Semmering, Austria: Proteome Informatics on the upslope

At the start of 2015, I was incredibly fortunate to attend the Midwinter Proteome Informatics Midwinter Seminar at Semmering, Austria.  Although I did not initially know many of the participants, I have subsequently become friends with many of them.  In some cases, we have even written papers and grants together!  I was thrilled to return to Semmering on January 8, 2017 to attend a sequel to this meeting, this time sponsored by the European Proteomics Association.  Our group had nearly doubled from fifty-six to one hundred and five!

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January 14, 2015 (Schneeberg appears in the distance behind us.)

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Jan. 11, 2017 (photo courtesy of Marc Vaudel)

Despite its small population (below six hundred permanent residents), Semmering is actually an interesting place.  The town is named for the eponymous pass through the Northern Limestone Alps.  The area gained special prominence in 1728 when Emperor Charles VI of Austria completed a road over the pass, a feat commemorated by a hefty monument near the ski resort.

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The 18th century monument bathes in the Zauberberg night lights.

One hundred twenty years later, the pass served as a key railway connection, tying together “Lower Austria” and Styria, one of the nine federated states of Austria.  The stylish and well-engineered construction of this railway has been listed by UNESCO as a World Heritage Site.  The railway reaches almost 900 m above sea level.  The tracks employ tunnels and graceful bridges through a ruggedly beautiful terrain.  These rail links accelerated development in the area, making Semmering a major resort destination.

Our conference had grown so much in size that we occupied almost the entirety of the Semmering Sporthotel.  A feature that I particularly enjoy about this conference is the chance to create new tutorials for a crowd of advanced researchers.  In 2015, I premiered a half-day workshop on the subject of algorithms to identify post-translational modifications.  I asked this year’s organizers what kind of tutorial they would most like.  They responded by asking what I was working on right now.  I described my work in preparing sequence databases for identifying proteins of non-model organisms, starting from RNA-Seq experiments.  They replied that this would be just great.  I found it was a very useful exercise to learn the individual methods well enough to teach them to others.  In the end, approximately 35 students worked through the resulting half-day tutorial.  We were pretty challenged by the weak Internet service at the hotel, split across so many users, but most of the crucial steps were possible with data I had provided via USB drives.

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My diagram of extant search engines from two years ago

Two years ago, I had chosen a somewhat controversial topic for my plenary lecture (one given to all the attendees at once rather than a subgroup).  In “The Hard Stuff: MS Bioinformatics Moves Beyond Protein Identification,” I argued that the era of publishing new database search engines for proteomics was drawing to a close, since more than thirty such tools have now been published!  I urged them to look beyond these basics to find challenges in non-conventional identification: MS/MS scans containing evidence for multiple peptides, proteins that vary in sequence from a database reference, and peptides bearing complex modifications like glycans or non-ribosomal peptides.

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A banner image from my 2013 review of quality control

This year, I decided to spend some attention on a question of importance since I am chairing a quality control working group for the HUPO-PSI.  What types of biological mass spectrometry are not well-served by existing quality control approaches?  I discussed some of the existing efforts in quantitative mass spectrometry within Spectrum Mill, SProCop, and MSstats.  I contrasted this situation with the emerging fields of data-independent acquisition, in which superior reproducibility is regularly claimed without metrics that could substantiate those claims.

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Jan 13, 2015: Johannes Griss and I discover our shared sense of humor. (Photo courtesy Lennart Martens)

With two meetings at Semmering under my belt, I must say I am hooked.  These meetings remind me of the lovely RECOMB Computational Proteomics meetings at UCSD from 2010 to 2012.  The quality of attendees is really substantial, and the free-wheeling conversations are highly entertaining and educational.  I must also say that there is nothing quite as thrilling as sledding down the designated path of the ski slopes head-first (NOTE: this posture is discouraged), the way I lost my lens cap in 2015!  If you are in our field, I hope I’ll get to see you at a 2018 meeting!

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Johannes Griss introduced me to Almdudler, a lovely tonic that is the taste of Austria for me.

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