TMT Reporter-Ion Mass Spectrum: 2D Peak-Fitting View

Sample Channels (true relative abundance)

MS Acquisition

Co-isolation interference 10%

MS2 ion sampling depth (AGC) 1.0×10⁵

Precursor charge state

MS1: the precursor isotope envelope is plotted around its m/z. Click Fragment to sweep to the resolved reporter-ion spectrum.

Readouts

Precursor m/z

—

Mean quant. error

—

Ch.	true	meas.	err

How it works

This is the instrument's own view of the data: a plotted mass spectrum (m/z on x, intensity on y), not a 3D scene. Two independent physical models drive it:

MS1 isotope envelope (averagine model):
n_res = M_peptide / 111.1254
n_C   = n_res · 4.9384
λ     = n_C · 0.0107          (¹³C natural abundance)
P(k)  = e^-λ λ^k / k!         (Poisson, k = 0,1,2,3 "+k" peaks)
spacing(k) = k · 1.003355 / z  Da in m/z

Orbitrap-style resolving power:
R(m/z) = R₂₀₀ · √(200 / (m/z))
FWHM(m/z) = (m/z) / R(m/z)   → peak σ = FWHM / 2.3548

Every peptide's isotope cluster is really a Poisson distribution over how many of its carbons happen to be the heavier ¹³C isotope — that's why real MS1 peaks come in a short descending "comb" (M0, M+1, M+2…) rather than one clean spike, and why the comb spacing halves at charge 3+ instead of 2+.

Shot noise — the instrument fills to a target total ion count (AGC). Each reporter channel gets a Poisson-distributed share, so relative precision improves roughly as 1/√N with sampling depth.
Ratio compression — any other peptide accidentally caught in the isolation window contributes an equal background to every reporter channel, pulling measured fold-changes back toward 1:1 even though the true abundances differ.

Move the abundance sliders, add interference, then Fragment to watch the isotope comb sweep across into six resolved reporter peaks and see how far the measured ratios drift from the truth.

MS1 — precursor isotope envelope