The Skyline Team is pleased to announce the Fifth Annual Skyline User Group Meeting, which will be held in San Antonio, TX on Sunday afternoon before ASMS.  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 proteomics techniques.  


When: Sunday, June 5, 2016
         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: Sheraton Gunter Hotel (http://www.sheratongunter.com), 205 East Houston Street, San Antonio, TX, 78205 (map)

  • The Sheraton Gunter is located about 15-20 walk northwest of the Henry B. Gonzalez Convention Center.
  • From the Convention Center northwest exit, take a right on South Alamo, left on E. Commerce, right on Navarro and a left on Houston. Sheraton Gunter is about a block more on the right side of the street.
  • Skyline User Group Meeting will be in the Crystal-Yellowrose rooms, on the first floor of the historic hotel.

[registration closed]

Confirmed Speakers

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

Josh Eckels (LabKey):Improved Quality Control Workflows and Other Panorama Updates
Panorama is a web-based complement to Skyline, used by more than a hundred organizations to manage, analyze, and share targeted mass spec data generated by Skyline. Since being unveiled at ASMS 2015, Panorama’s support for QC workflows has expanded significantly. (More info...)

Jay Kirkwood, Ph.D. (Colorado State University): The Flux Capacitor: Using Skyline for efficient processing of LC-MS/MS metabolic flux data
With the recent understanding that metabolic flux is often fundamentally altered with common disease states, there is now great interest in developing LC-MS based methods for the analysis of metabolic flux in living systems. Dependent on molecular formula, the fragment ion, and the isotopically labeled precursor, multiple SRM transitions are required to monitor for all the potential labeling patterns for a given metabolite (i.e. 36 transitions for argininosuccinate in our method).
(More info...)

Brendan MacLean, (MacCoss Lab, University of Washington): Status of the Skyline open-source software project 8 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 8 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...)

Diana A.T. Nijholt, Ph.D. (Erasmus MC): Validating PZP as a biomarker for presymptomatic Alzheimer’s disease using targeted proteomics approaches
Our group previously identified PZP as a potential serum biomarker for presymptomatic Alzheimer’s disease. A targeted MS method (SRM) including stable isotope labelled peptides was set up in our laboratory for absolute quantification of PZP. Measurements were performed on a Xevo TQ-S triple quadrupole (Waters) mass spectrometer. We make use of Skyline for method optimization (transition selection, collision energy) and data analysis of the PZP SRM method.
(More info...)

Lindsay Pino, (University of Washington): Applying lessons learned from targeted mass spectrometry to data-independent acquisition (DIA) assays
Advantages of a data independent acquisition (DIA)-MS workflow include comprehensive, unbiased, and reproducible sampling of ions, which coupled to peptide-centric analysis provides mass spectrometrists with data sets that make subsequent comparison quantification of target analytes much easier.
(More info...)

Thierry Schmidlin, (Utrecht University): Extending Selected Reaction Monitoring to Monitor Diet-Induced Neuropeptide Signaling
The analysis of neuropeptides has moved into focus in recent years, as their regulation is key in understanding a variety of functional processes, such as energy balance, drug addiction, etc. The biosynthesis of neuropeptides involves multiple trimming steps and post translational modification, thus impeding the prediction of the active peptide from the genome sequence or even the precursor protein.
(More info...)

Lightning Talks

Matthew MacDonald, Ph.D. (University of Pittsburgh): Synaptic Protein Networks in Neuropsychiatric Disease
Synaptic architecture and its adaptive remodeling require complex molecular events involving thousands of proteins. Many neuropsychiatric illnesses are complex trait disorders in which multiple genetic risk factors converge on neuronal protein networks, altering synaptic architecture and impairing brain function. A quantitative window into the synaptic proteome of brain tissue from patients is essential to understanding this neuropsychiatric disease pathogenesis. (More info...)

Bing Peng, (ISAS): Adaptation of Skyline for Targeted Lipidomics
In response to the urgent-need for analysis software that is capable of handling data from targeted high-throughput lipidomics experiments, we here present a systematic workflow for the straightforward method design and analysis of selected reaction monitoring data in lipidomics based on lipid building blocks. Skyline is a powerful software primarily designed for proteomics applications where it is widely-used. (More info...)

Chris Petzold, Ph.D. (Lawrence Berkeley National Lab): A Skyline-based workflow for rapid development of high-throughput quantitative proteomic assays
Quantitative proteomic assays are a key component of a wide variety of studies in biotechnology research, especially for synthetic biology and metabolic engineering applications that often involve sample sets in the hundreds or thousands. Complicating the analysis further is the fact that the target proteins and organisms of interest are often different across experiments. (More info...)

Qi Tang, (ProteinT Biotech): Edited transition and RT information in Skyline library improves DIA quantification of cerebral spinal fluid (CSF) proteomes
DIA-based proteomic profiling is an essential tool for molecular data collection in precision medicine. Skyline is one of very few available programs for deciphering DIA data. We performed proteomic comparison of CSF between 15 brain medullablastomas and 15 metastasis cases to seek for distinguishing biomarkers.( More info...)


Agilent Technologies Bruker
Shimadzu Thermo Scientific
Waters Cambridge Isotope Laboratories
LabKey Software SISCAPA Assay Technology