Since 2012, the Skyline team has been holding an annual User Group Meeting the Sunday before the annual ASMS conference. Made possible by the generosity of our vendor sponsors, the User Group Meeting has showcased the creative and innovative ways that Skyline has been used in mass spectrometry research over the many years that it has been freely available.
2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012
June 4, 2023
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 15 years after its inception
Abigail Burrows Franco Ph.D., (University of Kentucky):
Efficient generation of highly multiplexed serum biomarker panels using gas phase fractionation and DIA libraries
Philip Remes Ph.D., (Thermo Fisher Scientific):
A Skyline Tool for Creating Robust Large Scale Targeted MS/MS Assays
Julia Robbins, (Talus Bio):
How sweet it is: Leveraging the nuclear envelope glycome for the automated extraction of proteins from cell nuclei
Stoyan Stoychev Ph.D., (Evosep and ReSyn Biosciences):
Mag-Net: Bead based capture of membrane particles from plasma enables liquid biopsy measurements for >4,500 proteins
Gary Siuzdak Ph.D., (The Scripps Research Institute):
METLIN Ion Mobility: How to Analyze a Million Molecular Standards and Stay Sane
Lightning Talks
Ellen Casavant, Ph.D., (Genetech):
AutoQC enables efficient and reproducible LC-MS/MS chromatography and instrumentation
Gunnar Dittmar Ph.D., (Luxembourg Institute of Health):
Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics
Jeroen Demmers Ph.D., (Erasmus MC Proteomics):
Targeted mass spectrometry reveals that USP7 regulates the ncPRC1 Polycomb axis
Tom Lin Ph.D., (Washington University in St. Louis):
An Unbiased Proteomics Method to Discover Posttranslational Arginylation Sites from Whole Proteomes
Eduard Sabido Ph.D., (Center for Genomics Regulation and the University Pompeu Fabra):
High-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry
Ariana Shannon, (Ohio State University):
Generating fit-for-purpose targeted assays from a catalog of pre-screened peptides using data-independent acquisition (DIA) based figures of merit
June 5, 2022
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
Nathan Basisty, Ph.D. (NIH):
Accurate Calculation of Protein Half-Lives with the TurnoveR External Tool in Skyline
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.
Evan Hubbard (University of California - Riverside):
Finding and Quantifying Amino Acid Isomers in Data-independent Acquisition Data to Achieve Isomer Proteomics
Yishai Levin, (Weizmann Institute of Science ):
How Skyline Saved Us From Publishing Erroneous Data
Florence Roux-Dalvai, (CHU de Québec - Université Laval, Québec, Canada ):
Comparative analysis of library-based and library-free DIA strategies using Skyline software
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
Lilian Heil, (University of Washington):
Automating Transition Refinement for Unit Resolution PRM
Alison Porter (University of Kentucky College of Medicine):
Identifying and Validating Bisphosphonate Protein Biomarkers in Equine Sera Using Mass Spectrometry Methods
Yixuan (Axe) Xie, Ph.D., (Washington University in St. Louis):
Development of data-independent acquisition (DIA-MS) methods for Glycan and RNA modification analysis
October 27 - 28, 2021
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 13 Years after its Inception
Chris Ashwood, Ph.D., (Glycomics Core, BIDMC):
High-throughput Glycan Composition Profiling Enabled by MALDISkyLink and the Skyline Ecosystem
Natan Basisty, Ph.D., (NIH):
Analysis of Protein Turnover Rates in Skyline with the TurnoveR External Tool
Michelle Kennedy, (Cristea Lab, Princeton University):
Leveraging Skyline to Develop and Analyze Data from a Targeted Mass Spectrometry Assay for Pan-herpesvirus Protein Detection
Bini Ramachandran, Ph.D., (FARRP, University of Nebraska-Lincoln):
Matrix-independent Calibration: A Consensus Strategy to Quantify an Analyte from Different Types of Matrices.
Juan Rojas,, (University of Leipzig - Hoffmann Lab):
Skyline for the Parallel Analysis of LC-TWIMS-MS/MS DDA and DIA Data
Lightning Talks
Robert Ahrends, Ph.D., (University of Vienna):
Targeting the Lipid Metabolism with LipidCreator and STAMPS to Investigate Fat Cell Differentiation of Mesenchymal Stem Cells
Elena Barletta, (University of Zurich):
Mass Spectrometry-based Identification of Allergen Proteins Involved in Seafood-related Allergic Reactions
Muluneh Fashe, Ph.D., (University of North Carolina - Lee Lab):
Using Skyline to Quantify Drug Metabolizing Enzyme and Transport Protein Concentrations in Sandwich-Cultured Primary Human Hepatocytes
MaKayla Foster, (North Carolina State University)
Utilizing Skyline for the Evaluation and Quantitation of Per- and Polyfluoroalkyl Substances
Virag Sagi-Kiss, Ph.D., (Imperial College London):
Rapid Sample Preprocessing of a Large Number of Targeted Metabolites with Skyline
Nikunj Tanna, (Waters Corporation):
MassLynx Skyline Interface - Enabling automated MRM method development for targeted proteomics and peptide bioanalysis workflows
May 27 - 28, 2020
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
Josue Baeza, Ph.D., (Garcia Lab, University of Pennsylvania):
> Applications of Skyline for Method Development and Quantification of Histone Marks
Viktoria Dorfer, Ph.D., (University of Applied Sciences - Upper Austria):
MS Amanda goes West: Integrating a Search Engine into Skyline
Todd Greco, Ph.D., (Cristea Lab, Princeton University):
Unbiased and Targeted Mass Spectrometry Provides Insight into Huntington’s Disease Pathogenesis
Kaylie Kirkwood, Ph.D., (Baker Lab, North Carolina State University):
Developing Multidimensional Small Molecule Spectral Libraries for Rapid Lipid Detection and Quantitation
Roman Sakson,, (Heidelberg Molecular Biology Center):
Unleashing Versatile Skyline Features for the Everyday Needs of a Proteomics Core Facility
Lightning Talks
Karine Bagramyan, Ph.D., (Kalkum Lab, Diabetes and Metabolism Research Institute):
Using Skyline to Quantify Botulinum Neurotoxin Activity in Complex Biological Samples
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
Sebastien Gallien, Ph.D., (Thermo Fisher Scientific):
Towards Turnkey Targeted Proteomics Solutions Using SureQuant Internal Standard Triggered Acquisition on Orbitrap Mass Spectrometers
Benjamin Orsburn, Ph.D., (Johns Hopkins Medical School):
> Skyline -- A Comprehensive Package for Cannabis Testing Labs
Tobias Schmidt (Kuster Lab, Technical University Munich):
Real-time Spectrum Prediction in Skyline via ProteomicsDB’s gRPC Interface to Prosit
June 2, 2019
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 10 years after its inception
Birgit Schilling, Ph.D. (Buck Insitute) and Susan Abbatiello, Ph.D. (Northeastern):
Skyline: 10-year Retrospective: Part 1; Part 2
Pawel Sadowski, Ph.D. (Queensland University of Technology):
Teaching Old Dog New Tricks: Adaptation of Skyline to Analyze Untargeted Metabolomics Data Collected on GCMS Instrument
Tobias Schmidt, (Technical University Munich):
Using Prosit for PRM assay development and optimization
Selene Swanson, (Stowers Institute):
Absolute quantitative analysis of modified ribonucleosides in tRNA and mRNA using Skyline
Sebastian Vaca, Ph.D. (Broad Institute):
Avant-garde: A Skyline External Tool for automated data-driven DIA data curation.
Lightning Talks
Matthew MacDonald, Ph.D. (University of Pittsburgh):
Multi-omics Approach Identifies Pathological Phosphorylation Events Driving Synapse Loss in Schizophrenia
Sarah Michaud, (University of Victoria):
Development of Quantitative MRM Assays for the Measurement of 3,000 Proteins across 20 Mouse Tissues
Bhavin Patel, MD (Thermo Fisher Scientific):
Targeted Mass Spectrometry Assays for Absolute Quantitation of AKT/mTOR Signaling Pathway Proteins
June 3, 2018
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
Christopher Ashwood, (Macquarie University):
Applications of Skyline for automated profiling of cellular protein glycosylation
Paul Auger, (Genentech):
Automated quality control and system suitability in Panorama for peptide and small molecule analysis
Yao Chen, Ph.D., (Catalent Biologics):
Independent Digestion with Two Protease Enzymes Combining LC-HRMS Data Independent Acquisition (DIA)
Kristin Geddes, (Merck):
Implementation of Panorama into Daily Workflows and Quantitative Protein PK Analysis in the Pharmaceutical Setting
Lindsay Pino, (University of Washington):
Signal Calibration for Quantitative Proteomic
Lightning Talks
Robert Ahrends, Ph.D., (ISAS):
LipidCreator: A new skyline plugin for targeted LC-MS/MS-based lipidomics
Buyun Chen, (Genentech):
Important considerations for LC-MS based drug transporter quantitation
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
June 4, 2017
Michael J. MacCoss, Ph.D. (University of Washington):
Introduction and event host
Matt Rardin Ph.D.(Amgen):
Improved Quality Control Workflows and Other Panorama Updates
Eralp Dogu, Ph.D. (Mugla Sitki Kocman University):
MSstatsQC: An R-based Tool to Monitor System Suitability and Quality Control Results for Targeted Proteomic Experiments
Michael Schirm, Ph.D., (Caprion):
Analysis of Large Scale MRM Studies Using Skyline
Simone Sidoli, Ph.D., (University of Pennsylvania):
DIA for Differential Quantification of Isobaric Phosphopeptides and Other Protein Post-translational Modifications
Adam Officer, (Broad Institute):
Skyline Metadata Annotation and Automation of Robust Data Processing via Panorama Allows for Facile Analysis of High Throughput Targeted Proteomics Data
Brendan MacLean, (MacCoss Lab, University of Washington):
Status of the Skyline open-source software project 9 years after its inception
Lightning Talks
Shadi Eshghi, Ph.D., (Genentech):
A Workflow for Quality Assessment, Quantitation and Statistical Inference of Targeted Proteomics Data using Skyline and Panorama
Matt Foster, Ph.D., (Duke University):
A Targeted Proteomic Assay Quantifies the Periodic Expression of Cell-cycle Regulators in Yeast S. Cerevisae.
Tania Auchynnikava, Ph.D., (University of Edenburgh):
Deciphering Mechanisms of Epigenetic Inheritance with MSX-DIA
Juan Chavez, Ph.D., (Univerity of Washington):
A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry
Yang Zhang, Ph.D., (Amyris):
High Throughput Small Molecule Detection Using Automated Skyline Targeted Workflow
June 5, 2016
Michael J. MacCoss, Ph.D. (University of Washington):
Introduction and event host
Josh Eckels (LabKey):
Improved Quality Control Workflows and Other Panorama Updates
Jay Kirkwood, Ph.D. (Colorado State University):
The Flux Capacitor: Using Skyline for efficient processing of LC-MS/MS metabolic flux data
Brendan MacLean, (MacCoss Lab, University of Washington):
Status of the Skyline open-source software project 8 years after its inception
Diana A.T. Nijholt, Ph.D. (Erasmus MC):
Validating PZP as a biomarker for presymptomatic Alzheimer’s disease using targeted proteomics approaches
Lindsay Pino, (University of Washington):
Applying lessons learned from targeted mass spectrometry to data-independent acquisition (DIA) assays
Thierry Schmidlin, (Utrecht University):
Extending Selected Reaction Monitoring to Monitor Diet-Induced Neuropeptide Signaling
Lightning Talks
Matthew MacDonald, Ph.D. (University of Pittsburgh):
Synaptic Protein Networks in Neuropsychiatric Disease
Bing Peng, (ISAS):
Adaptation of Skyline for Targeted Lipidomics
Chris Petzold, Ph.D. (Lawrence Berkeley National Lab):
A Skyline-based workflow for rapid development of high-throughput quantitative proteomic assays
Qi Tang, (ProteinT Biotech):
Edited transition and RT information in Skyline library improves DIA quantification of cerebral spinal fluid (CSF) proteomes
May 31, 2015
Michael MacCoss, Ph.D. (University of Washington):
Introduction
Tom Dunkley, Ph.D., (Roche Innovation Center):
Targeted Proteomics (and Skyline) to Characterize an In Vitro Model of Human Neuronal Development
Martin Soste, M.Sc. (Picotti Lab, ETH Zurich):
A Sentinel Protein Assay for Simultaneously Quantifying Cellular Processes
Jim Bollinger, Ph.D. (MacCoss Lab, University of Washington):
Multiplexing Clinical Protein Targets in Dried Blood Spots
Sam Payne, Ph.D. (Pacific Northwest National Lab):
Viewing and Interpreting Data within a Biological Context
Chris Shuford, Ph.D. (LabCorp):
Real-world Application of Skyline in the Development of a Clinically Actionable Protein Measurement
Erin Baker, Ph.D. (Pacific Northwest National Lab):
Utilizing Skyline to Analyze Multidimensional LC-IMS(CID)-MS Data
Laura G. Dubois (Moseley Lab, Duke University):
Expanding Skyline’s Capabilities to Small Molecule Data Analysis
Sonia Ting (MacCoss Lab, University of Washington):
Application of PECAN for confident peptide detection directly from data-independent acquisition (DIA) MS/MS data
Bruno Domon, Ph.D. (Luxembourg Clinical Proteomics Center):
Development and Implementation of Parallel Reaction Monitoring Assays
Brendan MacLean (MacCoss Lab, University of Washington):
Status of the Skyline project seven years after its inception
June 15, 2014
Michael MacCoss, Ph.D. (University of Washington):
Introduction
Christopher Kinsinger, Ph.D. (National Cancer Institute):
The Skyline software project for clinical proteomics: lessons learned
Richard C. King, Ph. D. (PharmaCadence Analytical Services):
Skyline: Everyday tool for protein quantification
Michael Bereman, Ph. D. (North Carolina State University):
Statistical Process Control for Accessing Data Quality Throughout an LC MS/MS Experiment
Meena Choi (Vitek Lab, Purdue University):
MSstats as an external tool in Skyline – an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
Stephen Pennington, Ph. D. (University College Dublin):
Label-free LC-MS and MRM assay development for discovery and verification of biomarkers for organ confined prostate cancer
Dario Amodei, Ph. D. (Mallick Lab, Stanford University):
Multi-Instrument, Skyline-Based Comparison of DIA Peptide Detection and Statistical Confidence Tools
Kristin R. Wildsmith, Ph. D. (Genentech):
Skyline & Panorama Case Study: Targeted proteomics enables Alzheimer’s disease biomarker development
Christopher M. Colangelo, Ph. D. (Yale University):
The Integration of Skyline, Panorama, and LabKey Server Interface for R to Analyze the 2013-2014 ABRF sPRG Research Group Study
Jeffrey Whiteaker, Ph. D. (Paulovich Lab, Fred Hutchinson Cancer Research Center):
CPTAC Assay Portal: a community web-based repository for well-characterized quantitative targeted proteomics assays
Brendan MacLean (MacCoss Lab, University of Washington):
Status of the Skyline open-source software project five years after its inception
June 9, 2013
Joseph Brown, Ph. D. (Smith Lab, Pacific Northwest National Laboratory):
Effective design and analysis of multiplexed quantitative SRM data with Skyline
Christine Carapito, Ph. D. (IPHC/CNRS/University of Strasbourg, France):
Developing, transferring, sharing, combining, and bridging global and targeted quantitative methods and data in a platform-independent manner with Skyline
Josh Eckels (LabKey Software):
Panorama: targeted proteomics repository software for Skyline
Jarrett D. Egertson (MacCoss Lab, University of Washington):
Application of data independent acquisition techniques optimized for improved precursor specificity
Andy Hoofnagle, MD, Ph. D. (University of Washington):
Using Skyline for Lipidomics
Jacob D. Jaffe, Ph. D. (Carr Lab, The Broad Institute):
Discovery to Targets for a Phosphoproteomic Signature Assay: One-stop shopping in Skyline
Brendan MacLean (MacCoss Lab, University of Washington):
Status of the Skyline open-source software project five years after its inception
Brett Phinney, Ph. D. (UC Davis Genome Center):
Using Skyline to analyze the SPRG2013-2014 Targeted Proteomics Standard
Matthew J. Rardin, Ph.D. (Buck Institute for Research on Aging):
Label free quantitation of proteomic data using MS1 Filtering and MS/MSALL with SWATH acquisition
Olga Shubert (Institute of Molecular Systems Biology, ETH Zürich):
Development and application of assays for targeted mass spectrometric analysis of the complete proteome of Mycobacterium tuberculosis
May 20, 2012
Jeffrey Whiteaker, Ph.D. (Fred Hutchinson Cancer Research Center)
Developing quantitative assays for biomarker development
Andrew B. Stergachis (University of Washington)
Rapid empirical identification of optimal peptides for targeted proteomics
Christina Ludwig, Ph.D. (ETH Zürich)
Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline
Susan E. Abbatiello, Ph.D. (Proteomics Platform at the Broad Institute of MIT and Harvard)
Effectively Dealing with Transition Selection and Data Analysis for Multiplexed Quantitative SRM-MS Assays across Multiple Vendor Instruments
J. Will Thompson, Ph.D. (Duke Proteomics Core)
Using Skyline to Monitor Long-Term Performance Metrics of High-Resolution Mass Spectrometers
Birgit Schilling, Ph.D. (Buck Institute)
Platform Independent and Label-free Quantitation of Protein Acetylation and phosphorylation using MS1 Extracted Ion Chromatograms in Skyline
Jarrett D. Egertson (University of Washington)
Multiplexed Data Independent Acquisition for Comparative Proteomics
Brendan MacLean (University of Washington)
Status of the Skyline open-source software project four years after its inception
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