Users Meetings


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




2023 - Houston, TX

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


2022 - Minneapolis, MN 

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



2021 - Online

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



2020 - Online

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



2019 - Atlanta, GA

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 1Part 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



2018 - San Diego, CA

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



2017 - Indianapolis, IN

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


2016 - San Antonio, TX

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



2015 - St. Louis, MO

May 31, 2015

Michael MacCoss, Ph.D. (University of Washington):

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



2014 - Baltimore, MD

June 15, 2014

Michael MacCoss, Ph.D. (University of Washington):

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 


2013 - Minneapolis, MN

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


2012 - Vancouver, BC

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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