ASMS 2024!

I had the pleasure of attending the 2024 American Society for Mass Spectrometry annual meeting in Anaheim, California this June. It was a fantastic experience, and unlike any other conference I have been to.

I wanted to attend this meeting because I have been working with proteomes of marine microeukaryotes in a large informatic analysis (which I started 6 years ago!!). In our metaproteomic investigations, it was previously unclear how likely it would be to assign a peptide and its associated spectral counts to the incorrect taxonomic lineage. Do distinct lineages share many of their peptides? This is important because the different lineages of microeukaryotes have different ecological functions, with some contributing to primary production, some to carbon respiration, and a few to biomineralization.

To address this, I used metatryp2 software with MMETSP reference transcriptomes. These translated transcriptomes were digested into tryptic peptides in silico, and the number of shared peptides between pairs are computed. This software is great because you can build your own database like I did to explore peptide overlap between species, or you can use the WHOI website and its pre-populated database with marine prokaryotes. (We are planning to upload my eukaryotic database as well so others have a quick way to search their peptides). This is especially useful if you are conducting a targeted metaproteomics analysis and want to see whether a given peptide will be diagnostic of a specific taxon or more broadly represents a group. We found that in most cases, peptides are not shared across diverse lineages of eukaryotes. Within groups, there was a large degree of overlap, especially between species/strains. I had some really thoughtful comments on my poster, and I am grateful for the feedback. I hope others will find the metatryp tool useful for their own analysis.

This conference was an excellent venue to explore the nitty gritty of proteomics. Since I am most interested in the informatics sides of proteomics, I mostly browsed those posters and talks. There was such a huge range of topics covered, everything from instrument settings to environmental applications. I learned so much from the poster presenters! The statistical tests tend to be different for proteomics vs. transcriptomics, with all sorts of caveats and points to consider. For example, proteomics data has tons of 0 values. In the transcript world, if no reads are associated with a given transcript, we would assign this a count of “0”. I learned this is not recommened for proteins, because biologically it’s unlikely you found 0 proteins in a sample, yet many in another. It’s more probable that they were below your limit of detection. Because of this, you are better off imputing the missing data. There was tons of interest in new machine learning methods for assigning peptide spectrum matches de novo, and in using data independent acquisition (DIA) as opposed to data dependent aquisition (DDA), which gives you a lot more information per run. There is also a new mass spectrometer that appears to be really popular (Astral) and a lot of groups are starting to showcase the massive amounts of data obtained from these runs.

There was a small group of metaproteomics users, and it was interesting to hear their thoughts on where the field is going. They are working on intercomparisons just like we are on the RNA side. There was a lot of discussion regarding why metaproteomes are just as useful/more useful than transcripts, and it was exciting to hear interest in comparing these pools! My contribution was: there is value in both of these measurements :|

Some of my favorite parts of this conference were the vendors and their presence. There must have been 100 different vendor booths, with info on their software, equipment, and services. Over 250 Thermo Fisher representatives were there! In the evening, these vendors held events in the hotel suites with food, drinks, swag, demos, music and games. They were like 20 little nightclubs packed with scientists! I have never seen anything like it. All the fancy mass specs were on full display. I was talked into a protein extraction kit offered by Thermo. I am excited to try it!

I really loved the food and snacks at this conference. Somehow with 7,000 attendees, the food didn’t really run out. There were snacks at the posters and before the afternoon workshops. If you were up for it, you could also attend breakfast events with the vendors.

I also loved the opening and closing plenary talks. The opening was presented by Kim Prather at UCSD, and she gave a phenomenal talk about marine aerosols, their importance, and all that we have learned over the past decade about the role of the ocean in aerosol production. Seeing an ocean scientist give the opening talk made me feel a lot more at home!! The closing talk was probably the coolest I have ever seen. It was by Parag Mallick, a Stanford scientist who develops useful proteomics software. He is also a magician. He gave a talk about the history of magic and science, their intersection, and showed us a bunch of magic tricks. It was incredible.

I was also impressed with the collection of workshops and activities for students and postdocs. I loved to see such a diverse and international crowd with meet up opportunities for specific groups/communities. This seems like a solid networking opportunity for students. They can see academics alongside industry partners giving excellent research presentations. In ocean sciences, it can feel like academia is the only option, but it’s just not true. It was really nice to see the tons of positions and career paths available to students after they graduate if they so choose the non-academic path.

The days were long but very entertaining. I am removed from the mass spectrometry sphere so I don’t envision going to this conference every year, but I am really glad I got to experience it this time around.