The Skyline Team is pleased to announce the Seventh Annual Skyline User Group Meeting, which will be held in San Diego, CA 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 mass spec techniques.  


When: Sunday, June 3, 2018
         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: San Diego Central Library 330 Park Blvd., San Diego, CA 92101 - Downtown East Village, Park Boulevard at 11th Avenue, near Petco Park (map)

  • Designed by famed architect Rob Ellington Quigley, the San Diego Central Library will be the host of this year's Skyline User Group Meeting. The library is a 10 minute walk (.6 mile) from ASMS in the San Diego Convention Center.
  • From the Convention Center, cross over rail tracks on skybridge to get to 5th Ave. Continue on 5th Ave and turn right on J Street. Continue on J Street for seven blocks and turn right onto Park Blvd and the entrance of the library.
  • The meeting will be held in the Neil Morgan Auditorium on the ground floor of the library with lunch beforehand in the roped-off portion of the lobby.
  • Get a coveted, first-run Skyline and Panorama embossed coffee mug for your morning caffeine ritual!

[registration closed]

We have closed down our registration process but you can still attend! Please just come to San Diego Central Library for "day of" registration.


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 9 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 9 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...)

Christopher Ashwood, (Macquarie University): Applications of Skyline for automated profiling of cellular protein glycosylation
Our research examines automated methods to discriminate between structurally similar isomers and overcoming a bottleneck in the data analysis of LC-MS-based glycomics.(More info...)

Paul Auger, (Genentech): Automated quality control and system suitability in Panorama for peptide and small molecule analysis
Rapid and automated standard analysis and visualization was once a tedious chore for most routine mass spectrometry users. The introduction of AutoQC to Labkey’s Panorama module in 2015 was the culmination of a vision to place the assessment of multiple data metrics, inspired by Statistical Process Control in Proteomics(SProCoP), into an automated and easily accessed platform. (More info...)

Yao Chen, Ph.D., (Catalent Biologics): Independent Digestion with Two Protease Enzymes Combining LC-HRMS Data Independent Acquisition (DIA)
Peroxide and leachable metals induced chemical modifications are among the most import quality attributes in process development. However, overall characterization covering all common modifications in a therapeutic protein has not been previously reported. We describe a global characterization of a leachable metal- and/or peroxide- stressed human IgG1 mAb using bottom-up, liquid chromatography-high-resolution mass spectrometry to monitor 59 chemical modifications with maximum coverage. (More info...)

Kristin Geddes, (Merck): Implementation of Panorama into Daily Workflows and Quantitative Protein PK Analysis in the Pharmaceutical Setting
The transition from detailed data analysis within Skyline to routine outputs such as reports for customers and collaborators, and inputting processed data into standard pharmacokinetic data analysis workflows continues to be a time-consuming challenge. We have employed Panorama as a tool to facilitate the translation of Skyline documents into user friendly, interactive quantitation reports. In addition to the previously supported calibration curves and data tables, Panorama now calculates basic figures of merit and pharmacokinetic parameters. (More info...)

Lindsay Pino, (University of Washington): Signal Calibration for Quantitative Proteomic
We present a simple and inexpensive strategy for single point intensity calibration using a common external reference sample. We show that this calibration, minimizes quantitative variance between day, between instrument platforms, and between laboratories. As long as labs perform their measurements relative to the same reference, quantitative measurements are calibrated on the same scale. A strategy for defining the performance limits of each measured analyte using a novel strategy for creating a “matched matrix calibration curve” will be presented for assessment of the LOD and LOQ. (More info...)

Lightning Talks

Robert Ahrends, Ph.D., (ISAS): LipidCreator: A new skyline plugin for targeted LC-MS/MS-based lipidomics
We developed a native tool named “LipidCreator” to strengthen the LC-MS/MS-based targeted lipidomics workflow and to provide a user-friendly interface for lipid researchers. This tool has several features including i) using lipid building blocks, ii) latest lipid nomenclature, iii) lipid fragmentation rules, iv) transition mass-calculator, v) an in-silico spectral library generator and vi) a full integration with new small molecule support in Skyline (More info...)

Buyun Chen, (Genentech): Important considerations for LC-MS based drug transporter quantitation
When transporters play a major role in drug disposition, PBPK modeling faces challenges of lacking physiological data such as transporters’ expression abundance and their demographic differences. In our study we used MDR1 as an example to show how different surrogate peptide could impact the quantitation result and why. (More info...)

Don Davis, (Vanderbilt University): The Development, Validation and Clinical Application of a LC – MS/MS Method for Absolute Quantification of Anti-Epileptic Drugs in Serum
Routine quantification of Anti-Epileptic Drug (AED) small molecules in clinical laboratories is challenging as current methods, such as immunoassays and liquid chromatography - UV detection do not possess either the selectivity, or the low limits of detection and quantification required in clinical applications. This work reports a RPLC – MS/MS method to detect and quantify AEDs in human blood serum. (More info...)


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