg = peptide_meth_ox.getAverageWeight();

cout << "Average mass of the uncharged, full peptide: " << peptide_mass_avg << endl;

// mass of the 2+ charged b-ion with the given sequence

double ion_mass_b3_2plus = peptide_meth_ox.getPrefix(3).getMonoWeight(Residue::BIon, 2);

cout << "Mass of the doubly positively charged b3-ion: " << ion_mass_b3_2plus << endl;

// mass-to-charge ratio (m/z) of the 2+ charged b-ion and full peptide with the given sequence

cout << "Mass-to-charge of the doubly positively charged b3-ion: " << peptide_meth_ox.getPrefix(3).getMZ(2, Residue::BIon) << endl;

cout << "Mass-to-charge of the doubly positively charged peptide: " << peptide_meth_ox.getMZ(2) << endl;

// count AA's to get a frequency table

std::map<String, Size> aa_freq;

peptide_meth_ox.getAAFrequencies(aa_freq);

cout << "Number of Proline (P) residues in '" << peptide_meth_ox.toString() << "' is " << aa_freq['P'] << endl;

return 0;