week-10-hw-Imaging-and-Measurement
Homework: Final Project
1. Identify at least one aspect of your project that you will measure.
Answer:
- The expression level of the L lactate dehydrogenase Gene
- The concentration of lactic acid
2. Describe all the elements you would like to measure.
Answer: Lorem ipsum dolor sit amet.
3. What technologies will you use (e.g., gel electrophoresis, DNA sequencing, mass spectrometry)?
Answer: Lorem ipsum dolor sit amet.
Homework: Waters Part 1 — Molecular Weight
1. Based on the predicted amino acid sequence of eGFP, what is the calculated molecular weight?
Answer: 27052.56 kda (after reomving the H tag)
2. Select two charge states from the BioAccord data and determine z for each.
Answer: Lorem ipsum dolor sit amet.
3. Calculate the MW of the protein using the relationship between m/z, MW, and z.
Answer: Lorem ipsum dolor sit amet.
4. Calculate the mass accuracy of the measurement.
Answer: Lorem ipsum dolor sit amet.
Homework: Waters Part 2 — Peptide Map
1. How many Lysines (K) and Arginines (R) are in eGFP?
Answer: 20 and 6
2. How many peptides will be generated from tryptic digestion of eGFP?
Answer: 19
3. Based on LC-MS data, how many chromatographic peaks do you see between 0.5 and 6 minutes?
Answer: 19
4. Does the number of peaks match the number of peptides predicted?
Answer: Yes
5. Identify the m/z of the peptide shown in Figure 3b.
Answer: Lorem ipsum dolor sit amet.
6. What is the charge (z) of the most abundant charge state of the peptide?
Answer: Lorem ipsum dolor sit amet.
7. Calculate the mass of the singly charged form of the peptide ([M+H]+).
Answer: Lorem ipsum dolor sit amet.
8. Identify the peptide based on MS/MS fragmentation spectrum.
Answer: Lorem ipsum dolor sit amet.
9. What is the mass accuracy of measurement?
Answer: Lorem ipsum dolor sit amet.
10. What percentage of the sequence is confirmed by peptide mapping?
Answer: Lorem ipsum dolor sit amet.
Bonus Questions
1. Determine the peptide sequence for the fragmentation spectrum in Figure 4.
Answer: Lorem ipsum dolor sit amet.
2. Do the peptide map data make sense and confirm the protein is eGFP? Why or why not?
Answer: Lorem ipsum dolor sit amet.
Homework: Waters Part 3 — Secondary/Tertiary Structure
1. Explain the difference between native and denatured protein conformations.
Answer: Lorem ipsum dolor sit amet.
2. What changes do you see in the mass spectrum between native and denatured protein analyses?
Answer: Lorem ipsum dolor sit amet.
3. What is the charge state of the peak at ~2800 m/z in the native spectrum?
Answer: Lorem ipsum dolor sit amet.
4. Did I make GFP? Fill out the table with theoretical vs observed data.
Answer: Lorem ipsum dolor sit amet.