Q: If a protein sequence contains 5 residues, how many possible pentapeptides can be generated from it?

$$5 \times 4 \times 3 \times 2 = 120$$

Q: A protein of 200 residues can generate how many possible pentapeptides?

$$200 \times 199 \times 198 \times 197 \times 196 = 1,552,438,400$$

Question 1

Which of the following best describes the principle behind peptide mass fingerprinting (PMF)?

Accepted Answer

PMF uses the mass spectrum of peptides to compare with a database of known protein spectra to identify unknown proteins.

Question 2

In peptide mass fingerprinting, which type of chemical bond is primarily cleaved to generate peptide fragments for analysis?

Accepted Answer

Peptide bonds

Question 3

A protein is digested with trypsin for PMF analysis. Trypsin cleaves at the carboxyl side of which amino acid residues?

Accepted Answer

Lysine and arginine

Question 4

Why is it important that the database used in peptide mass fingerprinting already contains the protein to be identified?

Accepted Answer

PMF can only match the mass spectrum to proteins that are present in the database.

Question 5

If a protein sequence contains 5 residues, how many possible pentapeptides can be generated from it?

Accepted Answer

$$5 	imes 4 	imes 3 	imes 2 = 120$$

Question 6

A protein of 200 residues can generate how many possible pentapeptides?

Accepted Answer

$$200 	imes 199 	imes 198 	imes 197 	imes 196 = 1,552,438,400$$

Question 7

Which of the following is a limitation of peptide mass fingerprinting?

Accepted Answer

It cannot identify proteins unless their spectra are already present in the database.

Question 8

During PMF, why is it necessary to use an enzyme like trypsin for protein digestion?

Accepted Answer

Trypsin generates predictable peptide fragments by cleaving at specific amino acid residues.

Question 9

Which step in the PMF workflow directly produces the mass spectrum used for protein identification?

Accepted Answer

Mass spectrometry analysis of the peptide mixture

Question 10

If a protein sequence of $$N$$ residues can generate $$N-4$$ pentapeptides, how many pentapeptides can a 200-residue protein generate?

Accepted Answer

$$200 - 4 = 196$$

Question 11

Which of the following best explains why PMF is only necessary to analyze small portions of an unknown protein?

Accepted Answer

The mass spectrum of a few peptides is sufficient to uniquely identify the protein if the database contains its sequence.

Question 12

Which of the following is NOT a main chemical bond broken during tandem mass spectrometry in PMF?

Accepted Answer

Hydrogen bonds

Question 13

A researcher wants to identify an unknown protein using PMF. Which of the following steps should be performed first?

Accepted Answer

Digest the protein with a specific protease

Question 14

If a protein sequence of $$N$$ residues can generate $$N-4$$ pentapeptides, what is the formula for the total number of pentapeptides from a protein of length $$N$$?

Accepted Answer

$$N-4$$

Question 15

Which of the following scenarios would most likely result in a failed PMF identification?

Accepted Answer

The protein is not present in the database used for comparison.

Question 16

A protein sequence of 20 residues can generate how many possible pentapeptides?

Accepted Answer

$$20 - 4 = 16$$

Question 17

Which of the following is a key advantage of using PMF for protein identification?

Accepted Answer

It allows rapid identification of proteins using only small sample amounts.

Question 18

In PMF, what is the main reason for comparing the experimental mass spectrum to theoretical spectra in a database?

Accepted Answer

To identify the protein by matching peptide masses to known sequences.

Question 19

If a protein sequence of $$N$$ residues can generate $$N-4$$ pentapeptides, how many pentapeptides can a 50-residue protein generate?

Accepted Answer

$$50 - 4 = 46$$

Peptide Mass Fingerprinting and Peptide Sequence Combinatorics

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