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MCHM3001 · From Molecules to Therapeutics

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Chapter 2 of 13 · MCHM3001

Omics-Informed Target Discovery

Lectures 2–4 of MCHM3001 show how the 'omics — genomics, transcriptomics, proteomics and metabolomics — feed target discovery, and how mass-spectrometry workflows turn a cell lysate into a list of proteins. The examinable core is the MS-based proteomics pipeline (trypsin digestion, b/y fragment ions, quantitation) and worked disease examples such as Miller's syndrome. This underpins the target-identification half of the unit and appears in Test 1 and the final.

In this chapter

What this chapter covers

01The four omics layers (genomics static/predictive; transcriptome, proteome, metabolome dynamic/reflective) and why the same genome gives different proteomes
02Human genome scale: ~3.2 × 10⁹ bp, ~20,500 genes, ~1% protein-coding; falling genome-sequencing cost
03MS-based proteomics workflow: extraction → trypsin digestion → UHPLC → ESI → MS1 (precursor) → MS2 (fragments)
04Trypsin specificity: cleaves C-terminal to Lys (K) and Arg (R), but NOT when followed by Pro (P)
05Peptide fragmentation: b-ions (N-terminal) and y-ions (C-terminal); shotgun/bottom-up identification
06Quantitation methods: SILAC, isobaric tags (iTRAQ/TMT), ICAT, dimethylation; the Human Protein Atlas
07Worked disease example — Miller's syndrome: whole-genome sequencing filters millions of SNPs to the causal gene DHODH, corroborated by metabolomics
08Precision medicine and pharmacogenomics (VKORC1/warfarin, CYP2C19/clopidogrel)

Worked example · free

Predicting tryptic peptides from a sequence

Q [4 marks]. In a bottom-up proteomics experiment a protein is digested with trypsin. For the sequence Ala-Leu-Lys-Gly-Arg-Pro-Ser-Thr-Lys-Asp (ALKGRPSTKD), predict the peptides produced, and say which ion series identifies each peptide's N- and C-terminus in MS2. (4 marks)

+1State the rule: trypsin cleaves on the C-terminal side of lysine (K) and arginine (R), except when the next residue is proline (P).
+1Scan the sequence. K at position 3 is followed by Gly → cleave after K3. R at position 5 is followed by Pro → the Pro exception blocks cleavage, so do NOT cut here. K at position 9 is followed by Asp → cleave after K9.
+1Assemble the peptides between cut sites: ALK | GRPSTK | D — three peptides. Note GRPSTK survives intact precisely because the R-P bond is protected.
+1In MS2 each peptide is fragmented along the backbone: b-ions carry the N-terminal (amino) end and y-ions carry the C-terminal (carboxyl) end, so the b/y ladders read the sequence from both ends.

Three tryptic peptides: ALK, GRPSTK and D. Cleavage occurs after K3 and K9; the R5-P6 bond is NOT cut because trypsin skips K/R followed by proline. In MS2, b-ions define the N-terminus and y-ions the C-terminus of each peptide.

Sia tip — The trap is the proline exception — an R or K immediately before a P is not a cut site. Circle every K and R first, then strike out any that are followed by P. Ask Sia to give you fresh sequences to digest and to explain how the b/y ladder rebuilds the sequence.

Glossary

Key terms

Proteomics: The large-scale study of the proteins expressed by a cell or tissue. Because the same genome yields different proteomes over time and cell type, the proteome is a dynamic, reflective readout of state.
Trypsin digestion: Enzymatic cleavage of proteins C-terminal to lysine (K) and arginine (R), except when the next residue is proline (P); it generates predictably sized peptides for bottom-up MS.
b-ion / y-ion: Complementary backbone fragment ions from a peptide in MS2: a b-ion retains the N-terminal (amino) end, a y-ion retains the C-terminal (carboxyl) end. The ladders let you read the sequence.
Shotgun (bottom-up) proteomics: Digesting proteins to peptides, identifying tens of thousands of peptides by MS, then inferring the parent proteins; multiple peptides per protein give statistical confidence.
Isobaric tag (iTRAQ / TMT): A chemical label of equal total mass that fragments to distinct reporter ions, allowing several samples to be quantified in one MS run (relative quantitation).
Metabolomics: The measurement of small-molecule metabolites, a direct functional readout of cellular state; used, e.g., to corroborate a genomic target hit by showing substrate build-up and product depletion.

FAQ

Omics-Informed Target Discovery FAQ

Why does trypsin not cleave before a proline?

Proline's ring locks the peptide backbone into a geometry that trypsin's active site cannot accommodate for catalysis, so a lysine or arginine immediately followed by proline is skipped. This is a favourite exam point: when you predict tryptic peptides, always check the residue after each K or R and leave a K-P or R-P bond intact.

What is the difference between the genome and the proteome, and why does it matter for target discovery?

The genome is essentially static and the same in every cell; the proteome differs by cell type, time and condition because of regulated expression and modification (the butterfly-versus-caterpillar analogy). Since disease usually manifests as an altered proteome or metabolome, proteomics and metabolomics point more directly at druggable, disease-relevant targets than the genome sequence alone.

How did omics identify the cause of Miller's syndrome?

Whole-genome sequencing of an affected family filtered millions of candidate variants down to a handful of genes and pinpointed the causal enzyme DHODH (dihydroorotate dehydrogenase) in pyrimidine biosynthesis. Metabolomics corroborated it by showing the substrate accumulating and the product depleted — the pattern you expect if that enzyme is impaired — illustrating how multiple omics layers cross-validate a target.

Can AI help me with the omics and proteomics material in MCHM3001?

Yes. Sia can drill you on trypsin cleavage rules (including the proline exception), explain the b-ion/y-ion fragmentation ladder, contrast the labelling strategies (SILAC, iTRAQ, TMT), or walk through how a disease target like DHODH is triangulated across omics layers. It explains and checks your reasoning; it does not complete graded work, and University of Sydney academic-integrity rules apply.

Study strategy

Exam move

Anchor this chapter on the MS-proteomics workflow and be able to draw it end to end: extract → trypsin digest → UHPLC → ESI → MS1 precursor → MS2 fragments. Drill trypsin digestion on practice sequences until the K/R rule and the proline exception are automatic, and be able to say that b-ions mark the N-terminus and y-ions the C-terminus. Keep the four omics layers straight (which are static/predictive versus dynamic/reflective) and hold one disease case (Miller's syndrome → DHODH) ready as a worked example of omics triangulation. When the quantitation methods blur, ask Sia to tabulate SILAC versus iTRAQ/TMT by what is labelled and when.

Working through Omics-Informed Target Discovery in MCHM3001? Sia is AskSia’s AI Chemistry tutor — ask any MCHM3001 Omics-Informed Target Discovery question and get a clear, step-by-step explanation grounded in how MCHM3001 is taught and assessed. Read this chapter free, then take your hardest questions to Sia.

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