Mass Spectrometer

This page summarizes the Mass spectrometry wikipedia page

Purpose

For a given molecule $M$, the mass spectrometer generates a spectrum $\vec s$, where each element $s_i$ of the spectrum provides a confidence range that $M$ contained mass $i$. The spectrum can be used for peptide sequencing.

Details

The mass spectrometer are very complicated machines that can be dangerous to set up. Lab techs have told me that they must have power on at all times or else they can explode.

The diagram below depicts the mass spectrometry process.

1. The molecule $M$ is broken up into ionized particles, e.g. by vaporizing it.
2. The mass spectrometer shoots the particles into a magnetic arc. Since more massive particles have more momentum, they will deflect less than less charged particles in the magnetic field. The initial stream of ions will “refract” into several streams, therefore, based on the particles’ $\frac{mass}{charge}$ ratio.
3. The streams of ionized particles will then go to Faraday collectors, which measure the electrical current intensity of the separate beams.

Source: United States Geological Survey, via Wikipedia.

The mass spectrometer will emit mass/charge ratios. When the charge is +1, then the mass/charge ratio is equal to the mass $M + P$ where $P = \text{Mass of 1 proton} \approx 1 \text{ Dalton}$. The following plot depcits a spectrum reading, from wikipedia.

Source: Maciej Kotliński via Wikipedia.

De-noising

In practice, one must use a high-pass filter over these peaks to remove all but the highest intensity peaks. Many lower intensity peaks are actually false peaks.

Further, there can be sample contamination, so even the high-intensitiy peaks can be biologically inaccurate. Sometimes collagen from humans can make it into the sample, and the spectrum will create false positives for human proteins.

Tandem

The steps for tandem mass spectrometry are given below. At a high level, mass spectrometry seems most accurate with simple ions, so breaking down and ionizing a large molecule like a protein could require many steps. The tandem mass spectrometer specializes in performing these multiple steps at the same time.

Source: Hannes Röst and M. Steiner via Wikipedia.

METLIN Metabolite and Chemical Entity Database has lots of “real-world” tandem mass spectometry readings for known chemical compounds, and can be used to identify which molecules are showing up in experiments.