The American Society of Mass Spectrometry annual conference represents my one sure visit to the United States each year. What is it about this meeting that keeps bringing me back across the Atlantic Ocean? What makes this gathering feel like an academic home?
My first encounter with ASMS took place in 1998, when I attended the annual conference in Orlando. During this and other early years of the conference, I made it my goal to eat only free food during the four days of the conference. I remember ice cream breakfasts from a vendor at this first meeting! Being notoriously frugal did my waistline no favors, but then I was skinny as a rail during graduate school.
My Ph.D. project involved the creation of a automated sequence tag inference engine from low-resolution tandem mass spectra of peptides. That meant I had one particular talk on my agenda for ASMS 1998. I listened with rapt attention to talk WOF 3:10 given by Pavel Pevzner (then a scientist at Millennium Pharmaceuticals) describing his SHERENGA software: “Automated De Novo Peptide Sequencing.” I remember introducing myself to him after his talk. When I mentioned my project, I remember poking in that we were competitors! I was a frightfully competitive guy back then. I am grateful that Pavel let the comment pass; in the two decades since that meeting he and I have become friends.
I feel I must mention ASMS 2004, the year that John Yates, III won the Biemann Medal, which I consider to be mass spectrometry’s highest award. The conference was held at Nashville, TN, which was lovely given that I was a post-doc at Oak Ridge National Laboratory, just four hours down the interstate. I arrived at the conference to learn that Steve Gygi, a friend of mine from graduate school, had played an epic prank on John and me at one of the preliminary meetings. A student of his had captured a video of John and me encouraging people to get out onto the dance floor at a Keystone Symposium. Steve had used the video in a research talk to show that while John was an expert in biochemistry, analytical chemistry, and bioinformatics, he couldn’t dance!
To attend a yearly conference is one thing, but becoming part of its organization is quite another. After I joined the faculty of Vanderbilt University in 2005 as an assistant professor, I decided that ASMS was the organization that felt most like “home” to me, and I began paying my dues yearly rather than haphazardly on the years I planned to attend the conference. I became familiar with a growing number of its luminaries, both through the senior scientists with whom I collaborated and through smaller meetings, such as the Association of Biomolecular Resource Facilities and the United States Human Proteomics Organization. Happily, I gained a reputation as an energetic speaker who could make mass spectrometry informatics seem more approachable.
My three biggest public roles within ASMS have all been drawn from the field of mass spectrometry informatics. I feel deeply honored to have twice selected the speakers to appear in panels on the informatics of identification. My second big involvement was with the Bioinformatics Interest Group. After the main panels on each full day of the conference, ASMS features workshops for interest groups, running from 5:45 to 7:00 PM. Since the conference attendees tend to exhaustion after such busy days, the workshops function best when they feature passionate speakers that interact quite a lot with the audience. I am certainly not ashamed to stand outside the meeting room, inviting absolute strangers to join our group! I enjoyed my moments as Donahue, running between different members of the audience with the microphone.
My biggest engagement, however, has been a long-running ASMS short course. In 2011, Alexey Nesvizhskii, Nuno Bandeira, and I offered “Bioinformatics for Protein Identification” for the first time. In this two-day short course (on the Saturday and Sunday preceding the conference), we introduced the algorithms that enable protein identification for newcomers to proteomics. Happily, the course drew a good response, and we have now run the short course for eight consecutive years! It’s a lot of work, and it makes each ASMS visit six days rather than four, but I really draw a lot of satisfaction from working with the participants.
ASMS 2018: San Diego
What made this year such a busy program? I would start with the fact that I completed my Ph.D. at San Diego, and I had many friends to visit while there! I was very grateful to visit with friends from the “Darkstar” science fiction, gaming, yoga, and movie-making club; I hadn’t seen many of them for fifteen years! I was also happy to see Ben Winnick, a friend of mine since my undergraduate years at the University of Arkansas. It’s humbling to think I have known him since 1997. These social calls complemented the professional friendships I was able to renew at the conference.
Since John Yates has made his home in San Diego since 2000, I was also glad to attend the reunion dinner he organized on the Saturday before the conference. I was sitting down to dinner with my extended family of 200 friends, a bit worn out from running the first day of our short course, when I learned that the first speaker for the event had dropped out due to illness. I was soon penciled in to replace him! I frantically scribbled some notes while eating so that I could share some of my favorite stories from the early Yates Lab. I was glad I could make people laugh!
Although I was not part of this year’s bioinformatics interest group, I was included as a speaker for the Analytical Lab Managers Interest Group under Emily Chen and David Quilici at their Monday evening workshop. I emphasized the methods core lab managers need to incorporate “Big Data” into their work, emphasizing data repository use and careful statistics. I slumped into my hotel bed directly after this talk; I had been yammering about something or other almost continuously for three straight days.
Wednesday put me right back on stage. I was slated for a mock debate over at the Informatics Hub. I was paired with my friend Juan Antonio Vizcaino (responsible for PRIDE repository); he would argue that Big Data was transforming proteomics, and I would argue that Big Data was creating more problems than it was worth! It’s true that I have some doubts about the value of Big Data practices to date. I hope my talk caused participants to think about good strategies for its incorporation.
Of course, the “work” that most conference attendees incur still awaited me. I had submitted a poster reporting work I have conducted in agricultural proteomics with the University of the Western Cape. We created an ortholog mapping table via BLAST that allowed us to determine which protein in sorghum mapped to which protein in maize. We then used the mapping table to re-align our spectral count table so that the counts for each ortholog pair appeared on the same row. This means our statistical model can look for differences between our “wet” and “dry” cohorts in both species, simultaneously! I look forward to writing that paper. My poster had been slated for Thursday, so I dutifully stood beside my A0 format poster throughout the morning and into the early afternoon. I was glad to see that the poster hall was not completely deserted, even on the last day.
I am grateful to the people that launch the annual conference for ASMS each year. It’s wonderful to gather with friends and see what each of us has created in the course of our work!