Week 12: Imaging and Measurement
Context
This week pairs measurement with imaging and introduces protein characterization by LC–MS (liquid chromatography–mass spectrometry) using eGFP as a standard. Remote students use data produced at Waters Immerse Cambridge. :contentReference[oaicite:0]{index=0}
Timetable (work log)
| Date | Duration | Section |
|---|---|---|
| 2025/04/27 | — | Week 12 |
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Lecture (04/22)
- Class recording: https://mit.zoom.us/rec/share/SAo2w7ahtsPQpwaZ46TSje9j7BONJEErlzN0csIF7rlrKxTJUBBC5wZ_lNIInJik.jB4vClh4-tEIocbA :contentReference[oaicite:2]{index=2}
Recitation (04/23)
- Recitation recording: https://mit.zoom.us/rec/share/RsR-J97cySP2Yfl7lspXfCU0rKDSULuUZn-nGDvUrZaT74OkUr1v1MpYM_OWeSE4.kCXezBD9a3ewU8BV :contentReference[oaicite:3]{index=3}
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Homework
Prompt (per course page):
Characterize eGFP structure (primary, secondary/tertiary) using liquid chromatography and mass spectrometry data generated in the Waters Immerse Cambridge lab. Remote students will analyze the shared data. :contentReference[oaicite:5]{index=5}
What to do
- Skim the instruments & lab context used at Immerse Cambridge. (Public overview: Immerse Cambridge lab; Waters LC–MS systems.) :contentReference[oaicite:6]{index=6}
- Review LC–MS basics (what LC does vs. what MS measures; peptide mapping). :contentReference[oaicite:7]{index=7}
- Analyze the provided eGFP dataset (protein mass, peptide map coverage, PTM observations if present).
- Summarize your findings with 2–3 annotated screenshots (chromatogram, spectrum/peptide map).
Tip
Helpful background
- Immerse Cambridge (Waters): lab overview & purpose.
- LC–MS primer(s): quick refreshers on chromatography, ionization, and peptide mapping.
Deliverables
- A short methods note (what you looked at and why).
- Protein-level result: observed intact mass (or rationale if using only peptide-level data).
- Peptide-level result: coverage map (list or figure) and any notable PTMs.
- Figures: 2–3 screenshots (e.g., TIC, MS/MS spectrum with labeled ions).
- 1–2 paragraphs interpreting what these measurements tell you about eGFP.
References / resources
- Course page for Week 12 (schedule, homework text). :contentReference[oaicite:8]{index=8}
- Immerse Cambridge (Waters Innovation & Research Lab) overview. :contentReference[oaicite:9]{index=9}
- Waters LC–MS systems (platform overview). :contentReference[oaicite:10]{index=10}
- LC–MS basics primer (Agilent; Pitt LC–MS overview). :contentReference[oaicite:11]{index=11}
- Example eGFP MS dataset (public proteomics archive). :contentReference[oaicite:12]{index=12}