Dear Skyline Users:

The Skyline Team is pleased to announce the Second Annual Skyline User Group Meeting, which will be held in Minneapolis, MN on Sunday afternoon before ASMS.  We would like to thank the event sponsors (see below) for their generosity and interest in collaborating with the Skyline project on exciting new targeted and quantitative proteomics techniques.  Thanks to them, the meeting attendance is free, though registration is required.  We are also especially grateful to the investigators who have been deeply involved in helping to create some of the most exciting Skyline features available today or coming in the next version of Skyline, and who have agreed to speak about the research they are achieving with Skyline, described below.



When: Sunday, June 9th, 2013
               12:00 - 1:00 pm : Lunch served
               1:00 - 2:30 pm : Presentations
               2:30 - 3:00 pm : Snacks and break-out discussions
               3:00 - 4:30 pm : Presentations

Where: Minneapolis Central Library (, 300 Nicollet Mall, Minneapolis, MN

[registration closed]


Confirmed Speakers

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

Joseph Brown, Ph. D. (Smith Lab, Pacific Northwest National Laboratory): Effective design and analysis of multiplexed quantitative SRM data with Skyline
The first phase of a targeted quantitative study includes selection and optimization. These early decisions are the most crucial as they influence the entirety of the downstream process. This presentation will focus on how we have used the Skyline software package to effectively guide these initial phases for two large-scale NCI projects: CPTAC and EDRN. (More info...)

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
When working on biological applications for which MS data have been acquired on various LC-MS/MS and LC-SRM platforms (ABSciex, Agilent Technologies, Bruker Daltonics, Thermo Scientific and Waters in our case), using Skyline to combine and visualize those data in a platform-independent manner plays a crucial role. (More info...)

Josh Eckels (LabKey Software): Panorama: targeted proteomics repository software for Skyline
Panorama repository software was motivated by a need for labs to organize targeted proteomics experiments, securely collaborate, and build pools of representative data of targeted assays to inform future experiments. This talk will cover the current capabilities of Panorama and its integration with Skyline and LabKey Server. (More info...)

Jarrett D. Egertson (MacCoss Lab, University of Washington): Application of data independent acquisition techniques optimized for improved precursor specificity
Novel data independent acquisition (DIA) strategies optimized for improved precursor specificity are demonstrated and compared to existing strategies on a Q-Exactive. The optimization of these techniques for samples of varying complexity will be discussed along with applications to the study of aging in yeast. (More info...)

New! Andy Hoofnagle, MD, Ph. D. (University of Washington): Using Skyline for Lipidomics
Current software solutions for peak integration and data handling of mass spec data for lipidomics are limited. We have identified a workaround in Skyline that allows for the rapid analysis of many samples simultaneously. The solution takes advantage of the excellent peak identification and integration capabilities in Skyline and has greatly simplified the workflow for lipidomics in our laboratory. (More info...)

New! Jacob D. Jaffe, Ph. D. (Carr Lab, The Broad Institute): Discovery to Targets for a Phosphoproteomic Signature Assay: One-stop shopping in Skyline
The effective dimensionality of the phosphoproteome is actually much smaller than the number of phosphosites due to coordinate regulation by a limiting number of kinases and phosphatases. To study these properties, we generated a large perturbational phosphoproteomics data set across multiple cell types and compounds. We seek to collapse the phosphoproteome into a limited number of sites that can be monitored in a targeted MS-based assay. Skyline is our tool of choice for rapidly coöpting discovery data initially processed with MaxQuant into a framework for a targeted this assay, and we will distribute assay parameters and aggregate cross-laboratory results via Panorama. (More info...)

Brendan MacLean (MacCoss Lab, University of Washington): Status of the Skyline open-source software project five 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 5 years later, the Skyline project is a thriving proteomics community open-source collaboration with solid support for another 3 years, hundreds of users and thousands of instances started each week. In this presentation, the Skyline lead software engineer will present recent developments and a roadmap for the project's future. (More info...) 

Brett Phinney, Ph. D. (UC Davis Genome Center): Using Skyline to analyze the SPRG2013-2014 Targeted Proteomics Standard
The ABRF Proteomics Standards Research Group (sPRG) is currently conducting a study focused on generation of a standard for interassay, interspecies, and interlaboratory normalization in label-free as well as in quantitative stable-isotope label-based analyses. The standard has been formulated as two mixtures: 1000 stable isotope 13C/15N-labeled synthetic tryptic peptides alone, and peptides mixed with a tryptic digest from HEK 293 cell lysate. This presentation will detail how the sPRG used skyline to analyze this standard and will present several of the challenges we encountered when analyzing isotope labeled peptide standards in complex matrices. (More info...)

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
Skyline can now process both MS1 and MS2 ion intensity chromatograms from SWATH proteomic data sets. This presentation will focus on our efforts to explore the utility of MS1 and MS2 quantitation, either alone or in combination, using Skyline. (More info...)

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
Based on synthetic peptides, we developed a library of quantitative assays for the targeted analysis of the Mycobacterium tuberculosis proteome by selected reaction monitoring (SRM). The software tools Skyline and mProphet strongly supported the generation and validation of thousands of assays for 97% of the 4,012 proteins annotated in Mycobacterium tuberculosis. Currently, we are extending and optimizing the assay library for targeted data extraction of MS/MS spectra generated by data-independent acquisition (SWATH-MS), which allows us to consistently and accurately quantify hundreds of proteins in a single run. (More info...)



AB SCIEX Agilent Technologies
Bruker Thermo Scientific
Waters LabKey Software
Biognosys LabKey Software