Proteomics: Mass Spectra, Quantification and Interaction Maps
Mass spectrometry identifies peptides from mass and fragmentation, and quantification turns spectra into abundances that can be compared between conditions. This stop covers what a proteome measurement misses and how an interaction map is built and misread.
What a learner can do afterwards
- Describe how a peptide spectrum is matched to a sequence and what the false discovery rate there controls
- Compare label-free and isotope-label quantification for a stated comparison
- Explain why an affinity-purification interaction list needs both a control pull-down and a scoring step
1 · Read
Proteins carry out the work genes encode, and abundance plus modifications decide function, not just presence. That is why you study proteins directly instead of reading genes alone. In proteomics, proteins are digested to peptides, ionized, fragmented, and weighed in a mass spectrometer. The masses of the fragments spell out sequence, piece by piece.
A measured spectrum is searched against predicted spectra from a sequence database, and the top match above a threshold wins the peptide. The false discovery rate controls the share of false hits accepted among reported matches: a 1 percent rate means one in a hundred reported matches is bogus. Set the threshold loose and the list grows, but so does the junk inside it.
Quantification turns spectra into abundances you can compare between conditions. Label free comparison works run to run with no tags, which is cheap but noisy. Isotope labels multiplex samples in one run, which is precise at higher cost. Pick the method that fits your comparison: screen broadly on a budget, or measure tightly where small changes matter.
Interaction maps need the same skepticism as spectra. Beads pull down the bait plus sticky background, so an affinity purification list needs both a control pull down and a scoring step to separate true partners from junk. When you read any proteomics result, say which proteins were measured, which were inferred, and which were missed by design: peptides that never ionize never testify.
Digest, weigh, match against the database, quantify with honest error rates, and subtract the background.
2 · Watch
Take it off screen
Where it sits
Learn first
This opens up
Nothing builds on it yet.
8 questions wait behind this lesson, each with its answer explained. Every answer feeds the sky: stars light as they are learned, and dim when it is time to come back.