Skyline Workshop 2024

Skyline Software for Proteomics and Small Molecule Analysis

Date: 4th September 2024

Time: 09:00 to 14:30

Venue: Social Sciences Building, University of Warwick, CV4 7AL

Workshop Details:

Open a new window to understanding your mass spectrometry data for proteomics and small molecules with this introduction to the free and open-source Skyline software. Begin using Skyline data analysis and visualization for DIA, PRM, and DDA proteomics data and SRM for lipidomics data. This single-day workshop will get you started with using Skyline software in your quantitative LCMS experiments. In its 15 years of open availability, Skyline has routinely ranked as one of the most precise tools available for quantitative MS. Skyline is unparalleled in the field for its data visualization. See what you have been missing. This workshop will include case study examples of proteomics and targeted lipidomics.

For any questions relating to this workshop, please contact Brendan MacLean (


Dr Brendan MacLean, University of Washington

Dr Michele Woelk, Technical University of Dresden

Who is this workshop aimed at?

Mass spectrometrists and people analysing mass spectrometry data for quantitative proteomics and lipidomics.

What are the intended learning outcomes for this workshop?

Participants should leave with an introductory understanding of how to use the Skyline Targeted Mass Spectrometry software for method design and data analysis of proteomics and lipidomics data.

Do I require any previous knowledge or experience to complete this workshop?

The ideal participant should start with a working knowledge of liquid chromatography mass spectrometry (LCMS) having analysed and understood at least one data set. No prior knowledge of the Skyline software is required.

Will I need to do any pre-Workshop learning or activities (e.g. downloading software) to take part?

Ideally, you will download and install the free Skyline software on a Windows laptop before arriving. If your organization does not allow you to transfer files form a USB (A or C) drive to your laptop, you may be asked to download course files prior to arriving.

Workshop Sessions:

The sessions will be delivered as a mixture of in-person and live virtual deliveries, depending on the location of the presenter.

1. Introduction to quantitative proteomics and Skyline

Learn about the variety of chromatography-based mass spectrometry data applied to achieve a quantitative understanding of proteins and peptides in samples, and why Skyline is an important and useful tool for this.

2. Using Skyline for the first time with DDA, DIA, and PRM proteomics data

Learn how to use and learn more about Skyline for most of the mass spectrometry acquisition methods used in the field of proteomics.

3. Using Skyline for lipidomics data

Learn how Skyline can be used for quantitative analysis of small molecule mass spectrometry data with a specific example in lipidomics.

What course materials will be supplied alongside the Workshop?

Course participants will be supplied a flash drive (USB A and C) with all necessary data files for the hands-on tutorial sessions. All data and tutorials will be available before the workshop. Slides will be made available on-line during the workshop.

Registration Fees (includes a refreshment break and lunch):

  • BMSS/BSPR Concessionary Member (student/unwaged): £75.00
  • BMSS/BSPR Full Member (1 year/5 year): £100.00
  • Non-member: £150.00

Registration will close at midnight on 18th of August 2024.

Note: In proceeding with registration you will only be able to see options relevant to your membership status. 

  • BMSS Members: Please log in to your membership account to be able to access the relevant registration fees. 
  • BSPR Members: Please contact to obtain the BSPR discount code for the event, including the following information in your email:
    • Your BSPR membership type (full or student)
    • Your BSPR membership number
  • LIAM - Is this being offered for the workshops? Members of the Chromatography Society & the RSC-SSG: Are invited to register for this meeting at the BMSS Full Member rate. Please contact the BMSS Administrator to obtain your discount code.
  • Non-Members: Please follow the link to subscribe to the BMSS and gain access to discounted registration rates for this meeting.

Note: On-site registration for additional personnel will not be available.

Code of Conduct for BMSS & BMSS Related Events:

By registering for this meeting, delegates are agreeing to abide by the BMSS's Code of Conduct for BMSS & BMSS Related Events.

Cancellation Policy:

The BMSS will refund the registration cost, minus a £20 administrative charge, up to four weeks prior to the event start date. Thereafter, refunds will not be made; however, if a colleague is able to attend in the registrant’s place, this will be welcomed, subject to any charge adjustment accruing from the substitute’s membership status. To cancel or amend your registration for the course please email the BMSS Administrator at:

Personal Details