Welcome

The Skyline Team is pleased to announce the Eighth Annual Skyline User Group Meeting, which will be held in Atlanta, GA on Sunday afternoon before ASMS. This year we are also celebrating Skyline's 10th birthday. We plan to make this year's event extra special -- so be sure to register and attend! (Check out the coveted Skyline-branded hoodies as you register.) We would like to thank the event sponsors (see below) for their generosity and interest in collaborating with the Skyline project on exciting new targeted and quantitative mass spec techniques.  

--Brendan

When: Sunday, June 2, 2019
         12:00 - 1:00 pm : Lunch served
         1:00 - 2:30 pm : Presentations
         2:30 - 3:00 pm : Snacks and break-out discussions
         3:00 - 4:30 pm : Presentations

Where: Georgia Aquarium 246 Ivan Allen Jr. Blvd., Atlanta, GA 30313 (map)

• From the Georgia World Conference Building A, walk outside to Andrew Young International Blvd and head east towards Marietta Street
• Turn left on Marietta St. NW and walk three blocks to Ivan Allen Jr. Blvd
• Make a right turn at the crosswalk to heading towards Luckie Street -- the aquarium will be in front of you on the right side of Ivan Allen Jr. Blvd
• Just past the parking entrance, follow a blue walkway to the Ocean's Entrance
• From the Ocean's Ballrooms entrance, proceed to the Pacific Ballroom

Confirmed Speakers

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

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...)

Susan Abbatiello, Ph.D. (Northeastern) and Birgit Schilling, Ph.D. (Buck Insitute): Skyline: 10-year Retrospective
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. (More info...)

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): 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): 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...)

Lightning Talks

Matthew MacDonald, Ph.D. (University of Pittsburgh): Multi-omics Approach Identifies Pathological Phosphorylation Events Driving Synapse Loss in Schizophrenia
Schizophrenia is a complex trait disorder in which genetic risk factors converge on synaptic protein networks, altering synaptic architecture, and impairing brain function. Synaptic protein network features include protein expression, trafficking, and activity.  (More info...)

Sarah Michaud, (University of Victoria): Development of Quantitative MRM Assays for the Measurement of 3,000 Proteins across 20 Mouse Tissues
An ongoing effort at our center is the development of MRM-MS assays quantifying 3,000 proteins across 20 mouse tissues for use in molecular phenotyping. (More info...)

Bhavin Patel, MD (Thermo Fisher Scientific): Targeted Mass Spectrometry Assays for Absolute Quantitation of AKT/mTOR Signaling Pathway Proteins
Proteomics offers a deeper understanding of the protein events influencing cellular and biological function. However, Identifying key regulated proteins and their implicated signaling pathways represents a major analytical challenge to researchers. (More info...)

Sponsors