Determination of the mass of ions produced by fragmentation Use the following se

Question

Determination of the mass of ions produced by fragmentation

Use the following sequence: (NH2)-RTEQQASALEETAASMEQLTATVK-(COOH).

Access the Protein Prospector site: http://prospector.ucsf.edu/prospector/mshome.htm and select the utility program called “MS-Product”.

Enter the sequence of the peptide (replace the default sequence “SAMPLER” by “RTEQQASALEETAASMEQLTATVK”). Make sure that ONLY the b and y ions are selected. Do not change any of the other default parameters. Click "induce fragmentation".

a. What is the monoisotopic mass of the entire peptide?

b. What is the monoisotopic mass and sequence of y7. In your answer indicate the N and C-terminal ends of the y ion sequence

c. The sequence of the peptide shows that the trypsin digestion was incomplete. If the digestion was complete, what would be the sequence of the ion b7?

d. If the last residue E (the one closest to the C-terminal end) was methylated list all the b ions whose m/z ratio would be affected by modification (you don’t need to indicate the sequences of these b ions).

e. Assuming you were only given the m/z ratios of ions y1 to y7, you knew that there is only 1 missed trypsin cleavage, and the sequence of the analyzed protein was not in any database. Would the sequence of y7 be: QLTATVK? If not list any other possible sequence(s) (4 pts)

Explanation / Answer

Answer
a: Monoisotopic mass of the entire peptide: 2593.277 Da for the ion H-RTEQQASALEETAASMEQLTATVK-OH(H+)

b: Monoisotopic mass and srquence of y7=

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