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

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

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

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

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

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

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

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