nx_chem_mass.nx

nx_chem_mass.nx -- C2.8a milestone: monoisotopic mass + ion m/z prediction for LC-MS work. Standard atomic weight (Element.mass_q3 in milli-AMU, C1) is used for nominal molecular weight via nx_chem_mol_weight_q3 (C2.3a). For MS work, the EXACT MASS of the most-abundant isotope is needed instead -- e.g., glucose monoisotopic = 180.0634 Da (not 180.156 average) because LC-MS resolves a single isotope peak. This file composes on C1 AtomicData.iso_mass_q4 (Q4 micro-AMU) + C2.3a implicit-H to produce exact-mass + protonated-ion m/z. Units: iso_mass_q4 : exact isotope mass * 10000 (Q4 micro-AMU) monoiso_q4 : whole-molecule monoisotopic mass in Q4 proton_mass_q4 : 10073 (= 1.00728 Da, the proton mass; used for [M+H]+ ion m/z which differs from monoisotopic by adding a proton, not a neutral H atom; the difference is the electron mass = 0.00055 Da which is below Q4 precision) Honest gaps (DEFERRED): - Multi-charge ions [M+2H]2+, [M+nH]n+: trivially obtainable by dividing m/z by n; left for caller in MVP. - Isotopologue pattern prediction (M+1, M+2 peaks from natural abundance distribution): C2.8b composes on AtomicData iso_abund_ppm field; requires combinatorial expansion over all C/H/N/O isotopes. - Adduct ions [M+Na]+, [M+K]+, [M+NH4]+ common in ESI+: just substitute proton with respective ion mass.