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):  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 ): 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...)

Lightning Talks

Joanna Bons, Ph.D., (Buck Institute) ZenoTOF 7600 Acquisitions with Electron Activated Dissociation and Novel Skyline Features for Quantification of Protein Post-translational Modifications
Protein post-translational modifications (PTMs) are key players involved in many cellular processes and signaling. Proteomic analysis of PTMs however can be challenging, due to the presence of labile modifications, the low stoichiometry of PTMs, the presence of multiple PTMs per peptide, and modified isomeric peptides. (More info...)

Lilian Heil, (University of Washington): Automating Transition Refinement for Unit Resolution PRM
One benefit of parallel reaction monitoring compared to selected reaction monitoring is the ability to refine transitions after data acquisition. Transition refinement is a critical piece of quantitative analysis, particularly in unit resolution data where interferences are common. (More info...)

Alison Porter (University of Kentucky College of Medicine): Identifying and Validating Bisphosphonate Protein Biomarkers in Equine Sera Using Mass Spectrometry Methods
Bisphosphonates are a class of drugs used in humans and animals to treat resorptive diseases of the bone by inhibiting bone resorption. In equine, these anti-resorptive drugs are FDA-approved to treat clinical signs of navicular disease. Currently, there are two non-nitrogen containing bisphosphonate drugs approved for use in equine, tiludronate and clodronate. Bisphosphonates are heterogeneously distributed and tend to accumulate in areas of high bone turnover. (More info...)

Yixuan (Axe) Xie, Ph.D., (Washington University in St. Louis): Development of data-independent acquisition (DIA-MS) methods for Glycan and RNA modification analysis
The data-dependent acquisition (DDA) methods have been utilized to characterize biomolecules (such as proteins, RNAs, and glycocalyx). However, the information about low-abundant molecules is inconsistent and underrepresented. The limitations of DDA methods provide an opportunity for a recent MS technique, data-independent acquisition (DIA), to be used. (More info...)