Proteomics: Mass Spectra, Quantification and Interaction Maps · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.

Weighing proteins piece by piece

Science · Biochemistry & Molecular Biology · ages 23-24
Name ______________________   Date ____________

  1. How is a measured peptide spectrum matched to a sequence?

    • It is searched against predicted spectra from a sequence database
    • It is read by eye with no database
    • The heaviest peak alone names the protein

  2. In a proteomics run, proteins are digested to peptides, ionized, and fragmented. What is weighed?

    • Whole genomes still inside cells
    • The ionized peptide fragments
    • The culture medium around the cells

  3. A result reports matches at a 1 percent false discovery rate. What does that mean?

    • One in a hundred reported matches is expected to be bogus
    • One peptide in a hundred was measured twice
    • The instrument ran at 1 percent power

  4. Your beads pulled down the bait plus plenty of sticky background proteins. How do you find the true partners?

    • Publish the whole list as interactions
    • Keep only the heaviest proteins
    • Compare against a control pull down and apply a scoring step

  5. You compare protein levels across runs on a tight budget and accept some noise. Which quantification fits?

    • Isotope label multiplexing
    • Label free comparison across runs
    • Skipping quantification entirely

  6. Isotope labels allow several samples to be multiplexed and compared precisely in one run.

    Circle one:   True   False

  7. A peptide never ionizes, so the instrument never sees it. How should its protein be reported?

    • As absent from the sample for certain
    • As directly measured with full confidence
    • As inferred at best, or missed by design

  8. A bait pull down lists 40 proteins, but the control pull down shows 35 of them too. What do you conclude?

    • All 40 are true interaction partners
    • Only the 5 missing from the control are real candidates; the rest is background
    • The control failed because it found anything
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Answer key

For grown-ups. Fold this page away before handing over the rest.

Weighing proteins piece by piece W1-mt_a-8UHB2SFR-s1

  1. It is searched against predicted spectra from a sequence database · Predicted spectra give candidates, and the top match above a threshold wins.
  2. The ionized peptide fragments · Digestion plus ionization turns proteins into flyable fragments whose masses spell sequence.
  3. One in a hundred reported matches is expected to be bogus · The rate controls the share of false hits accepted among reported matches.
  4. Compare against a control pull down and apply a scoring step · The control shows the background, and scoring separates partners that beat it from junk.
  5. Label free comparison across runs · Label free needs no tags and runs cheap, trading precision for cost.
  6. True · Labels tag each sample, so they can mix in one run and still be told apart precisely.
  7. As inferred at best, or missed by design · No ionization means no testimony, so the protein cannot count as measured.
  8. Only the 5 missing from the control are real candidates; the rest is background · Proteins equally present without the bait are sticky background, not partners.
Worksheet · LightMySky