2019 User Group Meeting at ASMS

Thanks for helping us celebrate the 10th anniversary of the first release (in 2009) of Skyline at ASMS!

The celebration at our eighth annual Skyline User Group Meeting was held at the incomparable Georgia Aquarium on June 2, 2019. Enthusiasm ran high among the 250 attendees (a new record!) with standing room only both for lunch and the presentations. A 30' glass viewing window into one of the aquarium's largest saltwater displays with 20' whale sharks circling made even a standing lunch worth the visit. The aquatic theme continued into the presentation space with its aqua-toned walls and oceanic ceiling architecture (no sharks allowed) where nine speakers covered a diverse range of topics from developments in DIA peptide transition selection, analysis methods for metabolomics data collected on GCMS instruments and research of modified ribonucleosides in tRNA and mRNA -- all with Skyline as a critical research tool. Two longtime proteomics researchers who lead the original CPTAC studies that motivated Skyline development from the start -- Sue Abbatiello (Northeastern) and Birgit Schilling (Buck Institute) gave an informative and humorous retrospective of Skyline's early years up to the present. The original and now principal developer of Skyline (now a team of 9!) capped off the afternoon with his thoughts on 10 years of Skyline and his vision for 10 more years to come.

As our 10th anniversary gift, every attendee received a Skyline logoed sweatshirt "hoodie" in thanks.

All sessions were recorded and can be accessed, along with presentation PDFs, under the links for each speaker below.

The Skyline Team would once again like to thank all nine speakers for preparing and giving up their Sunday afternoon before ASMS to present at our forum. We'd also like to thank our sponsors for their continued financial support which allows us to keep our User Group Meeting free to participants. Lastly, we'd like to thank all our users for continuing to use Skyline and constantly pushing us to improve, adapt and make Skyline the best tool for your ongoing scientific research. Your enthusiasm for and support of Skyline has made the last 10 years incredibly rewarding.

Thank you! -- Brendan MacLean and Mike MacCoss Event Organizers

Michael J. MacCoss, Ph.D. (University of Washington): Introduction and event host

Full Talks

Brendan MacLean (MacCoss Lab, University of Washington): Status of the Skyline open-source software project 10 years after its inception
The Skyline project started just after ASMS 2008 as a 2-year effort to bring better SRM/MRM software tools to the NCI-CPTAC Verification Working Group that could support the variety of mass spectrometers in use in participating laboratories. Nearly 10 years later, the Skyline project is a thriving proteomics community open-source collaboration supporting 6 mass spec instrument vendors integrated with a wide variety of external software, with thousands of users worldwide and many thousands of instances started each week. (More info...)

Birgit Schilling, Ph.D. (Buck Insitute) and Susan Abbatiello, Ph.D. (Northeastern): Skyline: 10-year Retrospective: Part 1; Part 2 
Ten years ago a group of about 20 dedicated triple quadrupole operators met at the Broad Institute to learn about the features of Skyline -- this modest beginning evolved into the Skyline User Group Meeting -- the reason you are here today. Nowadays, the Skyline user base has grown significantly with 94,000 new installations of Skyline since 2009. 

Pawel Sadowski, Ph.D. (Queensland University of Technology): Teaching Old Dog New Tricks: Adaptation of Skyline to Analyze Untargeted Metabolomics Data Collected on GCMS Instrument
Processing untargeted metabolomics data collected on GCMS instruments comes with specific challenges and often requires specialized (or expensive) data analysis software. (More info...)

Tobias Schmidt, (Technical University Munich): Using Prosit for PRM assay development and optimization
We propose a novel cost-efficient approach which utilized our deep learning framework Prosit for the generation of in-silico spectral libraries with near reference data quality for virtually any peptide on a proteome-wide scale. (More info...)

Selene Swanson, (Stowers Institute): <a=href="https:>Absolute quantitative analysis of modified ribonucleosides in tRNA and mRNA using Skyline

Epitranscriptomics is a link between epigenomics and proteomics. Understanding the role of RNA modifications is important in elucidating many fundamental cellular processes such as RNA structural stability, splicing, and translation efficiency. Using a Lumos™ Tribrid™ Mass Spectrometer and Skyline, modified ribonucleosides (RNs) in E. coli tRNA and mammalian mRNA were identified and quantified based on calibration curves generated from known standard RNs. (More info...)

Sebastian Vaca, Ph.D. (Broad Institute): <a=href="https:>Avant-garde: A Skyline External Tool for automated data-driven DIA data curation.

Developments in Data-independent Acquisition data analysis have enabled the detection of large numbers of peptides. However, most tools focus on statistical validation of peptide detection (using target/decoy approaches) but do not address the quantitative suitability of the signals extracted.  (More info...)