2018 User Group Meeting at ASMS

The seventh annual Skyline User Group Meeting was held in June 3rd at the spectacular San Diego Central Library. Within the architecturally award-winning facility, our space featured a folding glass wall where attendees could enjoy lunch "al fresco" on the outside patio beforehand and then we moved into a lovely auditorium to hear about new "omic's" research approaches and methods using Skyline and Panorama. With about 200 in attendance, host Mike MacCoss from UW introduced the afternoon's talks and gave a brief overview of Skyline's nine-year history. The three and a half-hour program that followed featured speakers from all walks of mass spectrometry describing the ways that Skyline and Panorama have not only enhanced their research but in some cases, made their research even possible. As in previous years, the fast-paced meeting featured a mixture of full-length 20-minute talks as well as "lightening talks" -- five minutes to give an overview of one's research.

All the sessions were recorded and can be accessed under the link's for each speaker below.

Lastly the Skyline team would like to thank all eight speakers for preparing and giving up their Sunday afternoon before ASMS to present at our forum. Also, we'd like to once again, heartfully thank our instrument vendor sponsors who make the event possible each year and allow us to offer it without cost to attendees.

Thank you!

-- Brendan MacLean and Mike MacCoss
Event Organizers

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...)