When John conducts JW RRM research, he does not reduce an entire pathogen to a single overall frequency, nor does he analyse the complete genome all at once.

His first step is to select proteins associated with important pathogen functions.

These mainly include:

1. Proteins associated with infection of host cells.
2. Proteins associated with pathogen replication.
3. Proteins that maintain viral capsids, viral envelopes, or cellular structures.
4. Certain surface proteins, cell wall proteins, and important metabolic enzymes.

The focus of JW RRM is therefore not simply to search for the frequency of a pathogen. It is to study the proteins that the pathogen depends on to perform its essential functions.

John initially used methods that were closer to the original RRM approach when processing biological sequences. He later updated his method so that it begins with the atomic composition and electronic environment of the research target, examining the patterns presented by the molecule.

The information considered includes:

1. The valence electrons or outer shell electrons of atoms.
2. The effective influence of the atomic nucleus on electrons.
3. The shielding effects produced by inner shell electrons.
4. The arrangement of different atoms within a molecule.
5. The mass of the constituent nodes.
6. The structure and folding of the complete molecule.

John represents the electronic and structural information of a molecule as a numerical signal. He then uses methods including the Fourier transform to identify periodic patterns within the signal.

The result is a spectrum containing multiple peaks. John examines:

1. Which peaks appear in the spectrum.
2. Which peaks are more prominent.
3. Whether different targets share common peaks.
4. The relative power of each peak.
5. The overall pattern formed by multiple peaks.

Analysing a single protein may produce many spectral peaks that are unique to that particular sequence. To identify characteristics that may be more closely associated with the target function, John compares several proteins that perform the same or similar functions.

This work includes:

1. Collecting proteins associated with the target function.
2. Analysing the spectrum of each protein.
3. Comparing peaks across different spectra.
4. Identifying recurring common patterns.
5. Reducing interference from characteristics found only in individual samples.

Proteins and peptides can be studied through biological sequences. Drugs, nutritional supplements, and other small molecules usually do not possess the same type of linear amino acid sequence. To study these substances, John developed RRMD, a method with a greater focus on molecular structure.

The information considered includes:

1. SMILES
2. InChI
3. The atoms that make up the molecule.
4. The way the atoms are connected.
5. The chemical bonds within the molecule.
6. The overall physical structure of the molecule.
7. Molecular folding or conformation.
8. Different functional groups within the molecule.

This method does not consider only the mass of a substance. It also examines how atoms are organised to form a particular molecule.

As a result, it can distinguish between certain molecules that have the same mass or chemical formula but different atomic connections or spatial structures.