The ions are made in a discharge (the glow a current lights in low-pressure gas), and which one dominates depends on the source and how it is run. An ion is an atom or molecule that has lost or gained an electron and so carries a charge; H₂⁺ is a hydrogen molecule missing one electron. The physics was settled a century ago with magnetic analysis of discharge products. Electron impact on hydrogen makes H₂⁺ first, protons come from breaking it, and H₃⁺ forms when an H₂⁺ meets another molecule (Smyth (1925), p. 1). Hogness and Lunn summarised what their discharge tube showed: H₂⁺ dominated at low pressure, H₃⁺ at higher pressure and small drawing voltage, and H⁺ was favoured by a large voltage and an inert carrier gas (Hogness & Lunn (1925), p. 9). Those are tendencies observed in particular apparatus, and a source of another type can sit elsewhere. The documented cyclotron sources show the spread. The Rutgers 12-inch’s PIG source delivered protons and H₂⁺ together, about five to one (Koeth (2013), p. 2). A hooded cold-cathode source showed no H₂⁺ at its normal operating point and grew some when starved of gas (Forringer (2004), p. 89). Oliphant and Rutherford’s fresh discharge was mostly molecular ions and became “nearly all protons” only after running for some time (Oliphant & Rutherford (1933)). Residual gas, the air and water the pumps have not removed, adds N⁺, O⁺ and H₂O⁺ to the list, though their resonances fall far from hydrogen’s because they are far heavier. Choosing a different particle on purpose is a separate question (Could I accelerate electrons or other ions instead of protons? Would any of those be easier for an amateur?).
More than one peak is normal, and the extra peaks are information. Hold the RF fixed and sweep the magnet’s field, and each species resonates where B = 2πf·m/(q·k), with k the harmonic number, RF cycles per turn. At the same frequency H₂⁺ needs twice the proton field and H₃⁺ three times it, since they carry two and three times the proton’s mass on the same single charge. Each species then repeats at a third and a fifth of its own field. There the ion takes three or five RF cycles to go round once and still arrives at each gap crossing with the voltage pushing its way, so it gains energy (Prechtl & Wolf (2020); Yuly (2013), p. 4-5). Only odd multiples work. With one dee and grounded lids the ion crosses two accelerating gaps per turn, and an even multiple of its circling frequency gives no net energy gain over the two (hosted performance note, §5). Houghton labelled one scan’s peaks H⁺/3, H⁺/5, H⁺/7 and H₂⁺/9 (Yuly et al. (2010), p. 15-18), and the COLUMBUS workshop reads its one-third and one-fifth peaks on purpose (Wolf & Prechtl (2022), p. 2). The sweep is “a cheap first-pass mass spectrometer for the internal beam” (Yuly (2013), p. 4-5). COLUMBUS reads the field at each peak, computes q/m from it (the formula turned round, with f and k known), and compares with the table. Their proton peak came out within one percent of the tabulated value, and a second peak whose computed q/m was about half the proton’s (twice the mass per charge, so twice the field at the same frequency and harmonic) was assigned to H₂⁺ (Prechtl & Wolf (2020), p. 69-71, Prechtl & Wolf (2020), p. 71). A sweep can also carry peaks that are not accelerated beam: direct ions at low field (Prechtl & Wolf (2020), p. 74), a tank mode of the RF circuit (Koeth, p. 8) and collisions (Cressman (2006), p. 12) are the documented ones (How do I know my cyclotron is actually working? If I measure a current, how do I know it's accelerated particles rather than something else in the chamber?).
A peak’s position leaves some things open. Coincidences. H₃⁺ has three times the proton’s mass on the same charge, so its fundamental needs three times the magnet field a proton needs, and its third harmonic a third of that. At every frequency, H₃⁺ on its third harmonic lands at the field of H⁺ on the fundamental, because three times one third is one, and changing the frequency moves the two together. That is mass-number arithmetic. H₃⁺ is three protons with two electrons, so its real resonance field sits about 0.04 percent from the proton’s, far less than a peak’s width on a small machine. On the Mullins machine at 9 MHz the main peak at 593 mT can be either or both; a filament discharge in hydrogen at 10⁻⁵ torr indicated makes H₃⁺ readily, and a fixed-frequency sweep cannot separate them. The defensible identification from the log alone is “hydrogen ions” (hosted performance note, §5, Table 3; /library/amateur/#mullins). Fully ionised deuterium and He²⁺ nearly share a charge-to-mass ratio too: the deuteron has about twice the proton’s mass on one charge, the helium nucleus about four times on two, and the two differ by about 0.6 percent in mass per charge. The Rutgers group showed that even an embedded velocity filter does not split that pair in practice, since the cyclotron is itself a velocity filter at each radius (Koeth, p. 2). A velocity filter passes one speed only, and two ions with nearly the same charge-to-mass ratio at the same field and radius move at nearly the same speed. Energy. The peak’s position fixes q/m times k. It does not measure the energy, which is computed from the field and the collector radius once a charge state is assumed. The computed figure also depends on which field you use, centre or orbit-averaged (weigh-the-ion exercise; Livingston & Blewett (1962), p. 287-288). The meter. A field read with the RF on can be wrong in either direction on a cheap Hall meter, because the RF interferes with the meter, as the Mullins log recorded in 2019 (hosted instrumentation note, §6). A field approached from above reads differently from one approached from below (Gonski (2013), p. 3). A peak shifted by the meter looks like a different ion.
If your RF system can operate over a wide enough frequency range, lowering the RF frequency brings the fundamental resonances of several hydrogen ions within your magnet’s range. In the formula above every ion’s field scales with the frequency, so lowering the frequency lowers them all together. This can reveal additional peaks and help identify which ions are present. But some species-and-harmonic combinations overlap at every frequency, so even this scan may not uniquely identify the particles responsible for a particular peak. The H⁺ fundamental and the H₃⁺ third harmonic are the standing example. Lowering the frequency moves both together, and the peak at the proton field can carry either or both at every setting. The scan adds the H₃⁺ fundamental as a separate peak, three times higher in field. Its presence and size say whether H₃⁺ is in the source’s output at all, which is supporting information about the shared peak, not a separation of it. For the Mullins magnet, at or below about 4.3 MHz the H⁺, H₂⁺ and H₃⁺ fundamentals sit at 282, 564 and 846 mT, and a 2018 run at 3.26 MHz showed H⁺ and H₂⁺ as separate peaks at 214 and 427 mT (hosted performance note, §5, §12). COLUMBUS designed for the same kind of scan. At a fixed 2.82 MHz, protons resonate near 185 mT and H₂⁺ near 370 mT, and doubling the field was judged easier than doubling the frequency (Prechtl & Wolf (2020), p. 37-39). A tank (the dee’s resonant circuit) tuned near 9 MHz may not deliver useful dee voltage at 3 or 4 MHz without retuning or new parts (I keep seeing "cyclotron resonance", "RF resonance" and "impedance matching". Are these the same thing? What has to match what?; My RF circuit tunes up nicely on the bench. Why does it change when I close the chamber, pump down, turn on the source, or raise the power?). The energies at those settings are low, since energy at a given radius falls with the field; the scan is for identification.
If it does not work. A peak where none is predicted. Compute the candidates before concluding. Take every plausible species, including the residual-gas ions, times every odd harmonic up to seven or so. Add the tank’s other modes and the direct-ion field for your source-to-collector geometry. The Mullins note’s Table 3 is a model of the layout, one row per ion, one column per harmonic, with the magnet’s maximum marked. A strong peak at a third of the expected field and nothing at the field itself. Check whether the fundamental is inside your magnet’s range at all. On the Mullins machine the H₂⁺ fundamental at 9 MHz would need 1,185 mT against a maximum of 851. Peaks that move between runs. Hysteresis (the iron’s magnetisation lags the coil current, so the same current gives a slightly different field) and the meter are suspects before the species is (Gonski (2013), p. 3; Do I really need to map my magnet's field accurately? Is one reading in the middle enough, and which value goes into the frequency and energy calculations?). A peak whose height changes with gas flow or arc current (the source’s discharge current) while another does not. The difference is an observation about the source’s chemistry, consistent with the century-old recipe (Hogness & Lunn (1925), p. 9, Forringer (2004), p. 89). It suggests which peak is which; it does not establish it. A pronounced peak at a field that matches a simulated low-harmonic molecular ion. COLUMBUS saw that, H₂⁺ at a fifth of maximum speed, and the simulation and the measurement agreed (Wolf (2016), p. 3): genuine beam, of an unintended species.
To understand it. Species matters beyond the label. Molecular ions are destroyed more readily in residual gas than protons are. A proton is lost when it captures an electron from a gas molecule and becomes a neutral atom, which the magnetic field no longer steers; an H₂⁺ can also be broken apart. A cross-section is the likelihood of that per molecule passed. The compiled total destruction cross-section for H₂⁺ in hydrogen exceeds the proton’s electron-capture cross-section over the same energies, so at the same pressure the molecular beam survives fewer turns (Barnett et al. (1990), p. 629; Barnett et al. (1990), p. 44; What pressure should I aim for when the cyclotron is running? Don't I need more gas to make ions, but less gas to let them spiral around?). Once the machine is capable of a nuclear reaction the species sets the hazard. The Davis group deliberately ran H₂⁺ and alphas before protons until their shielding was complete (Jungerman (1966), p. 7; Can the machine make radiation, or hurt me some other way, before I've even detected a beam?). On the measurement side, the Rutgers 12-inch made its deflector (the extraction electrode at the edge) a q/m spectrometer by halving the field at fixed frequency and stepping the deflector voltage (Koeth, p. 6). COLUMBUS plans a Wien filter (a velocity filter) behind an extraction system to measure the ions’ speed directly (Wolf & Prechtl (2022), p. 3). A nuclear signature identifies by physics: the 63-inch concluded N³⁺ (nitrogen missing three electrons) from the energy a gamma burst implied (Howard (ed.), p. 9), and activation decay curves name the product and so the projectile (Howard (ed.)): the half-life of a target made radioactive names the nucleus formed, and so what formed it. Those are Level 3 instruments. The low-frequency scan is Level 1 where the RF allows it, and it informs the identification rather than settling it.