Reputation 0
CasualPro
PROTEOMICS · MASS SPECTROMETRY

Read a spectrum like a machine would.

A teaching game for the whole pipeline — from a tube of cells to a named protein. Every concept can be read (Codex), seen (Demos), or used (the games). Nothing is gated. Flip Casual ↔ Pro any time to add or hide the real numbers.

Follow the sample — the real workflow, end to end
01 · prepWet Lab Digest cells into peptides at the bench.
02 · measureInstruments LC, ionize, and weigh ions by m/z.
03 · strategyAcquire DDA, DIA or SRM — choose what to scan.
04 · identifySearch Match spectra to peptides, control FDR.
05 · biologyInterpret Find what changed — and the biomarker.
📖 Know it

Codex

An always-open encyclopedia. Read plain-language entries for ions, m/z, TOF, Orbitrap, DDA/DIA, b/y ions and more — each with a live diagram.

🎛 See it

Demos

Interactive, no-fail explorables. Drag a slider to watch charge change m/z; fire ions down a TOF tube and race them.

🧬 Use it

Decode

The flagship puzzle: read the gaps between fragment peaks to sequence a peptide. Earn Reputation, fill your Atlas.

The core loop: decode → earn Reputation → discover a peptide for your Atlas → unlock a harder one.

Codex — the Lab Manual

The instructive layer: read everything here without playing. Click a term.

Demos

No scores, no failing — just play with the controls and watch what happens.

Why the machine measures m/z, not mass

A peptide of fixed mass can pick up several protons. The instrument plots mass ÷ charge. Drag the charge — watch the same molecule appear at a different position.

Peptide mass (M)
2000.0 Da
Measured m/z = (M + z·1.007) / z
= 2001.0

Decode the spectrum Level 1

Each peak is a fragment of the peptide. The mass gap between two neighbouring peaks equals one amino acid. Click a ? gap, then pick the amino acid whose mass fits. Spell the whole peptide.

combo ×1
Click a “?” gap on the spectrum to begin.

Amino acids masses shown

Digest — cut the protein trypsin

Trypsin cuts a protein right after every K (lysine) or R (arginine) — except when the next residue is Proline (P), which trypsin skips. Click each correct bond to cut it; cutting anywhere else damages the sample.

Click the bonds after K or R to cut.
score 0

Acquisition Lab DDA · DIA · SRM

Solve a new acquisition challenge each round. Choose a method, adjust its settings, and check your answer. Questions and samples change; use the Learn buttons when you need a refresher.

Teaching model: peaks represent precursor ions. Selection does not guarantee peptide identification. In SRM, each chosen target represents a predefined precursor/product transition panel.

Instruments — play with the hardware

Each card is a live model of one part of a mass spectrometer. Drag the sliders and watch how it behaves in a simplified teaching model. Pause to inspect; scroll wide diagrams on small screens. Click “Codex” for the full explanation.

Wet-Lab Bench follow the protocol

You’re at the bench. Read the protocol paper, then pick the right chemical or tool for each step. Get it right and your sample advances — all the way to the mass spectrometer.

Reference Tables amino acids · instruments

Quick-reference tables to come back to any time.

Interpret — find the biomarker disease vs healthy

You quantified proteins in healthy and diseased samples. The volcano plot shows what changed. Set the cutoffs and click the protein that's strongly up in disease and highly significant.

Proteome Atlas

Every peptide you decode is catalogued here — your growing collection. (Real proteomics is, at heart, cataloguing the proteome.)