Dear Skyline Users,

Come show your support for keeping Skyline freely-available and open source at the last user group meeting before we apply for renewal of the NIH R01 that provides core funding for the Skyline project.

The Skyline Team is pleased to announce the Fourth Annual Skyline User Group Meeting, which will be held in St. Louis, MO 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.  Thanks to them, the meeting attendance is free, though registration is required.  We are also especially grateful to the investigators who have agreed to speak about the research they are achieving with Skyline, described below. Finally, we thank the National Institute of General Medical Sciences (NIGMS) without which the past threee years of Skyline development could not have happened.


When: Sunday, May 31st, 2015
               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: Old Post Office (, 815 Olive Street, St. Louis Mo 63101. (map)

  • The Old Post Office is located two blocks south of the ASMS convention hall (in America's Center).
  • Take North 8th Street south to Olive Street and turn right.
  • The entrance is mid-block between N 8th and N 9th Streets on Olive.

[registration closed]

Confirmed Speakers

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

Erin Baker, Ph.D. (Pacific Northwest National Lab): Utilizing Skyline to Analyze Multidimensional LC-IMS(CID)-MS Data
Ion mobility spectrometry (IMS) in conjunction with liquid chromatography separations and mass spectrometry offers a range of possibilities for analyzing complex biological samples.  In this presentation I will illustrate how Skyline has helped us understand the differences between acquiring LC-IMS(CID)-MS data taken in an all-ions fragmentation mode versus using a SWATH approach. (More info...)

Jim Bollinger, Ph.D. (MacCoss Lab, University of Washington): The Development of a Proteomic Wellness Assay Using Dried Blood Spots
This presentation will explore the development of a multiplexed SRM method for the establishment of personalized reference ranges in clinical protein diagnostics. (More info ...)

Bruno Domon, Ph.D. (Luxembourg Clinical Proteomics Center): Development and Implementation of Parallel Reaction Monitoring Assays
PRM is increasingly used for targeted proteomics experiments.  In this technique, the acquisition and the data processing are performed in two independent steps; a new workflow to design, execute the acquisition, and process data has been developed. (More info ...)

Laura G. Dubois (Moseley Lab, Duke University): Expanding Skyline’s Capabilities to Small Molecule Data Analysis
In this talk, I will show how Skyline is now able to help researchers develop targeted small molecule (metabolomics) methods with all of the features that are routinely used for proteomics. (More info...)

Tom Dunkley, Ph.D., (Roche Innovation Center): Targeted Proteomics (and Skyline) to Characterize an In Vitro Model of Human Neuronal Development
In this presentation, I will demonstrate how Skyline and Panorama have facilitated development of multiplexed methods, streamlined data analysis and ultimately enabled application of SRM-based protein profiling to neuroscience drug discovery. (More info ...)

Brendan MacLean (MacCoss Lab, University of Washington): Status of the Skyline project seven 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 7 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. In this presentation, the Skyline principal developer will present recent developments and a roadmap for the project's future. (More info ...)

Sam Payne, Ph.D. (Pacific Northwest National Lab): Viewing and Interpreting Data within a Biological Context
This presentation examines two Skyline plug-ins for data visualization and access: The first tool allows for better access and import processes to various proteomic datasets and assists in SRM assay design. The second plug-in receives data from Skyline and displays on biological pathways. (More info...)

Chris Shuford, Ph.D. (LabCorp): Real-world Application of Skyline in the Development of a Clinically Actionable Protein Measurement
Targeted quantification in a high throughput clinical setting (>100 samples/hour) requires consideration of all facets of LC-SRM measurement workflow to elucidate the one (or two) signature peptide(s) that will enable robust (CV < 15%), accurate (error < 15%), and sensitive (200 amole on column) measurement.  To that end, this presentation will focus on how Skyline was used to streamline the development work-flow of a single cancer biomarker, thyroglobulin, from in-silico selection of putative signature peptides, to optimization of peptide enrichment parameters. (More info ...)

Martin Soste, M.Sc. (Picotti Lab, ETH Zurich) A Sentinel Protein Assay for Simultaneously Quantifying Cellular Processes
This presentation will demonstrate a proteomic screening approach that uses a set of targeted mass spectrometry assays for ‘sentinel’ proteins which enables monitoring the activation of 188 yeast cellular processes in one hour. (More info ...)

Sonia Ting (MacCoss Lab, University of Washington): Application of PECAN for confident peptide detection directly from data-independent acquisition (DIA) MS/MS data
PECAN is a peptide-centric tool that enables peptide detection directly from DIA data without a spectral library. Its power as a DIA data analysis tool lies in its robustness and unrestricted querying space, enabling both targeted and discovery exploration of DIA data. (More info ...)



Bruker Agilent Technologies
SCIEX Shimadzu
Thermo Scientific      Waters
Cambridge Isotope Laboratories LabKey Software