Extracted ion mass window (source code)

= Extracted ion mass window

An \b[extracted ion mass window] is the set of <mass-to-charge ratio> coordinates included when reconstructing an <extracted ion profile> or <extracted ion chromatogram>. A common choice is an interval centered at $m_0$ with half-width $w$: $|m-m_0|\le w$. The profile definition permits one value or a set of values; specifying the window makes that selection reproducible.<Extracted ion profile in IUPAC Gold Book>[Entry12410, selected mass value or set of values.]{ref}

A relative half-width can be stated in parts per million:
$$
w=m_0\,p\times10^{-6},
$$
where $p$ is the stipulated ppm half-tolerance and $m,m_0$ use the same displayed mass-coordinate scale. At $m_0=500$, a5ppm half-tolerance gives $w=0.0025$ and interval $499.9975\le m\le500.0025$. At $m_0=1000$, the same relative tolerance gives $w=0.005$. Conversely, fixed $w=0.005$ corresponds to10ppm at500 and5ppm at1000. State whether a quoted width means half-width or full width.

Finite peak width makes window choice a signal-selection operation. A target whose measured center shifts from500.000 to500.003 moves outside the first window, although part of its broadened signal may remain inside. Widening the window can recover more target signal while admitting a neighboring ion. The <extracted-ion window capture fraction> depends on the peak shape, width and coordinate offset, not merely on the nominal target formula.

<Mass resolving power> describes separation of nearby ion peaks; coordinate accuracy and the chosen extraction tolerance are different properties. A narrow software window does not improve instrumental resolving power or recreate information that was not acquired. Nor does fitting the expected window establish a unique ion identity. The window should be interpreted together with acquisition conditions, reference measurements and the other evidence used for assignment.