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A mass analyzer is the part of a mass spectrometer that makes ions distinguishable or selectively transmits them according to mass-to-charge ratio. The measured coordinate can be position, arrival time or transmission under a specified field setting. A separate mass spectrometer detector records the resulting signal.

A quadrupole mass analyzer selects trajectories using combined static and time-varying electric fields: chosen mass-to-charge values remain on stable paths while others are lost from the transmitted beam.^[ref] A time-of-flight mass spectrometer instead encodes the ratio in arrival time after acceleration. Different physical designs can therefore provide the same kind of ionic-mass information through different observables.

An original magnetic example exposes an important assumption. For speed $v$ perpendicular to a uniform magnetic field $B$, balancing the Lorentz force and circular acceleration givesIf the incoming ions have the same selected speed and charge, mass values in the ratio $56/54$ give bending radii in that ratio, about $1.0370$. But if ions instead start negligibly slowly and gain energy from the same electric potential difference $U$, substituting $qU=m{v}^2/2$ gives $r=\sqrt{2mU/q}/B$. Their radius ratio is then $\sqrt{56/54}\approx 1.0184$. The initial-condition choice changes the mapping.

Analysis requires this mapping and its assumptions, not just separated peaks. Mass resolving power describes the ability to distinguish nearby peak coordinates under a stated width criterion; accurate assignment of those coordinates additionally needs instrument calibration and the correct charge-state interpretation.

A mass spectrometer is an instrument that produces or receives ions, separates them according to mass-to-charge ratio, and records their signals. Its major functions are supplied by an ion source, a mass analyzer and a mass spectrometer detector. The result is a mass spectrum; interpreting a peak also requires knowing which ionic chemical species produced it.

The 1955 instrument described by W. C. Wiley and I. H. McLaren provides a concrete apparatus example. An ion source and accelerating fields launch ions into an evacuated drift region toward a collector. Arrival times separate mass-to-charge ratios; the paper analyses how initial positions and velocities broaden the recorded peaks, and uses a two-field ion-gun geometry to improve focusing.^[ref] This is one analyzer design, not a definition requiring every mass spectrometer to measure flight time.

For an ideal time-of-flight mass spectrometer, neglect initial speed and acceleration duration. Across an electric potential difference $U$, an ion of positive electric charge $q$ gains $qU=m{v}^2/2$. A field-free drift of length $L$ then givesIf one peak arrives at $40\mu \mathrm{s}$ and another at $44\mu \mathrm{s}$, identical acceleration and drift conditions imply a mass-to-charge ratio ratio $(44/40{)}^2=1.21$. It is a mass ratio only if the charge states are also equal. Peak position, width and intensity answer different questions: ionic identity, resolving ability and response-weighted abundance.

A mass spectrometer detector turns arriving ions into a recorded electrical signal. It is distinct from the mass analyzer that makes mass-to-charge ratio information distinguishable. The measured response can depend on collection, conversion and amplification as well as on how many ions arrived.

A Faraday cup collects electric charge directly. Ideally, a flux $\Phi$ of ions with known charge $q$ gives $I=q\Phi$. For $10^6$ singly charged positive ions per second, the current is $1.602176634\times 10^{-13}\mathrm{A}$, about $0.1602\mathrm{pA}$. Escaping secondary electrons and background currents must be accounted for when inferring particle delivery.^[ref]

An electron multiplier instead uses secondary emission to amplify the initial conversion signal. The manufacturer's detector description shows discrete dynodes, a continuous-dynode alternative, and a conversion dynode before the multiplier.^[ref] In an illustrative equal-stage model, ten stages with mean yield $\delta =4$ give mean gain $G=4^{10}=1048576$. This is a model calculation, not a measured gain for a named instrument.

Detector gain and detection efficiency answer different questions: the size of an output event and the probability of registering an arriving ion. Increasing gain cannot recover missed ions. At high signals, mass spectrometer detector saturation can also invalidate proportionality between ion delivery and recorded response. Quantitative peak comparisons therefore need a tested response range and appropriate instrument calibration, not merely a large signal.

A time-of-flight mass spectrometer is a mass spectrometer whose analyzer infers mass-to-charge ratio from ion arrival times. A simple arrangement uses an ion source, pulsed acceleration, a drift region under vacuum and a mass spectrometer detector. The 1955 Wiley–McLaren instrument connected such an apparatus to calculations of how initial position and velocity spread affect resolution.^[ref]

In an ideal drift, $t_{\mathrm{drift}}=L\sqrt{m/(2qU)}$ for flight length $L$, positive charge $q$ and accelerating electric potential difference $U$. Recorded arrival time can also include a time-of-flight timing offset $t_0$. A useful ideal instrument calibration model iswhere $x$ is the numerical mass-to-charge coordinate in a declared unit and $k$ absorbs the instrument geometry and unit conversion.

For original invented standards, let $x=25$ arrive at $12\mu \mathrm{s}$ and $x=100$ at $22\mu \mathrm{s}$. Since the square roots are 5 and 10, $k=2\mu \mathrm{s}$ and $t_0=2\mu \mathrm{s}$. An unknown arriving at $17\mu \mathrm{s}$ then has $x=((17-2)/2{)}^2=56.25$. Ignoring the offset and scaling from the first standard alone would instead give $25(17/12{)}^2\approx 50.17$. A timing offset becomes a mass-assignment error when omitted from the model.

Real peaks have finite widths. Space focusing and time-lag focusing address specified sources of that spread; neither is simply a longer wait before detection. Calibration standards, acquisition timing and focusing conditions therefore belong in the interpretation of a measured spectrum.