2020 User Group Meeting at ASMS

Thanks for helping make this year's uniquely challenging Skyline User Group Meeting very much a success!

With coronavirus travel restrictions still in place, we were forced, like ASMS itself, to take our annual face-to-face event online in webinar form. Held over two days -- May 27 and 28, 2020, Skyline users came out spectacularly with over 1,000 registrations (a 3-fold record) to hear 11 speakers on a diverse spectrum of mass spectrometry topics plus Skyline Principal Developer Brendan MacLean's annual update on the year past and future aims of the Skyline project. Despite the much less interactive format, 450 attendees (nearly a 2-fold record) engaged in lively Q&A sessions after each presentation.

Session recordings including the Q&A sessions are now available from the Speaker's page under each speaker's bio below.

Written responses to the questions posed in the Q&A sessions are located in the Questions and Answers page. (see menu on right-hand side of this page)

We would like to thank our speakers who never wavered in their commitment to sharing their work. They volunteered their time to create and deliver informative presentations despite myriad timezones, practice sessions, and technical challenges. Thanks too for the ongoing support from instrument vendors who help fund our efforts and lastly, to our users who continually inspire us with the new and innovative applications for Skyline. That so many managed to join us in a time when we are all so confined meant a lot to us.

We look forward to seeing and conversing with you all at future ASMS conferences in person!

Thank you!

-- Brendan MacLean and Mike MacCoss Event Organizers


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

Full Talks

Brendan MacLean (MacCoss Lab, University of Washington): Status of the Skyline Open-source Software Project 12 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 12 years later, the Skyline project is a thriving multi-omics 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...)

Josue Baeza, Ph.D., (Garcia Lab, University of Pennsylvania): Applications of Skyline for Method Development and Quantification of Histone Marks
Despite a growing interest in epigenetics, performing proteomics studies of histone tail marks remains highly specialized. Mass spectrometry of histone tail marks is difficult due to the variety of modifications, coeluting isoforms, and dynamic range. Here, we have designed a robust histone DIA method and a flexible Skyline-based analysis workflow to more accurately and precisely quantify histone marks. (More info...)

Viktoria Dorfer, Ph.D., (University of Applied Sciences - Upper Austria): MS Amanda goes West: Integrating a Search Engine into Skyline
Mass spectrometry has become the method of choice for analysing proteins, demanding reliable and state-of-the-art software. Skyline has emerged as one of the most popular of these tools, supporting the generation and use of spectrum libraries from various analysis pipelines, however requiring separate pipeline execution. We present a fully integrated workflow for peptide identification and quantification within Skyline that incorporates the MS Amanda search algorithm. (More info...)

Todd Greco, Ph.D., (Cristea Lab, Princeton University): Unbiased and Targeted Mass Spectrometry Provides Insight into Huntington’s Disease Pathogenesis
The causative agent of Huntington’s disease (HD) is the CAG repeat expansion of the huntingtin gene, producing a mutant protein with an expanded glutamine tract (mHTT). mHTT toxicity selectively impacts the brain and liver. mHTT-induced proteome and protein interaction alterations have been investigated in the brain, yet those proximal to disease progression remain poorly understood. We detected 219 differential protein candidates in mHTT liver using MS1-based LFQ, which were all targeted for validation by PRM using Skyline. (More info...)

Kaylie Kirkwood, Ph.D., (Baker Lab, North Carolina State University): Developing Multidimensional Small Molecule Spectral Libraries for Rapid Lipid Detection and Quantitation
Multidimensional lipidomics data provides valuable polarity, structural and mass information, but results in large and complex datasets which are extremely difficult to process. Skyline offers rapid and targeted processing of lipid data which ultimately allows for confident detection of diverse lipid species. We have developed sample-specific lipid spectral libraries which include hundreds of target lipids from multiple lipid categories for human plasma, brain total lipid extract, zebrafish, bronchoalveolar lavage fluid, flies, and lettuce. (More info...)

Roman Sakson,, (Heidelberg Molecular Biology Center): Unleashing Versatile Skyline Features for the Everyday Needs of a Proteomics Core Facility
Proteomics Core Facilities need to support a set of robust qualitative and quantitative workflows for a broad customer base. We routinely use Skyline as a versatile, vendor-independent platform that helps us to address two major issues, namely quality control and sharing information between MS experts and users, especially if they are not located in the same place. Customized reports and integrated tools, such as Protter for protein sequence visualization, are extremely helpful while discussing results with customers. (More info...)

Lightning Talks

Karine Bagramyan, Ph.D., (Kalkum Lab, Diabetes and Metabolism Research Institute): Using Skyline to Quantify Botulinum Neurotoxin Activity in Complex Biological Samples
This presentation will highlight Skyline’s utility for the design and optimization of our PRM and MRM assays. This brilliant software provided us with a solid bioinformatics pipeline for the entire project: From the generation of calibration curves using stable isotope-labeled synthetic peptide standards, to the quantification of attomolar concentrations of BoNT, resulting in a novel assay that has unmatched limits of detection and quantification. (More info...)

Aivett Bilbao, Ph.D., (PNNL): Metabolite Profiling for Synthetic Biology using Ion Mobility-Mass Spectrometry and Data-Independent Acquisition with Improved Targeted Data Extraction Software
Combining liquid chromatography, drift-tube ion mobility spectrometry (DTIMS)-mass spectrometry (MS) and data-independent acquisition (DIA) with improved targeted data extraction software, we developed a workflow to enable more effective synthetic biology research of hundreds Aspergillus pseudoterreus strains engineered for production of organic acids of industrial relevance. (More info...)

Sebastien Gallien, Ph.D., (Thermo Fisher Scientific): Towards Turnkey Targeted Proteomics Solutions Using SureQuant Internal Standard Triggered Acquisition on Orbitrap Mass Spectrometers
An extension of HR-PRM, called SureQuant method, has recently been introduced to progress targeted proteomics. This method, implemented in the native instrument control software of Orbitrap instruments, uses spiked-in internal standards to dynamically control the acquisition process and maximize its productivity. This included new data processing functionalities implemented in Skyline, which is a key component of the optimized informatic pipeline supporting the workflow. (More info...)

Benjamin Orsburn, Ph.D., (Johns Hopkins Medical School): Skyline -- A Comprehensive Package for Cannabis Testing Labs
Recent changes in the laws regarding Cannabis in North America has created a profitable new market for agriculture and small batch production facilities. Due to the lack of federal oversight in the US, state and local municipalities are currently responsible for determining safety testing and product characterization requirements and these vary widely across the country. We demonstrate how the Skyline software can be utilized as a near solution for both the testing and quality control monitoring for Cannabis testing labs. (More info...)

Tobias Schmidt (Kuster Lab, Technical University Munich): Real-time Spectrum Prediction in Skyline via ProteomicsDB’s gRPC Interface to Prosit
Prosit is able to accurately predict fragment ion intensities and retention times of peptides by deep learning. However, deep-learning requires GPUs for predictions that are not yet readily available in many labs and thus limit its applicability. In order to circumvent this shortcoming, we made Prosit available via gRPC on ProteomicsDB, such that Skyline is able to directly request predictions in real-time and on-demand. (More info...)