2022 User Group Meeting at ASMS

Thanks to everyone who joined us in Minneapolis for the Skyline User Group Meeting before ASMS 2022. It was certainly a treat to share a beautiful space with passionate Skyline users presenting recent work enabled by the software -- in-person -- again!

Below are links to the speakers' pages with options to view their slides or watch their presentations. At the bottom of this page, you will also find some photos from the event.

Despite the uncertainty around travel and ambient concerns about attending large conferences this year, we were impressed by the turnout and enthusiasm of the audience! Thanks especially to the speakers for all the effort they gave to delivering great presentations. The presentations featured a range of Skyline-related topics, including everything from library-free-DIA pipeline comparisons, to enhancing newborn health screening, to improving thoroughbred horse blood doping detection. One presenter was even brave enough to share how Skyline saved his lab from inadvertently publishing erroneous data!

We hope these presentations long outlast the event itself, as previous years have.

Thank you! -- Brendan MacLean and Mike MacCoss Event Organizers

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 14 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 13 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...)

Nathan Basisty, Ph.D. (NIH): Accurate Calculation of Protein Half-Lives with the TurnoveR External Tool in Skyline
Loss of protein homeostasis is a hallmark of aging and age-related conditions, including neurodegeneration, sarcopenia, and type 2 diabetes. However, alterations in markers of proteostasis machinery do not necessarily reflect rates of protein turnover. Therefore, methods to measure the turnover rates of proteins directly, rather than surrogate measurements of translation and degradation machinery, are critically needed to accurately examine the stability of the proteome during aging and disease processes. (More info...)

James Dodds,   Ph.D., (North Carolina Statue University): <a=href="https:> Improving the Speed and Selectivity of Newborn Screening using Ion Mobility Spectrometry – Mass Spectrometry (IMS-MS) analyzed via Skyline.

Detection and diagnosis of congenital disorders is the principal aim of newborn screening (NBS) programs worldwide. Mass spectrometry (MS) has become the preferred primary testing method for high-throughput NBS sampling because of its speed and selectivity. However, the ever-increasing list of NBS biomarkers included in expanding panels creates unique analytical challenges for multiplexed MS assays due to isobaric/isomeric overlap and chimeric fragmentation spectra. (More info...)

Evan Hubbard (University of California - Riverside): Finding and Quantifying Amino Acid Isomers in Data-independent Acquisition Data to Achieve Isomer Proteomics
Some amino acids are capable of undergoing spontaneous chemical modifications to become a structural or enantiomeric isomer of the canonical residue. Confined to an individual amino acid and massless, these modifications are notoriously difficult to detect despite potentially affecting protein structure or inhibiting enzymatic digestion. Recently, we have shown that data-independent acquisition (DIA) is capable of detecting these modifications through retention time shifts of peptides containing these isomers.( More info...)

Yishai Levin, (Weizmann Institute of Science ): How Skyline Saved Us From Publishing Erroneous Data
Our story begins with a glycoproteomics project, with the aim of profiling glycopeptides from patient sera. We had two informatics tools at hand. One generates identifications, based on the MS/MS spectra, but not quantification (Byonic). The other, generates MS1 based, label free quantification from any list of peptide sequences (FlashLFQ). (More info...)

Florence Roux-Dalvai, (CHU de Québec - Université Laval, Québec, Canada ): <a=href="https:>Comparative analysis of library-based and library-free DIA strategies using Skyline software

Data independent acquisition (DIA) analysis has become a strategy of choice for the analysis of complex proteomes and a plethora of methods are now available in the literature. However, there is no consensus on the best acquisition parameters to use, whether a spectral library is needed, and which processing software is most efficient. In the most comprehensive comparative study of DIA pipelines ever published (Gotti et al. J.Proteome Res., 2021), we used a complex proteomic standard (E.Coli background + UPS1 Sigma) with 4 DIA acquisition methods on an Orbitrap Fusion instrument to benchmark 6 different processing tools. (More info...)