First Swim in the U.S.
Table of Contents
Sunday, April 20
167.6 lbs (Day 114, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★★☆
Today was my first time swimming in the U.S.! As I’ve probably said a hundred times already, the weather these days is insanely good, so my friend and I decided to try a rooftop swim. Before hitting the pool, we squeezed in a quick full-body workout. I’m used to swimming in indoor pools, so being outside in the sunshine was honestly a game-changer😝 The weather was perfect, and even though we only swam for about 15 minutes, it felt amazing. We agreed to make it a regular thing! At least once every weekend.
After the workout, we planned to go to Costco for groceries, but to our surprise, it was closed for Easter Sunday (April 20). So instead, we headed straight to Dumpling Home (298 Gough St, San Francisco, CA 94102), one of my favorite go-to spots in SF. This was already my third time there. Just so good. No regrets.
Once I got home, I took a quick nap and then realized I had left my swimsuit at the gym😩 I went back right away and even asked the staff, but no luck. I searched everywhere I could think of. If I still can’t find it by tomorrow (fingers crossed they collect lost items by the end of the day), I’ll go ahead and order a new one.
After that, I headed to the Hub to get some work done. I actually had a productive evening:
- Finished a blog post (finally didn’t postpone it. Let’s go 🤟),
- Replied to an email about a side project I’ve been working on,
- And organized all the notes I took during my first minicourse into one clean Obsidian file!
Monday, April 21
168.0 lbs (Day 115, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★
Outside of Work
Today, I decided to skip my morning workout because I planned to go to Costco in the evening with a friend. I thought I would get some light exercise beforehand instead.
The second block of this quarter has now started, and I begun attending a new class. I enrolled in this course because it offers a chance to gain an understanding of chemoproteomics during this rotation. The syllabus for the class is shown below.
Pharm Chem 219: Mass Spectrometry-based Proteomics (Spring 2025)
Proteomics is broadly concerned with gaining new knowledge of protein composition at the cellular, sub-cellular, or protein-complex level, and how protein functions are modulated by posttranslational dynamics, e.g. phosphorylation pathways or ubiquitylome/proteasome homeostasis, or how they are altered in disease states. Mass spectrometry is the technology of choice for detecting this information due to its ability to analyze complex samples for both discovery and quantification.
Mini-Course Description: This course will focus on the practical aspects (i.e. experimental and mass spectral interpretation) involved in the identification of proteins and their covalent modifications. It will cover the fundamental principles of currently important mass spectrometry instrument platforms. It will provide an overview of key scientific problems that are being tackled and solved at the protein-level relevant to cell function/dysfunction; the detection and assignment of protein posttranslational modifications; and studies of protein or modification dynamics using relative quantitation. It will also cover studies of the architecture of protein complexes and machines.
Participants will perform an analysis of supplied datasets to learn how to evaluate results, and time will be scheduled at the end of the course for presentation and discussion of the results obtained.
Schedule:
April 21 – May 9, 2025; Mo and Th 1-3 pm
Mission Bay Campus, BH-413
Student presentations will be scheduled during the course.
| Lecture | Lecturer | Topic |
|---|---|---|
| Apr 21st | Al Burlingame | Fundamentals: Ionization, Instrumentation; ion optics, resolution and mass accuracy; why these are important at protein vs peptide level. |
| Apr 24th | Robert Chalkley | Protein Identification. Basics of peptide fragmentation processes. Database searching. How to measure the reliability of assignments. |
| Apr 28th | Juan Oses | Sample preparation: Gels and Chromatography; IP/Affinity Tags, Digestion. What shouldn’t be in the sample – Contaminants. |
| May 1st | Jason Maynard | Posttranslational modifications: Protein vs peptide analysis. PTM enrichment, PTM cross-talk. |
| May 5th | Anatoly Urisman | Large-scale quantification strategies (Label-free, SILAC, iTRAQ, PRM, neucode). |
| May 8th | Mike Trnka | Architecture of protein complexes and machines (chemical cross-linking). |
The class is structured as a pretty intense two-hour straight lecture. It seems like each student will eventually receive a dataset and give a presentation at the end, but until then, it’s mostly just lecture-based. Today, after about an hour and a half of lecture, we got to spend the last 30 minutes visiting the instrument room to see an actual mass spectrometer in person!
As I’ve mentioned before, I believe that in experimental science, technical skills and access to good equipment are crucial. Of course, many places emphasize the importance of ideas (I completely agree), but I also think that understanding different experimental approaches and analysis techniques creates a kind of positive feedback loop. It helps you build a stronger foundation, which in turn can lead to generating even more meaningful ideas💡
After work, I went to the gym with a friend and then headed to Costco. On the way there, we listened to Guns N’ Roses’ Sweet Child O’ Mine and Welcome to the Jungle. The weather was perfect for a drive, and it really lifted my mood. We did a solid grocery shopping (although I ended up buying snacks in the end😇), and for dinner, we had some pre-cooked chicken drumsticks and boiled shrimp, though it turned out to be a lot more food than expected. After getting home, I spent some time watching YouTube and just relaxing. Later, I did some meal prep, took care of a few chores around the house, and went to bed early.
Lab Work
Chemistry
- SJ-1-13 check NMR
- Fortunately, I obtained the desired product, although the reaction was not as clean as it was with the Fmoc-protected substrate. I’m not entirely sure about the mechanism behind the formation of the side product with the Alloc-protected substrate, but I suspect that the Alloc group might be more susceptible to reduction.
- SJ-1-14 check NMR, Re-purification
- SJ-1-15 rxn
Tuesday, April 22
168.6 lbs (Day 116, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★
Outside of Work
I wasn’t particularly tired, but somehow I ended up oversleeping and missed my morning workout 😅 Today was the final journal club session, at least for a while, since I heard there won’t be any more scheduled soon. Interestingly, one of my cohort friends chose a paper titled Periodic Cooking of Eggs: Di Lorenzo, E. et al. Commun Eng 4, 5 (6 February 2025). Haha, it was so funny. He’s such a chill and hilarious guy.
The presentation was great, and honestly, it kind of made me want to try “periodic cooking” myself. In the method described, the eggs are alternately placed in boiling water (Th = 100 °C) for th = 2 minutes and then in cooler water (Tc = 30 °C) for tc = 2 minutes, for a total cooking time of 32 minutes. Apparently, the ideal cooking temperatures for egg whites and yolks are different, so this method helps maintain the yolk’s internal temperature consistently while preventing overcooking. They even showed data suggesting that it’s nutritionally a better method! If you’re curious, you should definitely check it out😊 Usually, journal club presentations are pretty heavy and focused on papers related to each person’s rotation project, so this one felt really refreshing and fun.
Right after class, I squeezed in a quick workout, then stopped by home for lunch before heading back to the lab. After work, I went to the library to sketch out some plans for upcoming experiments. It feels like I had a really productive day today!
Lab Work
Chemistry
- SJ-1-15 purification
- SJ-1-16, 17 rxn, work-up, check NMR
- Both SJ-1-16 and SJ-1-17 were DMP oxidations, but I recently realized that I might need to avoid using column chromatography as a purification method. This is because my aldehyde substrate has a chiral center at the alpha position, and the enantiomeric excess can decrease when the aldehyde forms an enolate.
- Some articles have reported that even a room temperature silica gel column run for about 30 minutes can reduce the ee by around 7%. However, the extent of this effect can vary. Some aldehydes are more resilient, while others are more susceptible. So the best approach would be to avoid chromatography altogether and rely solely on work-up methods.
- The challenge with the DMP reaction, despite it being a clean and reliable transformation, is the removal of excess DMP reagent and the byproduct (iodinane). To clean these up, salt washes are necessary.
- In the past, I typically evaporated the DCM after confirming reaction completion and then directly performed column chromatography, but that was when my substrates didn’t have a chiral center. This time, after doing only a few washes and checking by NMR, I still found impurities remaining. Tonight, I found a more reliable work-up method, and tomorrow I plan to try a few additional washes to see if it improves the purity.
Wednesday, April 23
168.0 lbs (Day 117, starting from 162.6 lbs on Dec 28) | 🏃🏻 Rest (2/6) | ★★★
Outside of Work
정희원의 저속노화
Nothing special today. I’m not feeling great (not sure why I’m so tired), so I just went straight home and passed out. I’ve been trying to give 100% focus on what I have to do, but it’s tough. Recently, I saw an image on YouTube that I really agree with: we need to save our energy for other important things other than work. Speaking of that channel, here’s another video I recommend: 과로가 내게 남기고 간 것들. Since coming to the U.S., I’ve kind of learned how to take my mind off work, but it’s still tough, since I was used to working as much as I could back in Korea. I really hope Korea becomes a place where people can live well without overworking, where just doing your job diligently is enough to live comfortably.
Lab Work
Chemistry
- SJ-1-16, 17 wash, and check NMR again
- Great. Adding one more wash with sat. NaHCO3 (aq.) and water completely removed the byproduct. I’ll use this work-up method from now on.
- SJ-1-18 rxn, purify
- SJ-1-19 rxn
- SJ-1-20 rxn
- Last time, during this reaction (aldehyde → alkyne transformation), I found that the Fmoc group was cleaved. So this time, I reduced the equivalents of both the Bestmann–Ohira reagent and base. However, even after just 2 hours, a significant portion of the substrate was deprotected.
- I tried the same method as before; evaporating both the aqueous and organic layers and dry-loading the crude onto a silica column. However, I came up with a new idea, just adding Fmoc-OSu and more base directly to the crude mixture to re-protect the amine.
- The reason I chose dry-loading was that the deprotected amine is highly water-soluble, making it difficult to fully extract from the aqueous layer. This method worked, but since I need to re-protect with Fmoc, it means one more round of reaction and purification.
- Next time, I might just evaporate the reaction mixture (solvent: MeOH) and directly proceed with Fmoc re-protection before purification.
Thursday, April 24
167.6 lbs (Day 118, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★☆
Outside of Work
It’s already my third week in a row going to the dentist🤣 I got in a solid workout in the morning, went to the clinic for a quick treatment, and scheduled my next regular check-up for around October. Hopefully, I won’t need to go back before then.
After a quick lunch, I dropped by the lab for a bit, then headed to class. Since it was already 3 PM, I pushed myself to focus hard on experiments and managed to finish up before 7. I had a lot to do afterward, so I went to the Hub to work on my side project.
Last time, I successfully ran AlphaFold3 with a covalent bond restraint, but now that I’m trying it again, it doesn’t work🧐 I reviewed the code I wrote before and realized I had simplified the CCD mmCIF file at the time. That got me thinking that it might have affected performance. So now, I’m trying to generate the mmCIF file using the original AlphaFold3 source code from GitHub, but it doesn’t seem to work in a regular Python environment. I ended up spending a ton of time troubleshooting.
Originally meant to write a blog post today too… but once I get sucked into debugging with GPT, Claude, and Gemini(my three AI tutors), hours just vanish. I’ll try to stay calm and take it one step at a time.
Lab Work
Chemistry
- SJ-1-18 check NMR
- SJ-1-20 purification, check NMR
- I think merging the two steps into one works well! However, neither compound shows a crystal-clear, obvious NMR spectrum. This has been a recurring trend with the pyrrolidine scaffold I’m working on. My mentor mentioned that after coupling with the diversifying part, the signals should become much clearer, even in LC-MS.
Friday, April 25
167.4 lbs (Day 119, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★★☆
Outside of Work
Another workout success~ Today, I finally attended Research in Progress in person again, which is my favorite class🤩 Last block, the class schedule overlapped with another, so I had to watch the recordings instead. Being there in person definitely helps me focus more.
Still… It’s a bit daunting to think that in just a month, I’ll be standing up there giving a flash talk. And a year from now, I’ll have to present everything I’ve worked on over the year. That’s a lot of pressure. Not to mention the qualifying exam haha…
After having lunch at home, I went to the lab and focused on experiments. I got off work a bit earlier today and headed to the Hub, where I spent time organizing my thoughts on the experiments and wrestling with my side project. In the end, it seems like I’ll have to use the Apptainer container image I previously built on the HPC and run the modules directly from there.
For dinner, I relaxed a bit watching 냉장고를 부탁해—a show I enjoy weekly. Then I got back to work for a bit before heading to bed. My nose feels a little itchy, I might be catching a cold, but it doesn’t seem serious enough to worry about yet.
Lab Work
Chemistry
- SJ-1-21 rxn, purification
- It’s just a simple Boc deprotection, but the deprotected amine is water-soluble. I tried five extractions, but I could still see UV signal on the TLC. So, I ended up dry-loading and purifying it. In this case, I think the best approach might be to isolate the TFA salt, which can be used directly in the next step in the next step in case the amine is water-soluble, by adding more base to neutralize the TFA salt. We can also use reverse-phase purification in case our product is not pure.
- SJ-1-22 rxn, work-up
Saturday, April 26
166.9 lbs (Day 120, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★☆
As always, I hit the gym with my friend and did another swim session. For some reason, my front legs were so sore that I couldn’t manage even a few laps. When I learned how to swim seriously (relatively recently, just before moving to the U.S.), I never had this issue, even though I used to swim five days a week. I don’t get it, but I’ll try to practice more over the weekend if I have time and get used to it again.
After the gym, I literally spent the whole day (until around 2 a.m.) focusing on my side project. I was trying to set up a pipeline that could automate the analysis I need, but it turned out to be more difficult than I expected. I had some success with specific parts of the process, but it’s still not perfect. For now, I’ve decided to wrap things up by handling it manually. If I have more time later, I’ll work on building a more efficient system that can handle multiple cases automatically.
